Chapter 1: Studying Life1.1: What Is Biology:

- Biology: the scientific study of living things- Living things: all the organisms descended from a single-celled ancestor. Biological science was founded with the development of (1) the cell theory, and (2) the theory of evolution by natural selection

- Unicellular organisms: a single cell carries out all the functions of life - Multicellular organisms: made of many cells that are specialized for different functions

- Characteristics of living organisms: Consist of one or more cells, Contain genetic information, Use genetic information to reproduce themselves, are genetically related and have evolved, can convert molecules from their environment into new biological molecules, can extract energy from the environment and use it to do biological work, can regulate their internal environment- Antony van Leeuwenhoek & Robert Hooke: improve microscope technology of Zaccharias and Hans Janssen (1590) while carrying out observations where he concluded – tissues were made of repeating units he called cells- Cell Theory: discovered by Scheilden and Schwann – States: (1) cells are basic structural n physiological units of living organisms, (2) cells are both distinct entities and building blocks of more complex organisms. At the time it was thought that life arises from nonlife by spontaneous generation (3) all cells come from preexisting cells, (4) similar in chemical composition, (5) most chemical reactions of life occur within cells, (6) complete sets of genetic info are replicated and passed on during cell division- Evolution: proposed by Charles Darwin (and Alfred Russel Wallace) is a process of natural selection – living organisms descended from a common ancestor; living systems evolve through differential survival and reproduction.

Species: a group of organisms, which look alike (morphologically similar), and can breed successfully with one another. Humans select for desired traits when breeding animals.Natural selection: could occur through differential survival and reproductive success. Adaptation: structural, physiological or behavioral traits that increase an organism’s probability of survival and reproduction in its environment.

- Genome: sum total of all the DNA in the cell. All cells in a multicellular organism have the same genome but different parts are exposed – creating the different types of cells - Nucleotides: A T G C are building blocks of DNA- DNA: the information that is passed from parent to daughter cells. 2 strands of long sequences of linked nucleotides. - Gene: consists of a specific sequence of nucleotides in a DNA molecule that contains the information on making proteins - Protein: Specific nucleotide sequence contain information to build a specific protein, they make up much of an organism’s structure and they are the molecules that govern the chemical reactions within cells - Mutations: alterations in the nucleotide sequence.

- Nutrients: living organisms require nutrients to supply the organisms with energy and raw materials for building biological structures. Breaking them down creates energy for biological work and allows the creation of new structures form the smaller chemical units - Internal environment: individual cells in multicellular organisms bathed in extracellular fluids from which they receive nutrients and excrete waste- Populations: Individuals are part populations that interact among themselves and populations of different organisms - Community: Interacting populations of many different species- Ecosystems: Interacting communities in a given area

1.2: How is All Life of Earth Related:- Fossil Record: investigate the fossils of organisms that lived in the distant past in order to discover evolutionary relationships between organisms (info about age and environment, anatomy) Evolutionary History:

- Chemical Evolution: complex biological molecules first arose from random association of chemicals in the environment – the appearance of molecules that could reproduce themselves - Cells formed: enclosure of complex biological molecules in membranes, which kept them close together and increased frequency of interaction.

- First Cellular Life: life arose 4 billion years ago, for 2 billion years, life consisted of single cells—prokaryotes. These cells were in the oceans (abundance of complex molecules for raw materials), protected from UV radiation.- Cyanobacteria: early photosynthetic cells, they became so abundant that the oxygen was accumulating atmosphere, only those that could tolerate this survived. - Aerobic Metabolism: metabolism based on the use of oxygen – more efficient allowing cells to grow larger - Organelles: intracellular compartments capable of taking on specialized functions- Nucleus: appearance of a dense kernel containing the genetic information – eukaryotes - Speciation: an event may isolate some members of a population structural and functional differences accumulate to an extent where evolutionary paths of 2 groups may diverge where members no longer reproduce with each other - Naming: a binomial: Genus name: a group of species that share a recent common ancestor, Species name: refer to a characteristic of the species. (Homo sapiens) - Tree of Life: shows the order in which species split and evolved into new species – based on evidence from fossils, structures, metabolic processes, behavior, and molecular analyses of genome- Taxonomy: Kingdom, Phylum, Class, Order, Family, Genus, and Species- Domains: 3 – Archea (prokaryotes), Eukarya (plants, fungi, animals – all evolved from unicellular microbial eukaryotes or protists), bacteria (prokaryotes) - Autotophes: (self-feeders) produces primary food fro nearly all-living organisms – bacteria, plants, protists, and archea

- Heterotophes: (other-feeders) require a source of molecules synthesized by other organisms – which they break down to obtain energy – fungi (in environment then absorb), animals (inside)

Chapter 2: The Chemistry of Life2.1 What are the Chemical Elements that Make Up Living Organisms:

- Atoms: all matter is composed of atoms with volume and mass consists of a dense positively charged nucleus with protons and neutrons, surrounded electrons. - Proton: Mass of one proton or one neutron = atomic mass unit (amu) or 1 dalton, or 1.7 × 10–24 grams. Positive charge, atomic number- Neutron: charge of 0, mass of 1 da, different in isotopes - Electron: Mass of one electron = 9 × 10–28 grams— negligible, determines reactivity - Atomic Mass: Protons + Neutrons- Charge: Protons + Electrons - Element: pure substance containing only one kind of atom. Elements are arranged in the periodic table.- 98% of a living organism is composed of 6 elements: hydrogen, carbon, nitrogen, oxygen, phosphorous, and sulfur- Approx. 11 ‘trace’ elements complete remaining 2%: Na, K, Mg, Ca, Mn, Fe, Co, Cu, Zn, Si, Cl- Isotopes: forms of an element with different numbers of neutrons, thus different mass numbers- Atomic weight: average of mass numbers of isotopes in their normally occurring proportions- Radioisotopes are unstable; they give off energy in the form of alpha, beta, and gamma radiation from the nucleus. This radioactive decay transforms the atom, including changes in the number of protons. Energy from radioactive decay can interact with surrounding material. Radioisotopes can be incorporated into molecules and act as a “tag” or label.- Reactivity: The number of electrons determines how atoms will interact. Chemical reactions involve changes in the distribution of electrons between atoms.- Orbital: describes locations of electrons in an atom. Region where electron is found at least 90 percent of the time. Orbitals are filled in a specific sequence.- Electron shells: (energy levels) series’ in which Orbitals occur fir one holds 2, beyond first holds 8. - Reactive: atoms have unpaired electrons in their outermost (valence) shell.Atoms can share electrons, loose or gain electrons, resulting in atoms bonded together to form molecules.- The Octet Rule: the tendency of atoms in stable molecules to have eight electrons in their outermost shells

