# BIO101 Study Guide

 Site: Saylor Academy Course: BIO101: Introduction to Molecular and Cellular Biology Book: BIO101 Study Guide
 Printed by: Guest user Date: Monday, August 15, 2022, 6:57 PM

## Navigating this Study Guide

#### Study Guide Structure

In this study guide, the sections in each unit (1a., 1b., etc.) are the learning outcomes of that unit.

Beneath each learning outcome are:

• questions for you to answer independently;
• a brief summary of the learning outcome topic; and
• and resources related to the learning outcome.

At the end of each unit, there is also a list of suggested vocabulary words.

#### How to Use this Study Guide

1. Review the entire course by reading the learning outcome summaries and suggested resources.
2. Test your understanding of the course information by answering questions related to each unit learning outcome and defining and memorizing the vocabulary words at the end of each unit.

By clicking on the gear button on the top right of the screen, you can print the study guide. Then you can make notes, highlight, and underline as you work.

Through reviewing and completing the study guide, you should gain a deeper understanding of each learning outcome in the course and be better prepared for the final exam!

## Unit 1: Introduction to Biology

#### 1a. List the basic characteristics of life that are common to all living things

• How is a nonliving thing (such as a rock) different from a living organism (such as a mouse)?
• Can you point to examples of nonliving things that have some characteristics of life?
• How is a dead organism different from a living organism?

Biology is the study of living things, which are also known as organisms. To determine what makes something alive, we must consider characteristics that are common to organisms. Chemistry is the study of non-living matter.

Though there are many different kinds of organisms, all organisms share these characteristics:

• Response to the environment

• Growth and developmental change

• Reproduction

• Energy processing and chemical metabolism

• Regulation and maintenance of homeostasis

• Orderly structure with cellular basis

• Evolutionary adaptation based on the transmission of heritable traits

Some nonliving things have some of these characteristics, but to be alive, something must have all of the characteristics. For example, a crystal has a high degree of order and can grow, but it does not maintain homeostasis.

Review this material in Advanced Characteristics of Life and Introduction to Biological Systems.

#### 1b. List the levels of organization of life and characteristics of each level

• What makes each level different from the one below it (or the level above it)?

The levels of organization in biology are characterized by increasing complexity and order. They are structured in a hierarchical (or nested) arrangement. For example, atoms of different types form more complex structures called molecules. Molecules can form more complex structures called organelles, and so on. You should be able to list the levels of organization – from atoms all the way up to the biosphere.

• Atom - basic building block of matter

• Molecule - multiple atoms bonded together

• Organelle - subcellular structure with specific functions

• Cell - basic unit of life

• Tissue - collection of cells

• Organ - multiple tissues packaged for a particular function

• Organ System - group of functionally related organs

• Organism - a living individual

• Population - group of individuals of the same species

• Community - different populations living together

• Ecosystem - a community along with the nonliving surroundings

• Biosphere - includes all living things and their surroundings

Review the levels of biological organization in Introduction to Biological Systems. It addresses the biological hierarchy starting at 15:10.

#### 1c. Describe the steps of the scientific method and the importance of using the scientific method in research

• What is science?
• How does science work?

Science is a logical system of inquiry. Consequently, science allows us to learn about ourselves and the universe we live in. A critically important aspect of science is that it is based on evidence and is observational. Beyond mere observation, science involves the systematic testing of hypotheses. A hypothesis is an explanation for an observation, the process of gaining information. A hypothesis (which might be correct or incorrect) is a prediction and attempts to explain why something is the way it is.

The active part of science is devising experiments to test hypotheses. A hypothesis is supported (although not proven) if an appropriate experiment yields the results the hypothesis predicted. Otherwise, you must modify or reject the hypothesis. This basic process has allowed us to learn about the universe. Biology is the corner of science that deals with living things in the universe, but biology is otherwise no different from science in general.

As you review the nature and process of science, pay particular attention to the steps in the following flowchart, which demonstrates how science is a process. You should also understand the distinction between basic and applied science.

To review this material, see The Process of Science.

#### Unit 1 Vocabulary

You should be familiar with these terms as you prepare for the final exam.

• atom
• biology
• biosphere
• cell
• chemistry
• community
• ecosystem
• environment
• experiment
• homeostasis
• hypothesis
• molecule
• observation
• organ system
• organelle
• organism
• population
• prediction
• reproduction
• science
• tissue

## Unit 2: Basic Chemistry

#### 2a. List the major components of an atom and their locations

• What are the three primary subatomic particles?
• What are the major differences between the various subatomic particles?
• Where are the various subatomic particles located within an atom?
• What is an electron shell?
• What is a subshell?
• What is an orbital?

The universe is made up of matter and energy. Matter (all of the material in the universe) is composed of almost unimaginably small particles called atoms. As tiny as atoms are, even smaller particles make up each atom. We call them subatomic particles because they are smaller than atoms.

The primary subatomic particles are protons, neutrons, and electrons. Protons and neutrons make up the nucleus of an atom. Electrons are outside the nucleus. A proton has an electrical charge of +1. A neutron is nearly identical in size to a proton, but it has no charge. An electron is much smaller than a proton or neutron. An electron is also a charged particle. Despite being much smaller than a proton, the charge of an electron is equal in magnitude to the charge of a proton. However, the charge is opposite, so each electron has a charge of -1.

Electrons occupy spaces around the nucleus. These spaces have a hierarchical arrangement. An orbital is a space that can be occupied by electrons. Each orbital can contain up to two electrons. There are different types and shapes of orbitals: $s$, $p$, $d$, and $f$. There is only one kind of s orbital, but there are three kinds of p orbital, five d orbitals, and seven f orbitals. A collection of orbitals of the same type makes up a subshell, and a collection of subshells makes up a shell (also called an energy level).

The first shell includes only one subshell (the $s$ subshell), which is made up of only one $s$ orbital. The second shell is made up of two subshells (an $s$ and a $p$ subshell), with the s subshell being made up of one s orbital and the p subshell being made up of three $p$ orbitals. Since different shells contain different numbers of orbitals, each shell has a different maximum number of electrons it can hold.

Review the atomic structure and orbitals in Elements and Atoms, More on the Atom, and Protons, Neutrons, and Electrons.

#### 2b. List the different types of bonds and how they lead to the formation of molecules and compounds

• What is a compound?
• How is a compound different from an element?
• How are compounds formed?

Atoms are the building blocks of elements, which are pure substances made up of only one kind of atom. Although there are just more than one hundred different elements, there are countless different substances in the universe. Most of these substances are compounds, not elements.

A compound is a substance made up of two or more different kinds of atoms. This is the fundamental distinction between an element and a compound. Rather than simply being a mixture of two or more kinds of atoms, compounds are formed when different kinds of atoms interact. This interaction gives the compound different properties compared to the properties of the constituent elements.

For example, sodium chloride (table salt) is comprised of the elements sodium and chlorine, but sodium chloride (the compound) is different from each of these elements. The interactions between atoms in a compound are called chemical bonds. There are three major categories of chemical bonds:

• Ionic bonds form when one or more electrons from one atom is transferred to another atom, creating a positive ion and a negative ion that are attracted to each other because of their opposite charges. Ions are charged elements.

• Covalent bonds form when two different atoms share one or more pairs of electrons which hold the two atoms together more strongly than an ionic bond.

• Metallic bonds consist of a "sea" of electrons that move about from one metallic atom to another, holding together many metallic atoms.

Molecules are particles that are bigger than atoms. They are made up of multiple atoms (of the same or different elements) held together by covalent bonds. For example, a molecule of water consists of an oxygen atom which is covalently and separately bonded to two hydrogen atoms.

You should appreciate the distinction between atoms, ions, molecules, elements, and compounds.

#### 2c. Describe the primary concepts of thermodynamics as they relate to heat, temperature, energy, and work

• What is energy?
• What is heat?
• What is temperature?
• What is work?
• What are the laws of thermodynamics?

Thermodynamics is the branch of science concerned with energy and energy transfer between objects. Although thermodynamics applies throughout the universe, we study it within biology because organisms are involved in many energy transactions. In other words, organisms are thermodynamic systems.

These are fundamental questions of thermodynamics. We can define energy as the capacity to do work. Work refers to some sort of change. For example, moving an object from one place to another requires work, and energy is required for that work. Heat is energy in the form of movement of particles (atoms, ions, or molecules) within a substance. Heat is energy that is unavailable for performing work. Temperature is a measure of the average speed of the particles in an object. Temperature and heat are not the same thing. Temperature does not depend on how much matter is present, whereas heat does.

For example, a swimming pool has the same temperature as a cup of water from that swimming pool, but the swimming pool contains much more heat than the cup of water because it contains much more matter.

Two of the four laws of thermodynamics are important in biology:

• The First Law of Thermodynamics states that energy cannot be created or destroyed, though it can be transferred and transformed. This is also known as the Law of Conservation of Energy.

• The Second Law of Thermodynamics states that every energy transaction increases the entropy (disorder) of the universe. An implication of this second law is that every energy transaction involves some loss of usable energy as heat, so no energetic process (including those occurring in organisms) can ever be perfectly efficient.

These thermodynamic concepts are important for understanding living things.

Review this material in Energy and Metabolism, More on Energy, The First Law of Thermodynamics, and Gibbs Free Energy.

#### Unit 2 Vocabulary

You should be familiar with these terms as you prepare for the final exam.

• atom
• chemical bond
• compound
• covalent bond
• electron
• element
• energy
• heat
• ion
• ionic bond
• metallic bond
• molecule
• neutron
• orbital
• proton
• shell
• subshell
• temperature
• thermodynamics
• work

## Unit 3: Biological Molecules

#### 3a. List the characteristics of water that make it important to life as we know it

• What is special about water?
• What is the electrical charge distribution on a water molecule?
• Why does the polarity of water make it well suited to its functions in biology?

Water is so indispensable for life that our primary method for searching for life outside of earth is to search for evidence of water.

A water molecule is composed of one oxygen atom that is simultaneously bonded to two hydrogen atoms. The covalent bonds between the oxygen and each hydrogen are polar because the sharing of electrons between oxygen and hydrogen is not equal. Because of this unequal sharing, the oxygen atom is partially negatively charged, and each hydrogen atom is partially positively charged. This makes the overall water molecule polar. This gives water several special characteristics:

• Water molecules can form hydrogen bonds with other polar molecules, including other water molecules.

• Water is less dense in the frozen state than in the liquid state. Because of this, bodies of water freeze from the top down, and thaw during seasonal warming.