2.2: How do Atoms Bond to Form Molecules: - Chemical Bond: attractive force that links atoms together to form molecules. Atoms with incomplete valence shells – reactive, interact with other atoms in order to complete shell

Covalent Bond: 1. Can share valence electrons, very strong a lot of energy is required to break them. Biological molecules are put together with covalent bonds and are very stable. Single—sharing one pair of electrons, Double—sharing two pairs of electrons, Triple—sharing three pairs of electrons Ionic Bond: 2. Can transfer valence electrons (attract opposite charges)

- Compound: a molecule made up of two or more elements.- Molecular Weight of a compound is the sum of the atomic weights of all atoms in the molecule.- Carbon: Carbon can form four covalent bonds - Electronegativity: the attractive force that an atomic nucleus exerts on electrons. Electronegativity depends on the number of positive charges (protons) and the distance between the nucleus and electrons.

Non-polar covalent bond: If two atoms have similar electronegativity, they will share electrons equallyPolar covalent bond: If one atom has more electronegativity, the electrons are drawn to that nucleus. Electrons not shared equally

- Ions: electrically charged particles— when atoms loose or gain electronsCations—positive (Na+)Anions—negative (Cl-)

- Ionic bonds are formed by the electrical attraction of positive and negative ions. Salts—ionically bonded compounds. In a solid, ions are close together and the ionic bond is strong. In water, the ions are far apart and the attraction is much weaker. Ions interact with polar molecules—salts dissolve in water.- Hydrogen Bond: sharing of H atoms - occur between strongly electronegative atoms and hydrogen atoms (the δ– end of one molecule and the δ+ hydrogen end of another molecule). Hydrogen bonds form between water molecules, and are important in the structure of DNA and proteins. They can also be two parts of one molecule. Hydrophilic: when a polar molecule interacts with water. Hydrophobic: interactions of water a non-polar atom- Vaan der Waals Interactions: interaction of electron of non-polar substances

2.3: How Do Atoms Change Partners in Chemical Reactions- Chemical Reactions: atoms bond or change bonding partners and involve energy changes

2.4: What Properties of Water make it So Important in Biology: - Origin: Life’s chemistry began in water. Water and other chemicals may have come to Earth on comets. Water was an essential condition for all life to exist and evolve: 45-90% of living organisms, humans are 70% water- Water: unique structure and special properties. A polar molecule that forms hydrogen bonds, it has a tetrahedral shape.

Properties: 1. Moderation of Temperature: high specific heat: the amount of heat energy required to raise the temperature of 1 gram of water by 1°C. Water gains / loses high amounts of heat when it changes state, high heat capacity, - moderate

earth’s climate. Water has a high heat of vaporization —the amount of heat energy required to change water from a liquid to a gas state.2. Cohesion & Adhesion: capacity of water molecules to resist coming apart when placed under tension – surface tension, allows to move through plants, helps insects float3. Ability to Act as an Insulator: since the solid is less dense it floats on water creating a barrier for the heat to get cold4. Ideal Solvent: Many important biochemical reactions occur in aqueous solutions. Most compounds are soluble in water due to its polarity. Water is the universal solvent. When acids dissolve in water, they release hydrogen ions—H+

(protons). H+ ions can attach to other molecules and change their properties. Bases accept H+ ions.5. Weak Acid: water has a slight tendency to ionize into hydroxide (OH-) and Hydronium (H+) H2O H+ + H3O-

- pH: negative log of the molar concentration of H+ ions. H+ concentration of pure water is 10–7 M, its pH = 7. Lower pH numbers mean higher H+ concentration then OH-, or greater acidity

Chapter 3: Macromolecules and The Origin of Life3.1 – What kinds of molecules characterize living things:

- Types of molecules in living organisms: proteins or polypeptides from amino acids (most), carbohydrates or polysaccharides from monosaccharide (sugar), lipids (least), and nucleic acids from nucleotides (second most common) and most are polymers of smaller molecules called monomers.- Macromolecules: polymers with molecular weights >1000- Functional groups: groups of atoms with specific chemical properties and consistent behavior; it confers those properties when attached to large molecules

- Isomers: molecules with the same chemical formula, but atoms are arranged differently- Structural Isomers: differ in how their atoms are joined together- Optical Isomers: mirror images of each other – occur when 4 different atoms or groups of atoms are attached to a single carbon atom - Biochemical unity: organisms can obtain required macromolecules by eating other organisms. One macromolecule can contain many different functional groups—determines shape and function.- Condensation Reactions Polymers: are formed when monomers are joined by covalent bonds. Water is removed—also called dehydration reaction.- Hydrolysis: Polymers are broken down into monomers – water is added

3.2 – What are the chemical structures and functions of proteins:- Functions of Proteins: Structural support, protection, transport, catalysis, defense, regulation, Movement - Amino Acids: (monomeric units) Proteins are made from 20 different - Polypeptide chain: single, un-branched chain of amino acids. The chains are folded into specific three-dimensional shapes. Proteins can consist of more than one type of polypeptide chain.- Composition: of a protein: relative amounts of each amino acid present- Sequence of amino acids in the chain determines the protein structure and function.- Acid and base: Amino acids have carboxyl and amino groups—they function as both - Asymmetrical: The α carbon atom is bonded to four different atoms or groups of atoms Amino acids exist in two isomeric forms: D-amino acids (dextro, “right”), L-amino acids (levo, “left”)—this form is found in organisms- R-groups: The side chains also have functional groups. Amino acids can be grouped based on side chains.

Hydrophilic: electrically charged side chains, attract ions of opposite charges, polar but uncharged side chains form hydrogen bondsHydrophobic: non-polar side chains of amino acidsSpecial Cases: cysteine, glycine, proline

- Peptide Bonds: Amino acids bond together covalently form the polypeptide chain. Condensation reaction Amino group + carboxyl group = water + peptide linkage- A polypeptide chain is like a sentence: The “capital letter” is the amino group of the first amino acid—the N terminus. The “period” is the carboxyl group of the last amino acid—the C terminus.- Primary structure (1o): of a protein is the sequence of amino acids. –N-C-C- backbone The sequence determines secondary and tertiary structure—how the protein is folded.The number of different proteins that can be made from 20 amino acids is enormous!- Secondary structure (2o): α helix—right-handed coil resulting from hydrogen bonding; common in fibrous structural proteins. β pleated sheet—two or more polypeptide chains are aligned in sheets- Tertiary structure (3o): Bending and folding results in a macromolecule with specific three-dimensional shape. The outer surfaces of 3o structure exposes functional groups that can interact with other molecules. Tertiary structure is determined by interactions of R-groups: Disulfide bonds, Aggregation of hydrophobic side chains, van der Waals forces, Ionic bonds, Hydrogen bonds - Quaternary structure (4o): results from the interaction of alpha and beta subunits (e.g. polypeptide chains) by hydrophobic interactions, van der Waals forces, ionic bonds, and hydrogen bonds.- The specific shape and functional groups of a protein determines function and allows it to bind non-covalently with another molecule (the ligand). Ex. Enzyme-substrate reactions, chemical signaling, antibody action, etc - Conditions that affect secondary and tertiary structure: High temperature, pH changes, High concentrations of polar molecules- Denaturation: loss of 3-dimensional structure and thus function of the protein- Chaperonins: are proteins that help prevent proteins from binding to the wrong ligands.

3.3 – What are the chemical structures and functions of carbohydrates:- Carbohydrates: molecules in which carbon is flanked by hydrogen and hydroxyl groups. Energy source - Carbon skeletons rearranged to form many other molecules- Monosaccharide: simple sugars- Disaccharides: two simple sugars linked by covalent bonds

- Oligosaccharides: 3-20 monosaccharides- Polysaccharides: hundreds or thousands of monosaccharides—starch, glycogen, cellulose- Glucose: (monosaccharide) Cells use as an energy source. Exists as a straight chain or ring form. Ring is more common—it is more stable.- Differ in H and Oh attached at carbon 1

- Monosaccharides: - CH2O have different numbers of carbons. Hexoses: six carbons—structural isomers, mannose, galactose, and fructose Pentoses: five carbons – Ribose, deoxyribose- Glycosidic linkages: when monosaccharides bind together in condensation reactions. Glycosidic linkages can be α or β. Α forms maltose, β forms cellobiose, α and fructose make sucrose- Oligosaccharides: may include other functional groups, often covalently bonded to proteins and lipids on cell surfaces and act as recognition signals. ABO blood groups- Polysaccharides are giant polymers of monosaccharides.

Starch: storage of glucose in plantsGlycogen: storage of glucose in animalsCellulose: very stable, good for structural components (plant cell wall)3.4 – What are the chemical structures and functions of lipids:

- Lipids: are non-polar hydrocarbons, Fats and oils—energy storage, Phospholipids—cell membranes, Carotenoids, Steroids. Fats serve as insulation in animals, lipid nerve coatings act as electrical insulation, oils and waxes repel water, prevent drying.- Triglycerides: Fats and oils are —simple lipids—made of three fatty acids and 1 glycerol. Glycerol: 3 —OH groups—an alcohol- Fatty Acid: nonpolar hydrocarbon with a polar carboxyl group—carboxyl bonds with hydroxyls of glycerol in an ester linkage.

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Saturated Fatty Acids: no double bonds between carbons—it is saturated with hydrogen atoms.- Unsaturated Fatty Acids: some double bonds in middle of the carbon chain.

Monounsaturated: one double bondPolyunsaturated: more than one double bond

- Animal Fats: tend to be saturated—packed together tightly—solid at room temperature.- Plant Oils: tend to be unsaturated—the “kinks” prevent packing—liquid at room temperature.- Phospholipids: fatty acids bound to glycerol, a phosphate group replaces one fatty acid. Phosphate group is hydrophilic—the “head”, “Tails” are fatty acid chains—hydrophobic - usually a phospholipid bilayer membrane- Carotenoids: Light absorbing pigments, beta-carotene is broken down into 2 vitamin A in humans- Steroids: multiple rings share carbons - Vitamins: small molecules not synthesized by the body—must acquire in diet.- Waxes: highly nonpolar, ester linkage between fatty acid and alcohol – impermeability to water

3.5 – What are the chemical structures and functions of nucleic acids:- Nucleic acids: DNA - deoxyribonucleic acid (missing an O in the OH group), RNA - ribonucleic acid- Polymers: the monomeric units are nucleotides.- Nucleotides consist of a pentose sugar, a phosphate group, and a nitrogen-containing base.

Pyrimidines: Cytosine, Thymine, Ur, single ringed Purines: adenine and guanine, double ringed

- Nucleoside: doesn’t contain a phosphate group- The “backbone” consists of the sugars and phosphate groups, bonded by phosphodiester linkages. “diester” = two bonds formed by hydroxyl (-OH) groups reacting with acidic phosphate groups (H3PO4). Strong covalent bonds within nucleic acid molecule holds DNA or RNA strands together- The phosphate groups link carbon 3′ in one sugar to carbon 5′ in another sugar- RNA: Instead of thymine, uses the base uracil (U). RNA is single-stranded, but complementary base pairing occurs in the structure of some types of RNA

- DNA is an informational molecule: information is encoded in the sequences of bases. RNA uses the information to determine the sequence of amino acids in proteins - Other roles for nucleotides: ATP: energy transducer in biochemical reactions, GTP: energy source in protein synthesis, cAMP & cGMP: essential to the action of hormones and transmission of information in the nervous system

Chapter 4: Cell Structure4.1: What features of cells make them the fundamental unit of life:

- Cells: separate external from internal environment; contain biomolecules that perform unique functions in cells- Cell Theory: 1.cells are the basic units of life; 2.all organisms are composed of cells, 3. All cells come from pre-existing cells - Surface Area-to-Volume Ratio: volume of a cell determines the amount of chemical activity carried out per unit area of time; the surface area of a cell determines the amount of substances the cell can take in from the outside environment & waste. As a cell grows larger its rate of activity (waste production and need for resources) grows faster than its surface area. – Cells must be small in volume in order to maintain a large enough volume to surface area ratio. Ratio limits size that functional cells can attain – Compartmentalization is key to eukaryotic cell function permitting much larger cells- All Life is Related: consist of organized cells, contain heritable genetic information for reproduction, show growth (and development), respond to environmental stimuli, maintain homeostasis, use/convert energy and matter for biological function (= metabolism), adapt to environmental change – with evolution through natural selection. - Microscopes: improve resolution so that cells and their internal structures can be seen- Plasma Membrane: cells are surrounded by a plasma membrane, separating it from its environment. Composed of a phospholipid bilayer (hydrophilic heads, hydrophobic tails), the heads face the aqueous interiors and the extracellular environment. – Allows a constant internal environment - homeostasis, acts a s a selectively permeable barrier – control substances that enter and exit, communication with adjacent cells through signals, protruding proteins that are there for binding and adhering to surrounding cells - Types of Cells: Prokaryotic – lack membrane-enclosed organelles – DNA in nucleoid region (no nucleus), Eukaryotic – have membrane-enclosed organelles – genetic information enclosed in the nucleus- Features of Cells:

1. With normal human vision, - smallest objects resolved ~200 m (0.2 mm) in size, cells are tiny microscopes are needed

2. Cells are unified by common (shared) characteristics: 1.cellular, 2.based on aqueous (= water) solutions, 3.consist of 6 elements (C, H, N, O, P and S), 4.similar macromolecules (carbohydrates , lipids, proteins), 5.have RNA and DNA from same nucleotides, 6.genome composed of RNA or DNA (replication), 7.have ribosomes acting as sites of protein synthesis, 8.undergo metabolic reactions catalyzed by proteins, 9.osmotically active membranes of similar structure, 10.use formation / hydrolysis of ATP for energy flow

3. Cells are distinguished by presence/absence of internal membrane-bound compartments: modern classification based on: 1. Obvious similarities, 2. Evolutionary relationships. 3 Domains: Archea: kingdom archea, Bacteria: kingdom Bacteria, Eukarya: kingdom protists, plantae, fungi, Animalia

4.2 – What are the characteristics of prokaryotic cells:- Structure: prokaryotes are small (< 10 mm)

Nucleoid: contains loosely organized hereditary material (DNA) of the cellCytoplasm: the rest of the material within the plasma membrane composed of the more fluid cytosol and insoluble suspended particles (ribosomes)

- Ribosomes: complexes of RNA proteins – the site of protein synthesis - Cell walls: located outside the plasma membrane, supports the cell and determines shape- Flagella: made of flagellin protein used as an appendage to aide in motion - Pili: hair-like help bacteria adhere to one another and animal cells- Cytoskeleton: internal filamentous helical structure inside plasma membrane to maintain cell shape

4.3 – What are the characteristics of eukaryotic cells: 4.4 – What are the roles of extracellular structures:

- Structure: - eukaryotes are larger than prokaryotes (> 10 mm) Surface Area: Volume- Eukaryote Cells: have internal membrane-bound organelles (nucleus, ER, GA, chloroplasts, mitochondria, vacuoles, lysosomes), have internal cytoskeleton for support. - Originate: led to: increase in size, increase in complexity.

Mechanisms of Formation: 1. Unfolding of cell membrane, 2. Endosymbiosis of membrane- bound organelles

- Functional groups of organelles: organelles are surrounded by a membranes to prevent inappropriate reaction, and traffic materials

1. Process information: Nucleus: contains DNA, the first step in decoding genetic info, Nucleolus, Ribosomes

2. Control function: ER and GA: proteins that are synthesized by ribosomes are sent to appropriate locations in cell via the ER or GA, Lysosomes/Vacuoles: Digestive system in which large molecules are hydrolyzed into unusable monomers 3. Process energy: Mitochondria: energy in the bonds of fatty acids and

carbohydrates are converted to ATP, Chloroplasts: perform photosynthesis 4. Provide structure: Cytoskeleton, Extracellular Components

ORGANELLE CATEGORY STRUCTURE FUNCTION

Nucleus Information Largest organelle- Surrounded by a nuclear envelop (2 membranes)- Pores

- Site of DNA replication- Genetic control of the cells; activities -

Nucleolus Information Within the nucleus - Begins assembly of ribosomes from RNA and specific proteins

Ribosome Information - Eukaryote: Float freely in the cytoplasm or on ER, inside mitochondria an chloroplasts, larger -

- Manufacture proteins

Endoplasmic reticulum (ER)

Regulation - Tubes or flattened sacs, ribosome studded- Interior is the lumen, separated from cytoplasm SER: more tubular

- Site of protein synthesis - ribosomes- Transports them to other locations - SER: lipid and steroid synthesis, hydrolysis of glycogen in animal cells and chemical modifications of proteins (drugs)

Golgi apparatus (GA)

Regulation - Cisternae: flattened membranous sacs piled up like saucers- 1um long

- Receives proteins from ER through vesicles and further modifies them - Processes and packages proteins

Lysosomes Regulation - Surrounded by a single membrane- Comes from Golgi

- Phagocytosis: Contain digestive enzymes, where macromolecules, are hydrolyzed into monomers

Vacuole Regulation Compartment in cytoplasm of plant cell

- Large vesicles for transport - Storage of toxic by-products- Provides structure - some contain enzymes to hydrolyze

Mitochondrion Energy - Double membrane – outer: smooth and

- Convert potential chemical energy of fuel

protective, inner: folds inwards forming a shelf-like structure called cristae

molecules 9degraded glucose) into ATP through cellular respiration

Chloroplast Energy - Contains green pigments called chlorophyll - Surrounded by 2 membranes- Made up of thylacoid membrane stacks called granna

- Harvest energy of sunlight to produce sugar- Site of photosynthesis

Cytoskeleton Structure - Microtubules, intermediate filaments, and microfilaments

- Support the cell shape- Involved in cell and organelle movement - Interacts with extracellular structures, helping to anchor cell in place

Extracellular matrix (ECM)

Structure - Fibrous proteins such as collagen and proteoglycans- Abundant in bone and muscles

- Holds cells together in tissues- Contributes to physical properties of cartilage, skin and other tissues- Helps filter materials-

Cell wall Structure - Cellulose fibers embedded in complex polysaccharides and proteins - plants

- Supports the plant cell- Barrier for infection- Contributes to form by growing as the plant grows.