• Water has a high specific heat capacity, requiring more energy than most substances to change its temperature. This stabilizes the temperature of bodies of water more than landmasses.

• Water has a high cohesion. This can create capillary attraction which can lift water through vessels to the tops of the tallest trees.

• Water is an excellent solvent. The chemistry of life is mostly aqueous solution chemistry.

• Water has high surface tension. This allows small organisms to walk on the surface of water.

• Water has a high latent heat of vaporization. This means water requires a lot of energy to change its state from liquid to gas. This allows for effective evaporative cooling by sweating.

• Water exists in all three states (solid, liquid, and gas) within a comparatively narrow range of temperatures that organisms can tolerate.

Because of these special characteristics, it is no surprise that life evolved in the water of the ocean. We can think of every living cell as a tiny bag of water and biological molecules. Keep these special properties in mind as you study biology, and be sure to review polarity and how it underlies these properties.

Review this material in Water and The Properties of Water.

#### 3b. Describe the role of acids, bases, and buffers in biological systems

• What are the definitions of an acid and base?
• How do buffers work?

In aqueous solutions, the hydrogen atom shifts from one water molecule to another. This creates H+ and OH- ions that are very reactive. These ions are equal in pure water, but an imbalance in concentration occurs when certain solutes are added. Acids increase the H+ concentration; bases decrease H+ concentration. Different environments in living organisms have different amounts of acids and bases.

For example, the stomach requires high amounts of acid to break down food. The bloodstream is a different environment. Buffers are chemicals that resist the changes that acids and bases make in a solution of the body environment.

Review this material in Acids, Bases, and the pH Scale, pH, pOH, and pKw, and Electrolytes and pH.

#### 3c. Define pH and the role of hydrogen ions in living systems

• What is the definition of pH?
• How do acids and bases alter the hydrogen ion concentration in a solution?

pH measures the H+ ion concentration in a solution. We define it as the negative log of H+ concentration. This creates an inverse comparison. When the H+ ion concentration increases, the pH value is low. When the H+ concentration is low, the pH value increases.

The pH scale is from zero to 14. Pure water has a pH of seven because the H+ concentration equals the OH- concentration. Acids increase the H+ ion concentration by 10 fold and lowers the pH, while bases decrease the H+ concentration. The pH of the stomach is two while the blood is around seven. Buffers are needed to maintain the pH in both of these environments.

Review Hydrogen Atoms in Acids and Bases, which describes the modification of H+ concentrations.

#### 3d. Recognize the structure of the four major biological macromolecules

• What are the four classes of biological macromolecules?
• What are the structural differences between the different classes of biological macromolecules?

All organisms feature four major classes of large biological molecules, or macromolecules:

1. Lipids are made up of a diverse set of hydrocarbon molecules (containing hydrogen and carbon). This makes them largely partially non-polar because the covalent bonds in hydrocarbons (between two carbon atoms or between a carbon atom and a hydrogen atom) share electrons equally.

2. Polysaccharides are complex carbohydrates made up of carbon, hydrogen, and oxygen in a 1:2:1 ratio, giving them an empirical formula generalized as (CH2O)n.

3. Proteins are enormously diverse in structure and function, yet they all feature the substructure of amino acids. Each amino acid features a central carbon atom simultaneously connected to a hydrogen atom, an amino group, a carboxyl group, and a variable $R$ group.

4. Nucleic acids are informational molecules with a basic structure in which each subunit includes a five-carbon sugar (either ribose or deoxyribose) attached to a phosphate group and a nitrogenous base.

Knowing the chemical structure that underlies these essential biomolecules not only allows you to recognize them. It allows you to understand how they are constructed within cells and how they chemically interact with each other in metabolism and to give rise to structural components of organisms.

Review this material in Biological Polymers, Carbohydrates, Lipids, Proteins, and Nucleic Acids.

#### 3e. Describe the functions of the four major biological macromolecules

• What are the major functions of the four classes of biological macromolecules?

Lipids are important for storing energy, thermal insulation, and providing protective padding. Phospholipids form the infrastructure of all cell membranes. Lipids also make up natural waxes and oils and many hormones.

Some polysaccharides (such as cellulose and chitin) are important for their structural strength, whereas other polysaccharides (such as starch and glycogen) are important for storing energy. Polysaccharides also serve as important identity markers on the surfaces of cells, so they play a role in immunity.

Proteins perform an impressively long list of biological functions. They function as enzymes, structural elements, chemical signals, transporters, and receptors. They also play important roles in cell-to-cell adhesion and immunity.

Nucleic acids include various DNA and RNA molecules. They serve informational purposes. DNA stores the genetic code, and various types of RNA help in the process of interpreting that code to build proteins. Certain RNA's can also function as catalysts.

Review these major functions in Lipids, Carbohydrates, Proteins, and Nucleic Acids. Try to make sense of why each macromolecule's basic structure is well suited to its particular function.

#### 3f. Indicate the monomers and polymers of carbohydrates, proteins, and nucleic acids

• What are the monomers that make up polysaccharides?
• What are the monomers that make up proteins?
• What are the monomers that make up nucleic acids?

A polymer is a particular category of macromolecule that is built by connecting together many ("poly-" means "many") smaller subunits, called monomers. Only three of the four biological macromolecules we have been studying are polymers. Lipids are not polymers, but the others are.

Polysaccharides are macromolecular carbohydrates. Be careful with the words "polysaccharide" and "carbohydrate". Sometimes these words are used interchangeably, but they should not be since they are different.

Carbohydrates include small and large molecules (macromolecules). Put another way, all polysaccharides are carbohydrates, but not all carbohydrates are polysaccharides. As the name implies, polysaccharides are polymers made up of multiple monosaccharides. Monosaccharides are monomers, and they can be connected in either a linear or branched arrangement.

Proteins are polymers that are made up of monomers called amino acids. Unlike polysaccharides, which may be branched, a protein must be a linear (or end-to-end) arrangement of amino acids. Organisms use 20 different kinds of amino acids (in an unlimited number of combinations and orders) to construct their proteins.

We can also call a nucleic acid a polynucleotide. This alternative name indicates it is a polymer made up of many nucleotides. In the case of DNA, the monomers are nucleotides that contain the pentose (five-carbon sugar) called deoxyribose. For RNA, the nucleotides contain ribose instead of deoxyribose. Although there are only four commonly used DNA nucleotides (and four commonly used RNA nucleotides), a typical DNA molecule contains millions of nucleotides. So there is an unlimited number of sequences of such nucleotides.

Be sure you can match each type of monomer to the type of polymer that can be made from such monomers. In addition to reviewing the various monomers, refresh your memory about how polymers are constructed using dehydration reactions and deconstructed using hydrolysis reactions in Biological Polymers.

#### 3g. Describe the four levels of protein structure

• What are the four levels of protein structure?
• How is each level distinct?

As a polymer, a protein is a large and complex molecule, and proteins have the most complex and most variable shapes among the three classes of biological polymers. Any given protein has its particular function because of its particular shape (also called its conformation). This is why proteins have such diverse functions. Some proteins function as enzymes, which are biological catalysts. We can describe protein structure up to four different levels:

• Primary structure refers to the particular sequence of amino acids (both the number and the order) making up a single polypeptide. A polypeptide is one continuous strand made up of some number of amino acids connected end-to-end in a particular order. If a protein consists of just one polypeptide, then that "polypeptide" is itself a "protein".

• Secondary structure refers to repeating patterns found within a polypeptide. The repeating patterns include alpha helices (a singular helix) and beta-pleated sheets.

• Tertiary structure refers to the particular three-dimensional structure of a single polypeptide. In other words, the particular shape that a single polypeptide assumes when it bends and folds is called its tertiary structure.

Every protein includes at least one polypeptide, so every protein features a primary, secondary, and tertiary structure. Only some proteins (called multimeric proteins) are made up of two or more polypeptides. For multimeric proteins, there is a fourth level of structure in addition to the other three levels.

• Quaternary structure refers to the particular way in which multiple individual polypeptides (each with their own primary, secondary, and tertiary structures) come together to form the overall shape of a multimeric protein. In this case, "polypeptide" and "protein" are not interchangeable terms. The polypeptides are just parts of the overall protein.

Review the section on protein structure in Proteins. Keep in mind that a protein cannot function properly unless it has the correct shape, regardless of its job in the cell.

#### Unit 3 Vocabulary

You should be familiar with these terms as you prepare for the final exam.

• amino acid
• amino group
• carbohydrate
• carboxyl group
• catalyst
• cohesion
• deoxyribose
• DNA
• enzyme
• hydrogen bond
• latent heat of vaporization
• lipid
• monomer
• monosaccharide
• multimeric
• nitrogenous base
• non-polar
• nucleic acid
• nucleotide
• phospholipid
• polar
• polymer
• polynucleotide
• polypeptide
• polysaccharide
• primary structure
• protein
• quaternary structure
• ribose
• RNA
• secondary structure
• solvent
• specific heat capacity
• surface tension
• tertiary structure

## Unit 4: Cells and Cell Membranes

#### 4a. Describe and diagram the structure and function of a typical biological membrane

• What is another name for the cell membrane?
• What types of molecules make up a cell membrane?
• How does the chemistry of the molecules in a membrane explain why a cell membrane forms?

The cell is the functional unit of life. Every organism features at least one cell; metabolism (the chemistry of life) occurs within cells. A membrane separates the cell from its surroundings.

Every cell features a cell membrane, which is also called the plasma membrane. The plasma membrane is a complex arrangement of several different types of molecules. The chief components are phospholipids. Each phospholipid molecule is an amphipathic molecule (polar at one end and non-polar at the other end). This explains why plasma (cell) membranes form.

In the presence of water, phospholipids self-assemble into a bilayer, with the non-polar tails in each monolayer pointing toward the non-polar tails of the other monolayer, and the polar heads of each monolayer pointing toward the watery solution on its side of the membrane (the water interior of the cell for one monolayer, and the water exterior of the cell for the other monolayer). In addition to the phospholipid bilayer, the plasma (cell) membrane features various other macromolecules, including proteins, sterols, and polysaccharides.

The plasma (cell) membrane is fundamental to life, so be sure to review its structure (and the structure of an individual phospholipid) in Parts of the Cell Membrane. Also, watch Review of the Cell Membrane and Structure of the Cell Membrane.

#### 4b. Describe characteristics of a membrane, solutes, and solvents, as well as predict where molecules will move and how the mass of a cell may change

• What are the components of a solution?
• What is the difference between a solvent and a solute?
• What happens to cell volume when osmosis occurs?