4.5 – How did eukaryotic cells originate?- Cell = a living unit greater than the sum of its parts: integrate structures in order to function, prokaryotes remained small with little internal structure, earliest eukaryotes solved problem of size limitation by maximizing surface area of membranes, eukaryotes became large and morphologically diverse, evolution of multi-cellular organisms (fungi, plants, animals) - not possible without evolution of eukaryotic cells - Life started as prokaryotes that absorbed their food directly from the environment- Some, like Cyanobacteria, became photosynthetic

- Endosymbiosis Theory: when smaller prokaryotes are engulfed by bigger ones, and survive grow and divide at the same rate in the cytoplasm. Successive generations contain the offspring of the last one

Chapter 6: Enzymes & Metabolism6.3 – What are enzymes:

- Enzymes: Specialized group of proteins that catalyze reactions without being altered by the reaction.- Substrates: Reactants- Active Site the region where the substrate molecules binds to the enzyme.- Substrate-Specific: Three-dimensional shape of the enzyme determines the specificity of enzymes- Activation Energy: Enzymes lower the energy barrier for reactions. The final equilibrium does not change ΔG (net free energy change) does not change.

6.4 – How do enzymes work:- Orient Substrates: Enzymes orient substrate molecules, bringing together the atoms that will bond.- Induce Strain: Enzymes can stretch the bonds in substrate molecules, making them unstable. And allowing them to bond more easily with other substances- Temporarily add chemical groups to substrates- The “lock and key”: Shape of enzyme active site allows a specific substrate to fit - Induced fit: ” Many enzymes change shape when they bind to the substrate- Require Partners: non- protein molecular partners in order to function

Prosthetic Groups: non-amino acid groups bound to enzymesCofactors: inorganic ions Coenzymes: not bound permanently to enzymes6.5 – How are enzyme activities regulated:

- Inhibitors regulate enzymes: a molecule that binds to the enzyme and slows reaction rates. Naturally occurring inhibitors regulate metabolism.- Irreversible inhibition: inhibitor covalently bonds to side chains in the active site—permanently inactivates the enzyme. Example: DIPF or nerve gas- Reversible inhibition: inhibitor bonds non-covalently to the active site, prevents substrate from binding—competitive inhibitors. When concentration of competitive inhibitor is reduced, it detaches from the active site. Noncompetitive inhibitors: bind to the enzyme at a different site (not the active site). The enzyme changes shape and alters the active site.- Allostery (allo, “different”; stery, “shape”) some enzymes exist in more than one shape: Active form—can bind substrate, Inactive form—cannot bind substrate but can bind an inhibition. Most allosteric enzymes are proteins with quaternary structure.

Catalytic Subunit: Active site is on one subunitRegulatory Subunits: to what Inhibitors and activators bind

- Optimal pH: pH influences the ionization of functional groups. Example: at low pH (high H+) —COO– may react with H+ to form —COOH which is no longer charged—affects folding and thus enzyme function.

- Optimal Temperature: At high temperatures, non-covalent bonds begin to break.Enzyme can lose its tertiary structure and become denatured.

Chapter 9: Chromosomes, The Cell Cycle & Cell Division:9.1 – How do prokaryotic and eukaryotic cells divide:

- Unicellular organisms use cell division primarily for reproduction.- Multicellular organisms, cell division is also important in growth and repair of tissues.- Four events must occur for cell division: Reproductive Signal: to initiate cell division, Replication: of DNA, Segregation: distribution of the DNA into the two new cells, Cytokinesis: separation of the two new cells- Prokaryotes: binary fission results in two new cells. External factors such as nutrient concentration and environmental conditions are the reproductive signals that initiate cell division. For many bacteria, abundant food supplies speed up the division cycle.

One Chromosome: Most prokaryotes have a single molecule of DNA; usually circular.Two Important Regions: ori—where replication starts, ter—where replication ends

- Replication occurs as the DNA is threaded through a “replication complex” of proteins in the center of the cell.- Segregation: The ori regions move towards opposite ends of the cell. Proteins in this region hydrolyze ATP for energy for this movement, perhaps by the cytoskeleton.- Cytokinesis: begins by a pinching in of the plasma membrane; protein fibers form a ring. As the membrane pinches in, new cell wall materials are synthesized, resulting in separation of the two cells - Eukaryotes: Originate from a single cell, the fertilized egg.- Gametes: the union of sperm and egg results in cell and contains genetic material from both parents.- Development is the formation of a multicellular organism from a fertilized egg. Development involves cell reproduction and cell specialization.- Eukaryote cell division: Signal for reproduction not related to the environment of a single cell, but to the needs of the whole organism. Eukaryotes usually have many chromosomes. - Mitosis: is the process that segregates the chromosomes (2 sister chromatids). Into 2 identical cells - Nucleus must be divided into two nuclei before cytokinesis can occur. Cytokinesis proceeds differently in plant and animal cells.- Meiosis occurs in cells that produce gametes. Mitosis results in two identical cells; the products of meiosis are not identical.

9.2 – How is eukaryotic cell division controlled: - The Cell Cycle: events that occur to produce two eukaryotic cells from one.

Interphase: most of the life of the cell—phase between divisions. A given cell lives for one turn of the cell cycle, and then becomes two cells. Chemical substances trigger the transition from one phase to another. Evidence of this came from cell fusion experiments.

G1: Gap 1 — each chromosome is single, unreplicated S phase: DNA replicates; one chromosome becomes two sister chromatids.G2: Gap 2 — cell prepares for mitosis.