A solution is a mixture that includes a solvent and a number of solutes. The solvent is the part of the solution that dissolves the solutes; the solutes are the parts the solvent has dissolved. In an aqueous solution, water is the solvent. A cell's plasma membrane forms a barrier between intracellular fluid and extracellular fluid (which are both aqueous solutions). The plasma membrane is selectively permeable, which means some particles easily pass through the membrane, while other particles cannot get through. Many solutes are effectively (although not perfectly) prevented from passing through the membrane, so we say the membrane is impermeable to these solutes. Water, on the other hand, can pass through to a certain degree.

Water passes through a plasma membrane using a mechanism called osmosis, a special type of diffusion process that is passive. The direction and rate of osmosis depend on the relative solute concentrations inside and outside the cell. Water always osmoses to the area that is less watery. This means water always moves away from the compartment that has a higher solute concentration. If the solute concentration of the extracellular fluid is higher than the solute concentration of the intracellular fluid, this means the extracellular fluid is less watery, so water will leave the cell by osmosis, and the cell volume will decrease.

If the reverse is true (the gradient is reversed), then water will enter the cell by osmosis, and cell volume will increase. In each case, notice that the water moves toward the less watery compartment. Organisms must regulate their osmotic conditions since changes in osmotic gradients can profoundly damage their cells.

#### 4c. Describe characteristics of a cell, and classify the cell as a prokaryotic, animal, or plant

• What distinguishes a eukaryotic cell from a prokaryotic cell?
• Are animal and plant cells eukaryotic or prokaryotic?

Although all cells share certain characteristics (for example, every cell has a plasma membrane), biologists recognize two fundamentally different categories of cells: prokaryotic cells and eukaryotic cells.

A prokaryotic cell does not feature membrane-bounded organelles; a eukaryotic cell does feature membrane-bounded organelles. A membrane-bounded organelle is an organelle (a tiny organ-like structure within a cell) that is enclosed by its own membrane, separate from the plasma membrane that encloses the entire cell.

Membrane-bounded organelles include diverse structures such as the nucleus, endoplasmic reticulum, lysosomes, mitochondria, chloroplasts, and others. Only eukaryotic cells feature these membrane-bounded organelles, though a eukaryotic cell might feature only some (but not all) of them.

For example, an animal cell (like one in a human body) features most of the membrane-bounded organelles, but it does not feature chloroplasts. A plant cell, on the other hand, typically includes the membrane-bounded organelles found in an animal cell, plus it also features chloroplasts. A bacterium, which is a prokaryotic cell, does not feature any of these membrane-bounded organelles. Ensure that you appreciate the differences between these major categories of cell types.

Review Prokaryotic Cells, Eukaryotic Cells, and Types of Cells.

#### 4d. Identify organelles that are found in typical prokaryotic, plant, and animal cells

• What are the names of the various organelles?
• Are all of the organelles membrane-bounded?
• What types of cells feature these various organelles?

You should recognize several organelles in this course:

• Ribosome - not membrane-bounded; found in prokaryotic and eukaryotic cells

• Plasma (cell) membrane - found in prokaryotic and eukaryotic cells

• Cell wall - found in most prokaryotic and some eukaryotic cells (though not animal cells)

• Nucleus - membrane-bounded; found only in eukaryotic cells

• Mitochondrion - membrane-bounded; found only in most eukaryotic cells

• Chloroplasts - membrane-bounded; found only in photosynthetic eukaryotic cells (plants and algae)

• Golgi body - membrane-bounded; found only in eukaryotic cells

• Central vacuole - membrane-bounded; found only in some eukaryotic cells, including plants and some protists

• Rough endoplasmic reticulum - membrane-bounded; found only in eukaryotic cells

• Smooth endoplasmic reticulum - membrane-bounded; found only in eukaryotic cells

• Lysosome - membrane-bounded; found only in eukaryotic cells

• Peroxisome - membrane-bounded; found only in eukaryotic cells

Notice that most of these organelles are membrane-bounded; therefore, they appear only in eukaryotic cells. These cells are structurally more complex than the prokaryotic cells they evolved from.

Review the structures of these important organelles in Cell Structure. Pay particular attention to Figure 1. Also, watch Parts of a Cell.

#### 4e. Indicate the functions of the various cellular organelles, including the nucleus, cell membrane, cell wall, mitochondria, chloroplasts, ribosomes, Golgi body, central vacuole, rough endoplasmic reticulum, smooth endoplasmic reticulum, lysosome, and peroxisome

• What are the major functions of the various types of organelles?
• What advantage is gained by some organelles being membrane-bounded?

One difference between the various organelles is their shapes. However, our primary reason for classifying organelles differently is because they perform different functions, just as different organs in our body perform different functions.

• Ribosome - molecular machines that interpret codes in mRNA to build proteins

• Plasma (cell) membrane - defines the cell and forms the boundary between the contents of the cell and its surroundings

• Cell wall - thicker, more rigid than, and exterior to the plasma membrane; withstands pressure and prevents the cell from bursting

• Nucleus - enclosed by two membranes; houses the DNA

• Mitochondrion - enclosed by two membranes; site for cellular respiration

• Chloroplast - enclosed by two membranes; site for photosynthesis

• Golgi body - receives newly-formed proteins, modifies them, and packages them for transport to the plasma membrane or out of the cell

• Central vacuole - largely water-filled organelle that can also house pigments and wastes

• Rough endoplasmic reticulum - site for synthesis of proteins that the Golgi body will package

• Smooth endoplasmic reticulum - site for synthesis of lipids and storage of calcium ions

• Lysosome - digests materials by subjecting them to enzymes

• Peroxisome - safely breaks down harmful chemicals in the cell

The organelles that are membrane-bounded form sub-compartments, so they can perform their functions in isolation from the rest of the cellular contents. Before proceeding, be sure you know which functions each organelle performs. Review this material in Parts of a Cell.

#### 4f. Explain how large signal molecules get their signal into the cell

• What are signal modules?
• What are receptors?

Signal molecules are examples of ligands, because they must bind to other molecules. We call the molecules that signal molecules bind to receptors. When a signal binds to a receptor, that binding causes changes in the cell. These changes are the responses to the signal. Some signals are small and non-polar, so they are easily able to pass through a cell's plasma membrane, and they bind to internal receptors. Most signals, however, are too large or too polar to pass through the plasma membrane, so they must bind to receptors on the exterior surface of the cell. Although these signal molecules do not actually enter the cell, they still cause changes inside the cell. This occurs using three primary mechanisms – the difference lies in what kind of receptor receives these signals.

• Ion-channel-linked receptors are transmembrane proteins that simultaneously serve as signal receptors and ion channels. When a signal molecule binds to this type of receptor, the ion channel either opens or closes its gate. This leads to changes in the flow of ions, which are charged particles. This redistribution of charge causes various responses.

• G-protein-linked receptors are transmembrane receptors that are associated with special proteins (G proteins) situated on the part of the protein that is in contact with the interior surface of the membrane. The binding of a signal molecule to the receptor activates (and frees) the G protein. This activation causes various responses.

• Enzyme-linked receptors are transmembrane proteins that simultaneously serve as signal receptors and enzymes. The binding of a signal molecule to the receptor activates the enzymatic portion of the receptor (which faces the interior of the cell). Once activated, the enzyme catalyzes various reactions, which causes various responses.

Be sure you understand the functional differences between these three classes of receptors; all three operate by binding to a signal molecule at the exterior surface. Since it helps to look at diagrams to make sense of the differences, review the text and figures in the section on types of receptors of Signaling Molecules and Cellular Receptors.

#### 4g. Describe the forms of transport across biological membranes

• What are the primary categories of transmembrane transport?
• What is the fundamental difference between these primary categories?

Particles pass through biological membranes (including the plasma membrane) by various mechanisms, which we can lump into two primary categories. We can classify transmembrane transport (transport of a particle through a biological membrane) as active or passive. The distinction between the two is the requirement of an external source of energy.

• Active transport requires an additional (external) source of energy to drive it. ATP is often the energy source, but other energy sources can be used. Since additional energy is applied, active transport can move particles against their gradient (see definition in next paragraph), which causes gradients to become even steeper.

• Passive transport does not require additional (external) energy for the transport to occur. The energy that drives passive transport is in the form of a gradient. A gradient is a difference in magnitude. A gradient that drives passive transport can be a concentration gradient (when the concentration of the particle type is higher on one side of the membrane than the other), an electrical gradient (when the charge distribution is different on one side of the membrane than the other), or both. In all cases of passive transport, the transport occurs down the gradient, such as from the place of higher concentration to the place of lower concentration. Passive transport never occurs in the direction against the gradient.

There are important subcategories of passive transport:

• Simple diffusion is passive transport of solute particles down the gradient for that type of solute and directly through the phospholipid bilayer of the biological membrane. This can occur only for particles small enough or nonpolar enough to pass through the bilayer.

• Facilitated diffusion is also diffusion, but it requires the help (facilitation) of a transport protein to get the particle through the membrane. This occurs for particles that are too big or too polar to cross the phospholipid bilayer directly.

• Osmosis is passive transport of solvent particles (not solute particles) down the gradient for solvent particles and through a selectively permeable membrane. In biological systems, the solvent is always water, so biological osmosis is movement of water.

These transmembrane transport processes are fundamental to life because organisms must continuously exchange materials with their surroundings to stay alive. Review the categories and subcategories by watching Review of the Cell Membrane and reviewing subunit 4.4.

#### Unit 4 Vocabulary

You should be familiar with these terms as you prepare for the final exam.

• active transport
• amphipathic
• aqueous
• cell membrane
• cell wall
• cellular respiration
• central vacuole
• chloroplast
• eukaryotic
• extracellular fluid
• facilitated diffusion
• Golgi body
• intracellular fluid
• ligand
• lysosome
• membrane-bounded
• mitochondrion
• non-polar
• nucleus
• organelle
• osmosis
• passive transport
• peroxisome
• phospholipid
• photosynthesis
• plasma membrane
• polar
• prokaryotic
• receptor
• ribosome
• rough endoplasmic reticulum
• selectively permeable
• signal
• simple diffusion
• smooth endoplasmic reticulum
• solute
• solution
• solvent

## Unit 5: Enzymes, Metabolism, and Cellular Respiration

#### 5a. Recognize and explain the difference between matter and energy

• What is energy?
• How is energy different from matter?

Organisms are examples of open thermodynamic systems because organisms must exchange matter and energy with their surroundings. As we reviewed in previous units, matter is the material stuff of the universe. Matter occupies space and has mass. Matter is made up of atoms.

Energy is not material. It does not have mass and it does not occupy space. We often describe energy as the capacity to perform work or bring about some sort of change. There are countless examples. A human performs work by flexing a muscle. A tiny cell within a human performs work by transporting particles into or out of the cell or by oxidizing fuel molecules. There are many different forms of energy (light energy, mechanical energy, heat energy, etc.), and we can broadly classify energy into two categories:

• Potential energy is energy in a stored form. It may be used, but it is not currently being used. The energy in food is an example of chemical potential energy.

• Kinetic energy is energy that is being used at the moment. A falling object, for example, has kinetic energy.

Energy can readily be converted between forms. For example, a book that falls from a shelf converts potential energy into kinetic energy. When someone moves the book back to the shelf, they convert kinetic energy into potential energy. The metabolism of life involves countless interactions between matter and energy and countless conversions between energy forms, so it is important to understand the distinction between matter and energy.

#### 5b. Apply the laws of thermodynamics and conservation of matter to metabolism

• What are the laws of thermodynamics?
• How do these laws affect biological processes?

Recall that the First Law of Thermodynamics states that energy is conserved (it cannot be created or destroyed; it can only be transferred and transformed). In ordinary chemical reactions (like biochemical reactions), matter is also conserved. Therefore, the overall amount of energy and matter entering the processes of glycolysis and cellular respiration is the same as the overall amount of energy and matter exiting these processes. What has changed are the forms of that energy and matter.

Energy enters as the potential chemical energy in the bonds of the glucose molecule. Some of that energy gets released as heat (unavailable for cellular work), and some of that energy ultimately gets stored in the bonds of ATP molecules. ATP is formed when ADP and inorganic phosphate combine. Matter enters as glucose and oxygen and, after many rearrangements of atoms, matter leaves as carbon dioxide and water. Review the principles of thermodynamics in subunit 2.2. Also review Energy and Thermodynamics, Metabolism Part 1, and Metabolism Part 2.

#### 5c. Describe the role of enzymes and how they function

• What is an enzyme?
• What kind of macromolecule makes up an enzyme?
• What is the function of an enzyme?
• What is a substrate?

Metabolism is the chemistry of life. Thousands of chemical reactions occur in a single cell – most of these chemical reactions rely on enzymes.

An enzyme is a protein that serves as a biological catalyst. A catalyst is a substance that greatly accelerates a chemical reaction, without actually being a reactant in that reaction. In other words, a catalyst (and therefore an enzyme) does not get changed into another substance (a product). The enzyme interacts with the reactants to make it more likely for the reactants to chemically react, turning them into products. We call the reactants of catalyzed reactions substrates. An enzyme operates by temporarily binding to substrates.

The rate of the reaction (its speed) when it is catalyzed by an enzyme is usually at least one million times faster than without the help of an enzyme. This is why enzymes are absolutely vital. Without enzymes, biochemical reactions of metabolism would occur much too slowly to support life.

Most importantly, enzymes are reusable since they do not get altered during the reaction – they can continue catalyzing the same sort of reaction until all of the substrate is depleted.

Review Energy and Metabolism and Metabolism Part 3 to make sure you are familiar with the basics of enzymes.

#### 5d. Explain the role of cellular respiration

• What is oxidation?
• What is reduction?
• How does cellular respiration accomplish its redox reactions?

Any living cell can extract energy from fuel and temporarily store that energy in the form of ATP, or a similar energy currency. This primary processing of fuel is called glycolysis. Only certain cells under the right conditions can continue where glycolysis leaves off, allowing much more usable energy to be extracted from the fuel. This additional processing of energy is called cellular respiration. Glycolysis and cellular respiration both extract usable energy from fuel by undergoing oxidation/reduction (or redox) reactions.

Oxidation is the loss of electrons from a particle (like a fuel molecule), whereas reduction is the gain of electrons. Since electrons are not destroyed in chemical reactions, oxidation occurs only if reduction also occurs. When something is oxidized (loses electrons), something else gets reduced (gains electrons). Organisms extract energy from fuel molecules by oxidizing these fuel molecules.

During cellular respiration, there is a substance (external to the process) that ultimately accepts the electrons that have been removed from the fuel. For aerobic organisms, that substance is oxygen, and when oxygen accepts these electrons (along with protons) from the fuel molecules, the oxygen gets reduced into water. Cellular respiration is important because it allows for maximal oxidation of fuels, which maximizes the amount of energy that can be extracted and stored as ATP.

Review glycolysis and cellular respiration in Introduction to Glycolosis, Cellular Respiration, The Citric Acid Cycle and Oxidative Phosphorylation, Glycolysis, More on Glycolysis, and The Process of Glycolysis.

#### 5e. Account for the matter inputs and outputs to glycolysis, pyruvate oxidation (preparatory reaction) the Krebs/Citric Acid Cycle, and the electron transport chain

• What are the material inputs and outputs for each of these processes?

Each component of the oxidation of glucose contributes to a series of reactions that can be summarized by a reaction equation that lists the inputs (reactants) and the outputs (products) of that process. The component processes that comprise the complete oxidation of glucose are glycolysis, pyruvate oxidation, the Citric Acid Cycle, and oxidative phosphorylation (including electron transport and chemiosmosis).

It is useful to review illustrations to make sense of these inputs and outputs, so pay careful attention to the figures in The Citric Acid Cycle and Oxidative Phosphorylation. You should also review subunits 5.5 and 5.6.

#### 5f. Describe the source and fate of energy in glycolysis, pyruvate oxidation (preparatory reaction), the Krebs/Citric Acid Cycle, and the electron transport chain

• What are the sources of energy and the fates of that energy in glycolysis, pyruvate oxidation, the Citric Acid Cycle, and oxidative phosphorylation?

The goal of the oxidation of a fuel (like glucose) is to transfer energy from that fuel into a versatile form of energy storage known as ATP (adenosine triphosphate). Many transfers of energy take place during the many reactions that make up glycolysis and cellular respiration. These transfers involve the original fuel (glucose), intermediate fuels, energy-carrying coenzymes (NAD and FAD), and ATP. Due to the third law of thermodynamics, some energy is lost as heat during each transfer. This lost heat energy becomes unavailable to perform work in the cell.

During glycolysis, energy starts out in the original fuel, glucose. By oxidizing glucose, some usable energy gets transferred into ATP and some into NADH. The intermediate fuel (pyruvate) that is left over contains usable energy, as well. During the oxidation of pyruvate, some of that usable energy gets transferred to more NADH. This leaves only acetyl coenzyme A as the remaining fuel, which still contains usable energy.

The citric acid cycle completes the oxidation of the remaining fuel (acetyl coenzyme A), and the usable energy that is extracted gets transferred to more NADH, to more ATP, and to FADH2. The carbon dioxide that remains from the fuel contains no usable energy (it is spent fuel). Oxidative phosphorylation serves to collect all of the usable energy that got transferred to NADH and FADH2 (in the earlier processes) and the usable energy is transferred to even more ATP.

The final acceptor of the electron is the molecule oxygen which subsequently changes to water as the final waste product. Refresh your understanding of this complex set of processes by reviewing subunits 5.4, 5.5, and 5.6.

#### Unit 5 Vocabulary

You should be familiar with these terms as you prepare for the final exam.

• acetyl coenzyme A
• ATP
• carbon dioxide
• catalyst
• cellular respiration
• chemiosmosis
• citric acid cycle
• coenzyme A
• electron transport
• energy
• enzyme
• glucose
• glycolysis
• kinetic energy
• Krebs cycle
• matter
• oxidation
• oxidative phosphorylation
• oxygen
• potential energy
• pyruvate
• pyruvate oxidation
• reaction rate
• redox
• reduction
• substrate
• water
• work

## Unit 6: Photosynthesis

#### 6a. Explain the role of photosynthesis

• What are the two ecological categories of organisms?
• What type of organism is capable of photosynthesis?
• How does photosynthesis relate to nutrient cycling?

We can ecologically classify any living organism as an autotroph or a heterotroph. Autotrophs ("self-feeders") are also known producers because they produce organic compounds from inorganic materials. They make their own food. Autotrophs require energy to do so, and most autotrophs use light energy in the process of photosynthesis.

We call heterotrophs ("feeders on others") consumers because they feed on organic compounds produced by other organisms. Maximally extracting energy from an organic fuel (food) involves the complete oxidation of the fuel (including glycolysis and cellular respiration); this leaves inorganic carbon dioxide.

Photosynthesis reverses these processes by starting with inorganic carbon dioxide and transforming it into organic compounds that can be used as fuel. In this way, photosynthesis is an important part of carbon cycling, because photosynthesis has a reciprocal relationship with glycolysis and cellular respiration.

Photosynthesis is of vital importance to organisms, because photosynthesis provides food for photosynthetic organisms (the producers) and the consumers of the world. As you review Overview of Photosynthesis, pay close attention to the summary reaction for photosynthesis (figure 5). Notice that photosynthesis is the reverse of the summary reaction for glycolysis and cellular respiration.

#### 6b. Describe where matter originates and ends up during photosynthesis

• What are the inputs and outputs of photosynthesis?

Recall that photosynthesis has a reciprocal relationship with the complete oxidation of glucose (glycolysis and cellular respiration). This means the summary reaction for each process is the reverse of the summary reaction for the other process. As you review the inputs and outputs of photosynthesis, appreciate this reciprocal relationship by noticing that the inputs into photosynthesis are the outputs from the complete oxidation of glucose and the outputs from photosynthesis are the inputs into the complete oxidation of glucose.

 Inputs Process Outputs Water (Includes oxygen and hydrogen) Carbon Dioxide (inorganic carbon source) Energy (in the form of sunlight) Photosynthesis Glucose (organic carbon product; includes hydrogen from water) Oxygen (from water after hydrogen is extracted) Glucose (organic carbon source; includes hydrogen) Oxygen Complete Oxidation of Glucose (Glycolysis and Cellular Respiration) Water (formed when oxygen joins with hydrogen) Carbon Dioxide (inorganic carbon product left over after hydrogen is extracted) Energy (in the form of chemical energy in the bonds of glucose)

Keep these inputs and outputs in mind as you review the biochemical components of photosynthesis in The Light-Dependent Reactions of Photosynthesis and The Calvin Cycle.