- A kinase is an enzyme that catalyzes phosphorylation.- Phosphorylation changes the shape and function of a protein by changing its charges.- Transitions depend on activation of the protein cyclin-dependent kinase (Cdk).- Cdk is activated by binding to cyclin (allosteric regulation); which exposes its active site. The cyclin-Cdk complex acts as a protein kinase and triggers transition from G1 to S. Several different cyclin-Cdk complexes control various stages of the mammalian cell cycle. - The Restriction Point: in G1 is a decision point beyond which the rest of the cycle is inevitable.- Progress past the restriction point depends on (RB) retinoblastoma protein. RB normally inhibits the cell cycle, but when phosphorylated, becomes inactive and no longer blocks the restriction point.- Tumor Suppressors: Proteins such as p21, p53, and RB that normally block the cell cycle- The cyclin-Cdk complexes act as checkpoints. Example If DNA is damaged during G1, p21 protein is made. p21 binds to G1 Cdks, preventing their activation. The cell cycle stops while DNA is repaired.- Cancer is a result of inappropriate cell division—the cyclin-Cdk controls are disrupted. A protein, p53, stimulates synthesis of p21, which inhibits Cdk and prevents normal cells from dividing. Over half of human cancer cells have defective p53.-Growth factors: external chemical signals that stimulate cells that no longer divide, or divide infrequently to divide.- Platelet-derived growth factor: from platelets that initiate blood clotting stimulates skin cells to divide and heal wounds.- Interleukins: produced in some white blood cells that promote cell division in other white cells.-Erythropoietin: produced in the kidneys stimulates division of bone marrow cells and production of red blood cells.- Cancer cells may produce their own growth factors, or no longer require growth factors for division.

9.3 – What happens during mitosis: - Chromatin: dense DNA complexed with proteins to form after replication- Condensins coat the DNA and make it more compact.- Sister Chromatids: are the replicated chromosomes are held together by cohesin. During mitosis, the cohesin is removed, except at the centromere.- DNA molecules are “packed” even during Interphase.- Nucleosomes: Chromosomes have many histones—proteins with positive charges that attract negative phosphate groups of DNA, results in the formation from interactions- During mitosis and meiosis, chromatin is coiled and condensed ever more tightly until the chromatids move apart.

- Centrosome: found near nucleus, doubles while DNA replicates. Centrosomes consist of two centrioles—hollow tubes lined with nine microtubules—at right angles to each other.-At G2 to M transition, the centrosomes move to opposite ends of the nuclear envelope. Orientation determines the plane at which the cell will divide; and the spatial relationship of the two new cells.- Tubulin dimers: in high concentration, surrounds the centrosomes. These initiate formation of microtubules, which leads to formation of the spindle structure. Plant cells lack centrosomes but have distinct microtubule organizing centers.- Mitosis can be divided into phases:

Prophase: cohesin disappears; chromatids become visible.Kinetochores develop in the centromere regions. Centrosomes serve as mitotic centers or poles; microtubules form between the poles to make the spindle. Spindle has two types of microtubules: Polar microtubules — form spindle; overlap in center. Kinetochore microtubules — attach to kinetochores on the chromatids. Sister chromatids attach to opposite halves of the spindle.

Prometaphase: the nuclear envelope and nucleoli disappear. Chromosomes are gradually pushed towards the equatorial plate.Metaphase: all centromeres have arrived at the equatorial plate.Anaphase: the sister chromatids separate and move to opposite ends of the spindle—now referred to as daughter chromosomes. Cohesin is hydrolyzed by separase. Separase is inactive before this point—it is bound to an inhibitory subunit called securin. When all chromatids are connected to the spindle, securin is hydrolyzed, separase breaks down the cohesin: the spindle checkpoint.Motor proteins at the kinetochores—cytoplasmic dynein—hydrolyze ATP for energy to move chromosomes along the spindle. Microtubules also shorten, drawing chromosomes toward poles. Motor proteins in region of overlap cause microtubules to slide past one another—increases the distance between the poles.Telophase: Spindle breaks down, Chromosomes uncoil, Nuclear envelope and nucleoli are reformed, and two daughter nuclei are formed with identical genetic information

- Cytokinesis: division of the cytoplasm. Animal cells: plasma membrane pinches in because of a contractile ring of microfilaments of actin and myosin. Plant cells: vesicles from the Golgi apparatus appear at the equatorial plate. These fuse to form new plasma membrane. Contents of vesicles form the cell plate—the beginning of the new cell wall

9.4 – What is the role of cell division in sexual life cycles: - Asexual reproduction is based on mitotic division of the nucleus. It may be a unicellular organism reproducing itself, or: Cells of multicellular organisms that break off to form a new individual, the offspring are clones—genetically identical to the parent.-Sexual Reproduction: the offspring are not identical to the parents. Meiosis produces gametes that differ genetically from the parents, and also from each other.

- Somatic Cells: body cells not specialized for reproduction. Each somatic cell contains homologous pairs of chromosomes with corresponding genes. Each parent contributes one homolog.- Haploid: number of chromosomes = n, Gametes contain only one set of chromosomes.- Fertilization: two haploid gametes (female egg and male sperm) fuse to form a diploid zygote; chromosome number = 2n- Sexual Life Cycles: - Haplontic Organisms: protists and many fungi; zygote is the only diploid stage. Zygote undergoes meiosis to form haploid spores. Mature organism is haploid; produces gametes by mitosis.- Alternation of Generations: most plants, some protists: meiosis gives rise to haploid spores. Spores divide by mitosis to form the haploid generation (gametophyte). Gametophyte forms gametes by mitosis. Gametes fuse to form diploid zygote (sporophyte).- Diplontic life cycle: animals and some plants; gametes are the only haploid stage.Mature organism is diploid and produces gametes by meiosis. Gametes fuse to form diploid zygote; zygote divides by mitosis to form mature organism.- Non-Identical: Sexual reproduction results in shuffling of genetic information in a population. No two individuals have exactly the same genes.- There is random selection of half a parents chromosomes that go into the haploid gamete; two such gametes fuse—offspring are not exactly like parents.- Cells in metaphase can be fixed in order to characterize the chromosomes.- Karyotype: the number, shapes, and sizes of the chromosomes in a cell.- Chromosome Recognition: Individual chromosomes can be recognized by length, position of centromere, and banding patterns.- Human Karyotype: in the diploid stages, the Karyotype consists of homologous pairs of chromosomes – 23 pairs – 46 chromosomes in total

9.5 – What happens when a cell undergoes meiosis:- Meiosis consists of two nuclear divisions that reduce the chromosome number to haploid. DNA is replicated only once. Products are different from the parent cell, and from each other.- Functions: Reduce chromosome number from diploid to haploid. Ensure that each product has a full set of chromosomes. Promote genetic diversity among the products.- Unlike mitosis: In meiosis I, homologous pairs of chromosomes come together and pair along their entire lengths. After metaphase I, the homologous pairs segregate; the sister chromatids remain together until after metaphase II.- S phase: precedes Meiosis I, during which DNA is replicated. Each chromosome then consists of two sister chromatids, held together by cohesin proteins.- Meiosis I:

Prophase I: the homologous chromosomes pair along the length: synapsis. Joining begins at telomeres; mediated by recognition of homologous DNA sequences. A protein scaffold—the synaptonemal complex—joins the homologous chromosomes (4 chromatids). The four chromatids form a tetrad or

bivalent. Example: humans have 46 chromosomes in 23 pairs. In prophase I: 23 tetrads form a total of 92 chromatids.Prophase I and Metaphase I: the chromatin continues to coil and compact. The homologs seem to repel each other but are held together at chiasmata that form between non-sister chromatids. Exchange of genetic material occurs at the chiasmata—also called crossing over forming recombinant chromatids. Crossing over increases genetic variability of the products. Prophase I may last a long time. Human males: about 1 week for prophase I and 1 month for entire meiotic cycle. Human females: prophase I begin before birth, and ends up to decades later during the monthly ovarian cycle.Prometaphase I: nuclear envelope and nucleoli disappear. Spindle forms; kinetochores of both chromatids of a chromosome attach to the same half-spindle. Which member of each homologous pair goes to which pole is random.Metaphase I: chromosomes are at the equatorial plate; homologous pairs held together by chiasmata.Anaphase I: homologous chromosomes separate; daughter nuclei contain only one set of chromosomes. Each chromosome consists of two chromatids.

Differences between meiosis II and mitosis: DNA does not replicate before meiosis II. In meiosis II the sister chromatids may not be identical because of crossing over. The number of chromosomes at the equatorial plate in meiosis II is half the number of those in mitosis.- Results: Meiosis results in four haploid nuclei. Genetic composition differs because of crossing over and the random segregation of homologous pairs during anaphase I.- Synapsis during prophase I allows crossing over; the resulting recombinant chromatids contain some genetic material from each parent.- Independent assortment: results from the random way in which homologous pairs line up on the equatorial plate at metaphase I.- Meiotic errors:

Nondisjunction: homologous pairs fail to separate at anaphase I; or sister chromatids fail to separate; or homologous chromosomes may not remain together. Either results in aneuploidy: chromosomes lacking or present in excess.

- Aneuploidy: may be caused by lack of cohesins that hold the homologous pairs together. Without cohesins, there is a 50 percent chance that both homologs will go to the same pole. Resulting gamete will have two of the same chromosome, or none.

- Down Syndrome: In humans, if both chromosome 21 homologs go to the same pole, and the resulting egg is fertilized, it will be trisomic for chromosome 21. - Monosomic: If the egg that did not receive a copy of chromosome 21 is fertilized, it will be.

Translocation: a piece of chromosome may break away and attach to another chromosome.

Down syndrome: An individual with a translocated piece of chromosome 21 plus two normal copies

- Trisomies and monosomies are common in human zygotes. Most embryos from these zygotes do not survive. Trisomies and monosomies for chromosomes other than 21 are lethal—many miscarriages are due to this.- Polyploid: Organisms with complete extra sets of chromosomes are called. Triploid (3n), tetraploid (4n), and even higher ploidy levels. Mitosis can occur because each chromosome behaves independently. •Polyploidy (e.g., 3n) can prevent meiosis because not all chromosomes will have a homolog, and anaphase I will not take place. Many modern crop plants are polyploid. Bread wheat plants are hexaploid—from crossing three different diploid grasses.

9.6 – How do cells die: - Necrosis—cell is damaged or starved for oxygen or nutrients. The cell swells and bursts. Cell contents are released to the extracellular environment. Can cause inflammation. Scabs are necrotic tissue.- Apoptosis—genetically programmed cell death. Cell is no longer needed, e.g., the connective tissue between the fingers of a fetus. Old cells may be prone to genetic damage that can lead to cancer; blood cells, epithelial cells die after days or weeks. Apoptosis: cell cuts up its chromatin into nucleosome-sized pieces, forms membranous lobes called blebs that break into fragments. Surrounding living cells ingest the remains of the dead cell.- Cell death cycle is controlled by signals: Lack of a mitotic signal (growth factor), Recognition of damaged DNA. External signals cause membrane proteins to change shape and activate enzymes called caspases—hydrolyze proteins of membranes.

Chapter 10: Genetics Mendel & Beyond10.1 – What are the Mendelian laws of inheritance?

- Plant Breeding: People have been crossbreeding plants and animals for at least 5,000 years. By the nineteenth century, plant breeding was widespread.- Two assumptions about how inheritance works: Each parent contributes equally to offspring. (Correct.) Supported by reciprocal crosses, 1770s, by Kölreuter. OR Hereditary determinants blend in the offspring. (Incorrect.) It was thought that once hereditary elements had blended they could never be separated. Gregor Mendel’s studies refuted this. - Mendel: was an Austrian monk. His studies in physics and mathematics were a strong influence on his use of quantitative experimental methods. Over seven years, he made crosses with 24,034 plants. His new theory of inheritance was published in 1866, but was largely ignored. Most biologists at the time were not used to thinking in mathematical terms. Even Darwin missed the significance of Mendel’s work.- Physical Explanation to Results: By 1900, meiosis had been observed. Three plant geneticists realized that chromosomes and meiosis provided a physical explanation for Mendel’s results.

- Garden Pea: what Mendel chose to work with; he could control pollination and fertilization—he could be sure of the parents of offspring. The peas naturally self-pollinate.- Character: observable physical feature (e.g., flower color).- Trait: form of a character (e.g., purple flowers or white flowers).- A heritable trait is passed from parent to offspring. - Mendel looked for well-defined, true-breeding traits—the observed trait is the only one present for many generations. True-breeding strains were isolated by inbreeding and selection. He concentrated on seven traits.- Mendel’s Crosses: Pollen from one parent was transferred to the stigma of the other parent. Parental generation = P. Resulting offspring = first filial generation or F1. If F1 plants self-pollinate, produce second filial generation or F2.- Mendel’s first experiment: Crossed plants differing in just one trait (P). F1 generation are monohybrids. The monohybrids were then allowed to self-pollinate to form the F2 generation: a monohybrid cross. Mendel repeated this for all seven traits.- Recessive: One trait of each pair disappeared in the F1 generation and reappeared in the F2