#### 6c. Describe how photosynthesis converts low-energy molecules into energy-rich carbohydrates

• How does photosynthesis transform low-energy, inorganic molecules into high-energy, organic molecules (fuels)?
• What is the name for the process of incorporating inorganic molecules into organic compounds?

Although cells can use many organic molecules for fuel, carbohydrates are the principal fuel for cells (this includes glucose). Carbohydrates make excellent fuels because they contain many C-H bonds. While energy is released by oxidizing an organic fuel molecule into carbon dioxide, it takes energy to reverse the process and reduce carbon dioxide into an organic fuel.

Incorporating carbon from an inorganic source, such as carbon dioxide, into organic compounds, such as glucose, is called carbon fixation. This is an extremely important function of photosynthesis. Carbon fixation results in products (organic compounds) that contain more chemical energy than the reactants (carbon dioxide molecules). This process requires an input of energy.

Sunlight provides the input of energy for the carbon fixation that occurs during photosynthesis. Powered by light energy, water molecules are split into oxygen and hydrogen atoms, and the hydrogen atoms from the water bond to the carbon atoms from carbon dioxide molecules to form high-energy carbohydrates. This occurs in two major pathways that comprise photosynthesis. Light-dependent reactions split the water, while the Calvin Cycle builds the carbohydrate molecules.

To review, see The Light-Dependent Reactions of Photosynthesis and The Calvin Cycle.

#### 6d. Explain the role of the light-dependent phase of photosynthesis

• What is the function of the light-dependent reactions?
• What are the requirements for (inputs into) the light-dependent reactions?
• What are the products of (outputs from) the light-dependent reactions?

Photosynthesis consists of two major components: the light-dependent reactions and the Calvin cycle.

The overall purpose of photosynthesis is to build carbohydrate molecules. This process requires energy from sunlight, but photosynthetic organisms cannot use sunlight energy directly to build these carbohydrates. Instead, the sunlight energy must be transformed into chemical energy that is temporarily stored in the forms of ATP and NADPH molecules. The Calvin cycle uses ATP and NADPH as energy sources to build carbohydrate molecules.

So, the main function of the light-dependent reactions is to produce ATP and NADPH. Overall, the light-dependent reactions require sunlight, water, NADP+, and ADP. The products are heat, oxygen, NADPH, and ATP. Make sense of these inputs and outputs as you review Photophosphorylation.

#### 6e. Explain the role of the light-independent phase of photosynthesis, and describe how it is related to the light-dependent reactions

• What is the function of the Calvin cycle?
• What are the requirements for (inputs into) the Calvin cycle?
• What are the products of (outputs from) the Calvin cycle?
• What is the relationship between the Calvin cycle and the light-dependent reactions?

The Calvin cycle, which is the light-independent reactions, is the component of photosynthesis where carbon fixation takes place. In other words, during the Calvin cycle inorganic carbon dioxide gets transformed into organic compounds (molecules of glyceraldehyde-3-phosphate, or G3P). This expensive process requires energy in the form of two energy-storing compounds (NADPH and ATP).

By using the energy stored in NADPH and ATP, the Calvin cycle takes in carbon dioxide and (after several rearrangements of atoms, forming several different intermediates) produces a three-carbon compound called G3P. These G3P molecules are chemically transformed into other organic molecules for various uses in the organism.

Light energy indirectly powers the Calvin cycle, because the Calvin cycle requires NADPH and ATP, and the light-dependent reactions (using sunlight) produce NADPH and ATP for the Calvin cycle. As you review the particulars of the Calvin cycle, ensure that you understand how the light-dependent reactions must operate first if the Calvin cycle is going to operate at all.

To review, see The Calvin Cycle and Photophosphorylation.

#### 6f. Explain how energy is transformed and transferred during photosynthesis

• How is energy transferred stepwise from sunlight to carbohydrate molecules?
• What energy-carrying compounds are used as intermediates in the process?
• What is the fate of the products of photosynthesis?
• How can plants store usable energy that is incorporated during photosynthesis?
• How does photosynthesis contribute to the accumulation of biomass?
• What part of photosynthesis directly produces biomass?

Photosynthesis uses sunlight energy to fix carbon dioxide into carbohydrates. However, the transfer of energy from sunlight to the chemical energy of the carbohydrate product is not direct.

Photosynthetic organisms, such as plants, algae, and cyanobacteria, are not able to use sunlight directly to power the fixation of carbon dioxide into carbohydrates. The carbon fixation requires stored energy in the bonds of two important energy-carrying compounds:

• ATP is important as a general energy currency in cells, and it's also required in parts of the Calvin cycle of photosynthesis. The light-dependent reactions transform ADP into ATP, storing some of the energy originally in the sunlight.

• NADPH temporarily stores energy for use in the Calvin cycle of photosynthesis, just as the highly related compound, NADH, stores energy during cellular respiration. The light-dependent reactions transform NADP+ into NADPH, storing some of the energy originally in the sunlight.

As you review the light-dependent reactions and the Calvin Cycle, pay attention to how energy gets transformed from light energy into chemical energy as energy gets transferred from sunlight to ATP and NADPH and finally to the C-H bonds of the carbohydrates produced.

##### Energy Storage in Plants

The major accomplishment of photosynthesis is carbon fixation, the production of organic compounds from inorganic compounds. The direct, organic product of the Calvin cycle is a three-carbon carbohydrate. That organic product can then be used as a precursor to building organic macromolecules, including proteins, lipids, nucleic acids, and polysaccharides, or it can be used to build monosaccharides like glucose.

If a plant needs to store energy in the form of oxidizable fuels, the primary sugar that is produced to store chemical energy is sucrose. Sucrose is a disaccharide consisting of the two monosaccharides, glucose and fructose. Sucrose is a major component of sap that travels through a plant's vessels to deliver that stored energy to different parts of the plant. Plants can also store energy in lipid forms (fats and oils) as occurs, for example, in nuts.

##### Biomass

Biomass is matter produced by living organisms. It consists of the material making up both living and dead organisms. As such, biomass is organic material.

Since biomass is organic matter, any biological process that transforms inorganic matter into organic matter – any process that fixes carbon – is a process that produces biomass. Carbon fixation occurs in all autotrophs (producers), but the vast majority of autotrophs are specifically photoautotrophs, because their method for carbon fixation is photosynthesis.

The Calvin cycle is the component of photosynthesis that actually fixes the carbon from carbon dioxide into the organic form of carbohydrates that are produced, so the Calvin cycle directly contributes to the accumulation of biomass. Recall that organic biomass can be converted back into inorganic carbon dioxide in autotrophs and heterotrophs by oxidizing the organic compounds using glycolysis and cellular respiration. As you review the Calvin Cycle, pay particular attention to the fact that inorganic carbon dioxide enters the process and organic carbohydrate molecules (G3P) exit the process.

To review, see The Light-Dependent Reactions of Photosynthesis and The Calvin Cycle.

#### 6g. Explain how plants have adapted to deal with the problem of photorespiration

• What is photorespiration?
• Why is photorespiration problematic for a plant?
• What kinds of plants are able to minimize the occurrence of photorespiration?
• How do plants minimize the occurrence of photorespiration?

A crucial step in the Calvin cycle is the fixation step, which takes in carbon dioxide and joins it with an intermediate compound (ribulose bisphosphate), thus incorporating inorganic carbon dioxide into an organic compound. RuBisCO (ribulose bisphosphate carboxylase oxygenase) is the enzyme that catalyzes this step. RuBisCO can operate to join either carbon dioxide or oxygen to ribulose bisphosphate. However, joining oxygen instead of carbon dioxide is counterproductive, because no carbon fixation (the purpose of the Calvin cycle) takes place.

We call this counterproductive process (incorporating oxygen instead of carbon dioxide) photorespiration. Two major categories of plant species have evolved ways around this problem:

• C4 plants separate the process of carbon dioxide intake (which occurs in superficial cells called mesophyll cells) from the process of carbon fixation in the Calvin cycle (which occurs in deeper cells called bundle sheath cells).

• CAM plants take in carbon dioxide and store it in the form of organic acids during the night when their stomata are open. During the day, the organic acids get broken down to release the carbon dioxide for the Calvin cycle, while the stomata are closed (preventing oxygen from interfering).

These two types of plants operate the Calvin cycle more efficiently because photorespiration is minimized. As you review C4 plants and CAM plants, notice they accomplish the same thing in two different ways.

To review, see C-4 and CAM Photosynthesis.

#### 6h. Identify the differences in photosynthesis in reference to CAM and C4 plants

• How is a C4 plant different from a CAM plant?

Both C4 plants and CAM plants have evolved mechanisms to minimize the costly and wasteful occurrence of photorespiration. Both types of plants accomplish their avoidance of photorespiration by separating two processes: the intake of carbon dioxide, and the operation of the Calvin cycle.

The major difference between C4 and CAM plants is that C4 plants avoid photorespiration by separating the two processes spatially (they occur in separate spaces), whereas CAM plants avoid photorespiration by separating the two processes temporally (they occur at separate times).

A C4 plant takes carbon dioxide into mesophyll cells, then it transfers that carbon dioxide into different cells (bundle sheath cells) that are farther away from the atmospheric oxygen. The Calvin cycle then occurs in this separate space (the bundle sheath cells).

A CAM plant opens its stomata only at night, taking in carbon dioxide that gets stored in acid form until the next day. During daylight, the stomata are closed (disallowing oxygen from entering), and the acids are processed to release the carbon dioxide to the Calvin cycle, which occurs at a separate time compared to the intake of carbon dioxide.

As you compare C4 plants to CAM plants and review the avoidance of photorespiration, keep in mind that a typical plant (C3) operates less efficiently, because there is no separation of the processes of carbon-dioxide intake and Calvin-cycle operation.

To review, see C-4 and CAM Photosynthesis.

#### 6i. Explain what the "carbon cycle" is and how it relates to the conservation of matter

• What is the carbon cycle?
• Why is it a cycle?
• How does the carbon cycle exemplify conservation of matter?

The carbon cycle refers to the many chemical transformations that involve compounds containing carbon. The carbon cycle is cyclic because there is a continuous alternation between the carbon of organic compounds and the carbon of inorganic compounds. Inorganic carbon dioxide gets fixed (by autotrophs) into organic compounds. These organic compounds get converted into other organic compounds (including simple organic compounds like monosaccharides, nucleotides, and amino acids, as well as complex macromolecules like polysaccharides, nucleic acids, lipids, and polypeptides).

The carbon in these organic compounds gets passed from organism to organism as they feed on each other. Organisms use some of the organic molecules as fuel, and the oxidation of these organic fuels (to provide energy for the organisms) returns the carbon to inorganic form (carbon dioxide) to complete the cycle. In this cycle of transformations, carbon (matter) remains in the ecosystem (it is conserved). It is not destroyed; it is merely transferred and transformed.

Review this material in The Carbon Cycle.

#### Unit 6 Vocabulary

You should be familiar with these terms as you prepare for the final exam.

• ATP
• autotroph
• biomass
• bundle sheath cell
• C3 Plant
• C4 Plant
• Calvin cycle
• CAM Plant
• carbohydrate
• carbon dioxide
• carbon fixation
• cellular respiration
• conservation of matter
• consumer
• disaccharide
• energy
• G3P
• glucose
• glycolysis
• heterotroph
• inorganic
• light-dependent reactions
• light-independent reactions
• lipid
• mesophyll cell
• monosaccharide
• nutrient cycling
• organic
• oxidation
• oxygen
• photoautotroph
• photorespiration
• photosynthesis
• producer
• reduction
• RuBisCO
• sucrose
• stomata
• water

## Unit 7: Cellular Reproduction: Mitosis

#### 7a. Differentiate DNA from RNA

• How are DNA and RNA chemically different?
• How are DNA and RNA functionally different?

As their names indicate, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are both nucleic acids. Any nucleic acid is a polymer made up of monomers called nucleotides. Any nucleotide consists of three components:

1. A pentose (five-carbon sugar)

2. A nitrogenous base attached to the pentose

3. A phosphate group also attached to the pentose

For DNA, the specific pentose in each of its nucleotides is deoxyribose, whereas RNA features ribose as the pentose in each of its nucleotides. There are normally four kinds of DNA nucleotides, because there are four normal nitrogenous bases used in DNA:

• Guanine

• Cytosine

• Thymine

RNA also features four kinds of nucleotides, and the nitrogenous bases are nearly the same as for DNA, except that RNA uses uracil instead of thymine.

DNA functions for self-replication (before a cell divides into two cells) and for transcription, a process that produces RNA. There are different functional categories of RNA including mRNA, tRNA, rRNA, and others.

Watch DNA and RNA to review the similarities and differences between these important macromolecules.

#### 7b. Describe how different organisms reproduce

• What are the different ways that organisms reproduce?
• Why do organisms go through cell division?

To continue survival, organisms must pass their traits on to reproduced offspring. Prokaryotic organisms reproduce by binary fission. These unicellular organisms divide to continue the existence of the species. Multicellular organisms divide for growth, development and repair. Eukaryotic organisms reproduce asexually and sexually. Asexual reproduction involves transferring 100% of DNA to their offspring. Sexual reproduction involves offspring sharing DNA from different parents.

Review this material in The Genome. Pay particular attention to the diagram in Figure 6.1.

#### 7c. Recognize the phases of mitosis

• What is mitosis?
• What are the phases of mitosis?
• What types of cells undergo mitosis?

Mitosis is the division of a cell nucleus. Since only eukaryotic cells feature a nucleus, only eukaryotic cells undergo mitosis. Mitosis is part of eukaryotic cell division (the other part is cytokinesis, which is the division of the cytoplasm). Mitosis occurs in the following phases, listed in the order in which they occur:

• Prophase

• Prometaphase

• Metaphase

• Anaphase

• Telophase

Review these phases in Mitosis.

#### 7d. Describe the stages of the cell cycle

• What are the phases of the cell cycle?
• What are the major events occurring in each phase of the cell cycle?

The cell cycle includes all parts of the normal lifetime of a single, eukaryotic cell. The cell cycle begins when a cell is created via the division of a previous cell and ends when the cell undergoes its own cell division to produce two new cells. A single cell cycle consists of four major phases of unequal length:

1. The G1 phase includes most of the normal lifetime of the cell. During G1, the cell goes about using its DNA as instructions for building proteins that allow the cell to metabolize and function for its specific purpose. During this time, the DNA has not yet replicated.

2. The S phase is the first step in a cell's preparation for cell division. During the S phase, the DNA is replicated, yielding two identical copies of the DNA (one for each of two cells that will be created when this cell divides).

3. The G2 phase follows the S phase. Like the G1 phase, the G2 phase features much protein synthesis and metabolism, but most of this activity is concentrated on preparing for cell division.

4. The M phase includes mitosis (the division of the nucleus) and cytokinesis (division of the cytoplasm). By the end of the M phase, two separate cells have been created from the original cell, and each of these two cells enters its own cell cycle.

Review this material in The Cell Cycle. Pay particular attention to the diagram in Figure 1.

#### 7e. Describe what occurs in each of the phases of mitosis

• What are the five phases of mitosis?
• What happens in each phase?

Mitosis (the division of a eukaryotic cell's nucleus) occurs in five phases:

1. Prophase: The first phase of mitosis. The microtubules that make up the mitotic spindle begin forming on the two centrioles, and these centrioles start to move to opposite poles.

2. Prometaphase: Construction of the mitotic spindle is completed, and the nuclear envelope disintegrates, allowing microtubules of the mitotic spindle to connect to replicated chromosomes.

3. Metaphase: Replicated chromosomes (each consisting of two identical sister chromatids) move along the spindle tubules until all replicated chromosomes are aligned at the metaphase plate, midway between the poles.

4. Anaphase: Each pair of sister chromatids (one pair for each replicated chromosome) separate and move toward opposite poles. At this point, they are no longer called chromatids; rather each is an unreplicated chromosome.

5. Telophase: The unreplicated chromosomes reach opposite poles. Each pole becomes a new nucleus, as each pole becomes enclosed by a new nuclear envelope.

In most cases, cytokinesis (division of the cytoplasm) occurs near the end of telophase, when the original cell separates into two distinct cells, each with its own nucleus.

Review the events of each mitotic phase in this lecture, A Tour of Mitosis.

#### 7f. Explain the purpose of mitosis

• Why is mitosis important?
• Under what conditions does a cell undergo mitosis?

Recall that mitosis is the division of a eukaryotic cell's nucleus. One of the hallmarks of mitosis is that two genetically identical nuclei are produced when the original nucleus divides. The chromosomes in one nucleus are exactly the same as the chromosomes in the other nucleus. Moreover, each nucleus is genetically identical to the nucleus in the original cell (before mitosis). Mitosis creates two nuclei from one, and each of these nuclei can serve as the nucleus of a new cell.

When cytokinesis accompanies mitosis, the cytoplasm divides, forming two distinct cells. Each cell contains its own nucleus (created by mitosis). Cell division that features mitosis allows one parent cell to divide into two, genetically identical daughter cells. Creating new cells is important for several reasons:

• Mitosis allows for cell proliferation for the purpose of development of a unicellular zygote into a multicellular organism.

• Mitosis allows for cell proliferation for the purpose of growth of a multicellular organism.

• Mitosis allows for creation of new cells to replace cells that have been damaged by injury or infection in a multicellular organism.

• Mitosis is a means for a unicellular, eukaryotic organism to reproduce.

As you review, think about how mitosis (as part of the M phase) fits into The Cell Cycle.

#### Unit 7 Vocabulary

You should be familiar with these terms as you prepare for the final exam.

• anaphase
• asexual reproduction
• cell cycle
• centrosome
• chromatid
• chromosome
• cytokinesis
• cytosine
• deoxyribonucleic acid
• deoxyribose
• DNA
• eukaryotic
• G1 phase
• G2 phase
• guanine
• M phase
• metaphase
• metaphase plate
• microtubule
• mitosis
• mitotic spindle
• multicellular
• nitrogenous base
• nuclear envelope
• nucleic acid
• nucleotide
• nucleus
• pentose
• phosphate
• prometaphase
• prophase
• replication
• ribonucleic acid
• ribose
• RNA
• sexual reproduction
• S phase
• telophase
• thymine
• unicellular
• uracil

## Unit 8: Cellular Reproduction: Meiosis

#### 8a. Identify the different types of daughter cells produced by meiotic cell division

• What is the difference between the gamete and somatic cell?
• How do diploid and haploid cells differ from each other?

Organisms that reproduce sexually must create cells that have half of their chromosomes. A gamete is a cell formed by meiosis that is non-identical to the original parent cell. We call the cells that contain all of the chromosomes somatic cells, which we also call body cells. Some body cells are in sex organs that reproduce gametes. Somatic cells are diploid; gametes are haploid.

Review The Cellular Basis of Reproduction for an overview of the different cells meiosis produces.

#### 8b. Diagram and label the phases of meiosis given a number of chromosomes or chromosome pairs

• What happens during each phase of meiosis?

Meiosis proceeds in essentially the same way in any eukaryotic cell that undergoes meiosis. The main difference is the number of chromosomes involved. The number of chromosomes depends on the species. The variable, $N$, represents the number of different kinds of chromosomes. We also call it the haploid number. This is because a haploid cell contains just one of each type of chromosome. A diploid cell is characterized as $2N$, because a diploid cell has two of each type of chromosome (one from each sexual parent).

Meiosis allows one diploid cell to become four haploid cells. Each haploid cell is not only genetically different from the original diploid cell, but each haploid cell is also genetically different from the other three haploid cells produced. The stages of meiosis are illustrated below for a species with $N=2$. The original, diploid cell in this example ($2N$) therefore has $2\times 2=4$ overall chromosomes. Each of the four cells produced has $N=2$ overall chromosomes (they are haploid). Whatever the value of $N$, during metaphase of meiosis I, $N$ pairs of homologous, replicated chromosomes line up, and during metaphase of meiosis II, $N$ individual, replicated chromosomes line up.

Review Meiosis. You should be able to draw what the stages look like for any other value of $N$.

#### 8c. Compare and contrast mitosis and meiosis

• How are mitosis and meiosis similar?
• How are mitosis and meiosis different?

Mitosis and meiosis are two alternative processes that can be involved in eukaryotic cell division. Here are key similarities:

• Mitosis and meiosis are both processes that divide the nucleus of a cell.

• Both processes occur in phases including prophase, prometaphase, metaphase, anaphase, and telophase.

• Meiosis II is essentially identical to mitosis, but meiosis II occurs in each of the two cells previously produced in meiosis I.

Here are key differences:

• Mitosis produces two cells that are genetically identical to the parent cell; meiosis produces four cells that are genetically distinct from each other and from the parent cell.

• Mitosis is used to produce duplicate cells for the purpose of growth of a multicellular organism or replacement of lost cells; meiosis is used to produce haploid cells out of a diploid cell for the purpose of sexual reproduction.

• Mitosis involves only one round of division; meiosis involves two rounds of division (meiosis I and II).

• In mitosis, chromosomes act individually, and homologous chromosomes do not synapse; in meiosis, homologous chromosomes go through synapsis or come close together, and each homologous pair acts throughout meiosis I as a unit.

• Mitosis does not feature crossing over; meiosis I features crossing over.

• During the metaphase of mitosis, individual, replicated chromosomes line up midway between poles (without pairing of homologs); During the metaphase of meiosis I, homologous pairs of chromosomes line up as tetrads midway between poles.

• During anaphase of mitosis, sister chromatids separate; in anaphase of meiosis I, homologs separate.

• Mitosis maintains the ploidy; meiosis cuts the ploidy in half.

Review Meiosis and Mitosis, Meiosis, and Sexual Reproduction to compare and contrast these important processes.

#### 8d. Explain the role of meiosis

• What is the purpose of meiosis?
• How do aspects that make meiosis different from mitosis allow meiosis to fulfill that purpose?

While there are several similarities between mitosis and meiosis, there are some critically important differences that allow the two processes to serve different purposes.

The life cycle of any sexual species features fertilization, which is the fusion of unicellular gametes (one male gamete and one female gamete) to produce a unicellular zygote. The unicellular zygote that fertilization produces carries chromosomes from both gametes. Therefore, the ploidy of the zygote is double the ploidy of the gametes.

If fertilization were the only process occurring each generation, the ploidy would double each generation (tetraploid, then octaploid, etc.), and the zygote would not be able to contain the DNA.

To prevent the ploidy from doubling each generation, a separate process is needed to cut the ploidy in half. That process is meiosis.

Specifically, the reduction of ploidy occurs in meiosis I, when homologs separate and go to distinct daughter cells. Since a diploid cell that undergoes meiosis will produce haploid cells (gametes), when these haploid gametes fuse (in fertilization), the zygote will be diploid. By alternating meiosis and fertilization each generation, the ploidy simply goes back and forth between haploidy and diploidy (rather than continually increasing).

Another important purpose of meiosis is to drastically increase the genetic variability of the gametes produced. This increase in genetic variability comes in the forms of crossing over (during prophase of meiosis I) and independent assortment (during metaphase of meiosis I).

Review Mitosis, Meiosis, and Sexual Reproduction. Crossing over and independent assortment produce new genetic combinations, and separation of homologs reduces the ploidy.

#### Unit 8 Vocabulary

You should be familiar with these terms as you prepare for the final exam.

• 2N
• anaphase
• chromosome
• crossing-over
• diploid
• eukaryotic
• fertilization
• gamete
• genetic variability
• haploid
• homolog
• homologous
• independent assortment
• meiosis
• meiosis I
• meiosis II
• metaphase
• mitosis
• N
• nucleus
• ploidy
• prophase
• synapsis
• telophase
• zygote

## Unit 9: Mendelian Genetics and Chromosomes

#### 9a. Explain how information flows from genotype to phenotype at the molecular level

• What is a genotype?
• What is a phenotype?
• How are genotype and phenotype different?
• What is the connection between genotype and phenotype?

We often say our genes give us our traits. This is true, but only indirectly. Genes are sequences of DNA, and these genes provide instructions for how to make corresponding sequences of RNA. These sequences of RNA, in turn, serve as instructions for how to build proteins.

Proteins are the final product of gene expression. The particular proteins that are built in the cells of an organism are what give that organism its traits. The proteins directly determine the traits, but the genes indirectly determine the traits, because the genes indirectly instruct the cells how to build the proteins.

There may be multiple possible traits for any given characteristic, such as black, brown, or red hair color. We call the trait an individual exhibits for a given characteristic, such as the black hair trait for the hair-color characteristic, that individual's phenotype. That phenotype depends on the proteins produced, which depends on the version of the corresponding gene (DNA) that individual possesses.

An individual's genotype refers to the DNA sequence for a particular gene. Consequently, your genotype indirectly determines your phenotype.

Review how these terms relate, and how they differ, in the section Phenotypes and Genotypes.

#### 9b. Explain how the terms: genotype, phenotype, homozygous, heterozygous, dominant, recessive, co-dominant, and sex-linkage are used

• Distinguish between genotype and phenotype.
• Distinguish between homozygous and heterozygous.
• Distinguish between dominance and recessivity.
• What is co-dominance?

When scientists study organisms genetically, they usually focus on one single gene. A gene is a stretch of DNA coding for a particular protein – a gene controls a particular characteristic. Alternative versions of a gene (with different nucleotide sequences) are called alleles. A diploid cell features two alleles for any particular gene because a diploid cell features two of every kind of chromosome, one from each parent.

An individual's genotype is the sequence of symbols that represent the particular alleles an individual possesses for the gene being studied. Since alleles code for proteins, and proteins give organisms their traits, alleles indirectly determine phenotype. A phenotype is the observable trait an individual exhibits for the characteristic being studied. Since a diploid cell contains two alleles for a gene, there are two possibilities:

• Both alleles for the gene under study are the same version (they are identical). In this case, the individual is homozygous.

• The two alleles for the gene under study are different versions. In this case, the individual is heterozygous.

One allele is typically dominant over another allele, which is called recessive. When one or two dominant alleles occur in a cell, the dominant phenotype shows itself. For example, if there is just one dominant allele and the other allele is recessive, the single dominant allele will dominate over the recessive allele. The dominant phenotype is expressed (shows itself), but the recessive phenotype is not expressed. The only way a recessive phenotype is expressed is when both of the alleles are recessive. This individual is homozygous recessive.

A heterozygous individual features one dominant allele and one recessive allele and expresses the dominant phenotype. A homozygous dominant individual (both alleles are dominant) also expresses the dominant phenotype. Codominance describes a special case when two different alleles are both simultaneously expressed. In other words, one allele does not dominate the other. A good example is Type AB blood, which expresses both Type A and Type B phenotypes.

Sex linkage refers to a gene that is part of a sex chromosome. Consequently, the expression is different in males compared to females. For example, in humans, females have two X chromosomes, so they have two alleles for sex-linked genes. Males, on the other hand, have one X chromosome and one Y chromosome, but the Y chromosome does not have all of the genes that an X chromosome has. Therefore a male has only one allele for a sex-linked gene.

Make sure you understand these important definitions for the laws of inheritance before you proceed. Review Extensions of the Laws of Inheritance.

#### 9c. Given a pedigree, infer whether the trait in the diagram is dominant or recessive, and indicate individual genotypes when possible

• What is a pedigree?
• How does a pedigree use symbols to indicate phenotypes?

A pedigree is merely a symbolic representation (or chart) of the phenotypes and sexes of individuals, with the ancestral relationships between these individuals. Keep the laws of inheritance in mind, as you study a pedigree to determine whether a given trait is dominant or recessive.

Once you determine the dominance/recessivity relationship, a pedigree is a useful tool for determining the possible genotypes of individuals, based on the phenotypes indicated in the chart.

For example, in this pedigree, the original parents (square and circle at the top) both carry the unaffected phenotype (because their symbols are not filled). They produced some offspring that were unaffected and some that were affected. The only way for this to be possible is if the affected phenotype is the recessive trait. An offspring with the affected (recessive) phenotype must be homozygous recessive; otherwise, that individual would have the unaffected (dominant) trait.

Therefore, each original parent must be heterozygous, because each parent must pass on a recessive allele to produce a homozygous recessive offspring. We can make the same inference about the two parents listed rightmost in the generation enclosed by the red dashes because they also produced recessive offspring. A good example of this is when two parents with black hair (dominant) have a child who has red hair (recessive).

Review Pedigrees for more on the laws of inheritance.

#### 9d. Solve genetic problems involving monohybrid crosses with dominant and recessive traits, codominant traits, and sex-linked traits

• What is a genetic cross?
• How do you use a Punnett square?

A genetic cross is an incidence of sexual reproduction that involves a male and female from a particular species. A monohybrid cross is a cross where you are studying only one gene (one characteristic), and the two parents usually differ in their genotypes. For example, one parent might be homozygous dominant (AA) and the other might be homozygous recessive (aa).

Knowing the genotypes of the parents allows us to draw a Punnett square to represent the possible fertilization events involving these two parents. Fertilization is the fusion of a male gamete and a female gamete to produce a zygote.

A Punnett square lists (on adjacent sides of the square) all possible gametes that can be produced by each parent. By matching up each possible gamete from one parent with each possible gamete from the other parent, the boxes within a Punnett square list all possible zygotes that can be produced by these parents. Moreover, the ratio of different possible genotypes (the genotypic ratio) and of different corresponding phenotypes (the phenotypic ratio) can be computed for the generation created by the particular cross.

Review crosses in Introduction to Heredity. Practice constructing Punnett squares to make sure you understand the concepts they represent.

#### 9e. Solve genetic problems involving dihybrid crosses with dominant and recessive traits, codominant traits, and sex-linked traits

• How is a dihybrid cross different from a monohybrid cross?
• How are they similar?

Once you know the genotypes (for a particular characteristic or gene) for two parents, it is possible to compute the probabilities of various genotypes or phenotypes in the offspring they produce. This is because the genotype of an offspring results from randomly selecting one of the two alleles for the gene in one parent, and randomly selecting one of the two alleles in the other parent.

The sperm and egg carry these randomly selected alleles. When the sperm and egg fuse (fertilization) to produce the zygote of the offspring, the genotype of the offspring is a combination of an allele from the father and an allele from the mother. For example, when a male with genotype Aa mates with a female with genotype $aa$, we symbolize this mating (or cross) as $Aa \times aa$.

The probability of an offspring having the $AA$ genotype

Having the $AA$ genotype requires receiving an $A$ allele from the father and an $A$ allele from the mother. The mother in this example has no $A$ allele, so the probability is zero.

The probability of an offspring having the $Aa$ genotype

Having this genotype requires receiving an $A$ allele from one parent (either one) and receiving an $a$ allele from the other parent. The probability of receiving an $A$ allele from the father is one-in-two (50% or 0.5). The probability of receiving an allele from the mother is two-in-two (100% or 1.0), because that is all she has to give. The overall probability for $Aa$ is the product of these two individual probabilities.

In this case, it is 0.5 × 1.0 = 0.5. In other words, there is a 0.5 (50%) probability that any given offspring of these parents will have the $Aa$ genotype.

The probability of an offspring having the $aa$ genotype

Using the same reasoning we used to compute $Aa$, there is also a 0.5 probability for the aa genotype, because there is a 0.5 probability of receiving an $a$ allele from the father, and a 1.0 probability of receiving an $a$ allele from the mother. The overall probability is 0.5 × 1.0 = 0.5.

In this example, aa is the only other possible genotype besides $Aa$.

You can think about fertilization as if you were to randomly choose a card from two cards a father holds, and then randomly choose a second card from two cards a mother holds. The two cards you draw (representing the sperm and egg) determine the two cards you (the offspring) will have (representing the genotype of the zygote). Keep this in mind as you review Mendel's Laws of Inheritance.

Like a monohybrid cross, a dihybrid cross is a genetic cross. This means it involves fertilization of a female gamete (from the female parent) by a male gamete (from the male parent) to produce zygotes that can develop into adult offspring. The fundamental difference between a monohybrid cross and a dihybrid cross is that a monohybrid cross tracks only gene (corresponding to one characteristic), whereas a dihybrid cross simultaneously tracks two different genes (corresponding to two different characteristics).

Since two different genes are studied, the genotypes in a dihybrid cross are longer sequences of symbols (both for the alleles and for the zygotes), because they need to indicate alleles for two genes. Also, because there are more possible combinations of alleles, a dihybrid cross will feature more boxes in its Punnett square compared to a monohybrid cross. These differences are illustrated in the generic examples shown below.

Monohybrid cross: $Aa$ (heterozygous male) $\times Aa$ (heterozygous female)

• Number of genes under study: One (Gene $A$)
• Genotypes of possible male gametes: $A$, $a$
• Genotypes of possible female gametes: $A$, $a$
• Punnett square:

Dihybrid cross: $AaBb$ (doubly heterozygous male) $\times AaBb$ (doubly heterozygous female)

• Number of genes under study: Two (Gene $A$ and Gene $B$)
• Possible male gametes: $AB$, $aB$, $Ab$, $ab$
• Possible female gametes: $AB$, $aB$, $Ab$, $ab$
• Punnett square:

Review the dihybrid example in the second video in Introduction to Heredity to ensure you understand how dihybrid crosses differ from monohybrid crosses.

#### 9f. Define mutation and explain how mutations can result in an altered phenotype

• What is a mutation?
• How can mutation affect phenotype?

A mutation is an accidental change in the DNA sequence of an organism. An organism's DNA is arranged in chromosomes. Each chromosome is a long sequence of DNA nucleotides. A gene is a subsequence of DNA nucleotides within the longer sequence that makes up the chromosome. A mutation arises when the sequence gets changed – either by an error during DNA replication or by some other accident, such as exposure to certains chemicals or forms of radiation. The reason a gene is able to serve as a code (stored information) is due to its particular sequence of DNA nucleotides.

Mutation changes that sequence. The code is changed, and the RNA will also be altered when the altered code is used to make RNA. Similarly, when the code from the altered (mutated) version of RNA is used to build a protein, the protein may be different from the unmutated version.

Since proteins directly determine phenotypes, a mutant protein (resulting from a mutant form of DNA for the corresponding gene) may alter the phenotype. Mutation is the original source of genetic variation. It explains why we have different species and differences among individuals of the same species.

In the case of heterozygote advantage, heterozygous individuals are more fit than both types of homozygous individuals (homozygous dominant and homozygous recessive). For example, a mutant allele for a human hemoglobin gene codes for a mutant form of the hemoglobin protein. This situation is deleterious (causes harm or damage) because it causes sickle cell disease. However, the mutant form of hemoglobin also confers higher resistance to malaria.

A homozygous recessive individual will develop sickle-cell disease, which drastically reduces fitness. A homozygous dominant individual will not develop sickle-cell disease, but that person will not be resistant to malaria. However, a heterozygous individual will not develop sickle-cell disease (because the one normal allele will prevent the disorder), and they will also have increased resistance to malaria (because of the mutant allele).

Therefore, heterozygous individuals have the greatest chance of passing on their alleles to the next generation – this includes the mutant allele. The population maintains the sickle-cell allele by natural selection. To make sense of heterozygote advantage, review the laws of inheritance. Keep in mind that each allele is a code for a particular protein, and therefore each allele corresponds to a particular trait.

Review Mutations and Laws of Inheritance. As you continue to study genetics, keep in mind that accidental mutations are the source of differences in genotypes and phenotypes.

#### Unit 9 Vocabulary

You should be familiar with these terms as you prepare for the final exam.

• allele
• characteristic
• chromosome
• co-dominant
• cross
• dihybrid cross
• diploid
• DNA
• dominant
• egg
• fertilization
• fitness
• gamete
• gene
• genotype
• haploid
• heterozygous
• homozygous
• homozygous dominant
• homozygous recessive
• inheritance
• monohybrid cross
• mutant
• mutation
• natural selection
• nucleotide
• offspring
• parent
• pedigree
• phenotype
• probability
• protein
• Punnett square
• recessive
• RNA
• sperm
• trait
• zygote

## Unit 10: Gene Expression

#### 10a. Explain the molecular basis of heritable traits, and how information in DNA is ultimately expressed as a protein

• What is the Central Dogma?

DNA indirectly controls traits, because the trait is a direct result of the version of protein the individual can produce. The individual's gene (which is made of DNA) determines the type of protein they can produce. The term gene expression refers to the molecular process of building a particular protein using the code that is stored (in DNA form) as a gene. The central dogma is the teaching of the flow of genetic information to the level of the protein. DNA is used as a template to transcribe RNA, and RNA is used to translate proteins.

Simply diagram how information flows from a gene to a protein and pay particular attention to figure 9.14 in More on Transcription.

#### 10b. Define the role of DNA and its means of replication

• What is the structure and function of DNA?
• Why and how does DNA self-replicate?
• What are the enzymes involved in DNA replication?

Deoxyribonucleic Acid (DNA) is one of the most celebrated molecules in history. It is a double-helical nucleic acid made up of nucleotides. DNA has two functions:

1. It offers semiconservative replication

2. It provides a template for RNA transcription

DNA nucleotides consist of phosphate, deoxyribose sugar, and four nitrogenous bases (adenine, guanine, cytosine, thymine). You should understand how the structure of DNA represents a code template for gene expression.

DNA replication is a complex process that has different mechanisms and employs a great variety of enzymes. Two new strands are copied, the leading strand is synthesized continuously, while the lagging strand is synthesized as Okazaki fragments. This is because DNA synthesis can only take place in the 5'-3' direction and the DNA polymerases create the two strands simultaneously.

The main enzymes involved are helicase, primase, DNA Polymerase I and III, and DNA ligase:

• Helicase: unwinds the DNA

• Primase: creates an RNA primer

• DNA Polymerase III: elongates the two strands separately by adding complementary bases.

• DNA Polymerase I: removes the RNA primer and replaces it with DNA, but leaves a gap between fragments.

• DNA Ligase: fills in the gap and joins DNA fragments to create fully joined identical copies of DNA.

Review DNA, which demonstrates the role of complementary nucleotide bases in DNA. Review DNA structure in The Chemical Structure of DNA. Review the semiconservative process of DNA replication in DNA Replication. Review Visualizing DNA Replication and pay attention to the steps that involve enzyme catalysis.

#### 10c. Distinguish between the two main phases of gene expression: transcription and translation

• What are the processes involved in gene expression?
• In what order do these processes occur?
• What specifically occurs in these processes?
• How are these processes regulated?

Gene expression consists of two serial processes, occurring in the following order:

Transcription is the only part of gene expression that directly involves the gene. The cell "reads" the DNA nucleotide sequence of a gene, and uses the sequence as a code to construct a complementary sequence of RNA nucleotides.

That RNA sequence is known as messenger RNA (mRNA), because the mRNA carries the original code, as a message, to a ribosome. DNA's job is done until the gene is read again in a later round of gene expression.

Translation refers to the part of gene expression where the polypeptide (protein) is constructed. A polypeptide is a sequence of amino acids. The code in mRNA (produced earlier by transcription) instructs the cell's ribosomes how to build the polypeptide by conveying how many amino acids to string together, which amino acids to use, and how to order the amino acids in the sequence.

As a ribosome reads each codon (a sequence of three nucleotides) in the mRNA, a type of RNA called transfer RNA (tRNA) delivers the correct type of amino acid to the ribosome. Amino acids are added in this way, one by one, until the polypeptide is complete.

A completed polypeptide (produced by translation) assumes a particular shape, depending on its particular sequence of amino acids. Because of that particular shape, that polypeptide will have a particular function, and it will therefore give the individual a particular trait.

Gene expression occurs differently in organisms. Transcription and Translation occur simultaneously in prokaryotes. However, in eukaryotes, there are several modifications post-transcriptionally and post-translationally. This allows for more regulation.

Review transcription in More on Transcription and the lectures DNA Transcription. Read translation in More on Translation and the lectures Translation and Synthesis. Review How Genes Are Regulated to observe the different ways organisms regulate gene expression.

#### 10d. Discuss some technological advances of molecular biology

• What is a gene and how is it edited?
• Why are DNA technologies important?

Biotechnology is the field that uses practical knowledge to solve problems in living organisms. DNA biotechnology incorporates gene modification and other tools to advance certain goals. For example, DNA technology has helped solve problems in the criminal justice system, agriculture, and the medical field.

We know genes reflect specific DNA sequences that help the body produce specific proteins, which in turn express a certain genotype or phenotype. Scientists are learning how to modify problematic genes to alleviate and eradicate disease. For example, they are using gene-editing tools to remove and replace harmful genes that cause certain dysfunctions. CRISPR is a specific type of gene editing method.

Review Biotechnology, What is Gene Editing and How Does it Work? and CRISPR: A Game-Changing Genetic Engineering Technique to understand how scientists use CRISPR in living organisms. Scientists use technology to learn about all of the genes and the phenotypes they represent. Review some genetic advances in Genes, Health, and Moving Beyond Race.

#### Unit 10 Vocabulary

You should be familiar with these terms as you prepare for the final exam.

• amino acid
• biotechnology
• central dogma
• codon
• CRISPR
• cytosine
• DNA
• gene
• gene editing
• gene expression
• guanine
• lagging strand
• mRNA
• nucleotide
• Okazaki fragments
• phenotype
• plypeptide
• protein
• regulation
• ribosome
• RNA
• semiconservative
• thymine
• trait
• transcription
• translation
• tRNA