- Dominant Trait: The trait that appears in the F1 - Mendelian Ratio: The ratio of dominant to recessive in the F2 was about 3:1.- Reciprocal crosses: yielded the same results: it made no difference which parent contributed pollen. The idea that each parent contributes equally was supported. - Particulate Theory: Mendel proposed that the heritable units were discrete particles each plant has two particles for each character, one from each parent.- Mendel also concluded that each gamete contains only one particle (or unit), but the zygote contains two—because it is produced from the fusion of two gametes. The “particles” are now called genes. The totality of all genes in an organism is the genome.- The true-breeding plants in the P generation had two identical copies of the particle (gene) for each character. Example: spherical SS ; wrinkled ss gametes from SS will have one S, gametes from ss will have one s, offspring (F1) will be Ss, S is dominant; s is not expressed in F1

- Alleles: different forms of a gene. True-breeding individuals have two copies of the same allele—they are homozygous for the allele (e.g., ss). Heterozygous individuals have two different alleles (e.g., Ss).- Phenotype: physical appearance of an organism (e.g., spherical seeds). - Genotype: the genetic makeup (e.g., Ss). - The Law of Segregation: the two copies of a gene separate when an individual makes gametes. When the F1 self-pollinates, there are three ways to get the dominant trait (e.g., spherical), only one way to get the recessive (wrinkled)—resulting in the 3:1 ratio.- Punnett Square: Allele combinations can be predicted- A gene is a sequence on a DNA molecule that resides at a particular site on a chromosome—the locus—and encodes a particular character. Genes are expressed as proteins with particular functions. Different alleles of a gene separate during meiosis.- Test Crosses: determines whether an individual is homozygous or heterozygous for a trait by crossing it with the homozygous recessive.

- Mendel’s next experiment: Crossing peas that differed in two characters—seed shape and seed color. true-breeding parents: SSYY—spherical yellow seeds ssyy—wrinkled green seedsF1 generation is SsYy—all spherical yellow.- Dihybrid Cross: Crossing (self-pollinating) the F1 generation is a - Recombinant Phenotypes: If linked, gametes would be SY or sy; F2 would have three times more spherical yellow than wrinkled green. If independent, gametes could be SY, sy, Sy, or sY. F2 would have nine different genotypes; phenotypes would be in 9:3:3:1 ratio.- The Law of Independent Assortment: Alleles of different genes assort independently during gamete formation. Doesn’t always apply to genes on the same chromosome; but chromosomes do segregate independently - Probability: If an event is certain to happen, probability = 1, If an event cannot possibly happen, probability = 0, All other events have a probability between 0 and 1- Probability of two independent events happening together: multiply the probabilities of the individual events.-The multiplication rule: multiply probabilities - The probability of an event that can occur in two different ways is the sum of the individual probabilities.- The Addition Rule: In F2, there are two ways to get a heterozygote; thus ¼ + ¼ = ½ - Result: 1:2:1 ratio of genotypes; 3:1 ratio of phenotypes- Human pedigrees can show Mendel’s laws. Humans have few offspring; pedigrees do not show the clear proportions that the pea plants showed. Geneticists use pedigrees to determine whether a rare allele is dominant or recessive.- When there is a rare recessive phenotype in a family, there is usually marriage of relatives. If a recessive allele is rare in the general population, it is unlikely that two people that marry will both carry it unless they are related (e.g., cousins)

10.2 – How do alleles interact:- Mutation: rare, stable, inherited changes in the genetic material.- Wild type: allele present in most of the population. Other alleles are mutant alleles. Locus with wild-type allele present less than 99% of the time is polymorphic.- A given gene may have more than two alleles.- Incomplete dominance: Some alleles are neither dominant nor recessive—heterozygote has an intermediate phenotype- Codominance: two alleles at one locus produce phenotypes that are both present in the heterozygote. Example: ABO blood group system—three alleles at one locus.- Pleiotropic: A single allele can have multiple effects. Example: allele for coloration pattern in Siamese cats; the same allele results in crossed eyes—both result from the same protein.- Epistasis: phenotypic expression of one gene is influenced by another gene. Example: coat color in Labrador retrievers. allele B (black) dominant to b (brown), allele E (pigment deposition) is dominant to e (no pigment deposition—yellow)

10.3 – How do genes interact:- Inbreeding: mating among close relatives; can result in offspring of low quality. Close relatives tend to have the same recessive alleles.

- Heterosis: A cross between two different true-breeding homozygotes can result in offspring with stronger, larger phenotypes: hybrid vigor or heterozygote advantage. First discovered with corn by G.H. Shull.- Environment also affects phenotype. Light, temperature, nutrition, etc., can affect expression of the genotype. Siamese cats and certain rabbit breeds—enzyme that produces dark fur is inactive at higher temperatures.

Penetrance: proportion of individuals with a certain genotype that show the phenotype.Expressivity: degree to which genotype is expressed in an individual.

- Mendel’s characters were discrete and qualitative. For more complex characters, phenotypes vary continuously over a range — quantitative variation, or continuous. Quantitative variation is usually due to both genes and environment.- Quantitative trait loci: Genes that determine these complex characters.- Much genetic research has been done with the fruit fly Drosophila melanogaster.

10.4 – What is the relationship between genes and chromosomes:- Beginning in 1909 in Thomas Hunt Morgan’s lab at Columbia—the “fly room.” Identifying these loci can help improve crop yields, understand disease susceptibility and behavior, etc.- Some crosses performed with Drosophila did not yield expected ratios according to the law of independent assortment. Some genes were inherited together; the two loci were on the same chromosome, or linked.- All the loci on a chromosome form a linkage group. - Absolute linkage is rare. Genes may recombine during prophase I of meiosis by crossing over. Chromosomes exchange corresponding segments. The exchange involves two chromatids in the tetrad; both chromatids become recombinant.- Recombinant offspring phenotypes (non-parental) appear in recombinant frequencies: Divide number of recombinant offspring by total number of offspring. Recombinant frequencies are greater for loci that are farther apart.- Recombinant frequencies can be used to make genetic maps showing the arrangement of genes along a chromosome. Distance between genes = map unit = recombinant frequency of 0.01. Map unit also called a centimorgan (cM)- Sex determination varies among species. Corn: each adult produces both male and female gametes — monoecious (“one house”). Some plants and most animals are dioecious (“two houses”) — male and female gametes produced by different individuals.- Many animals have a pair of sex chromosomes; all others are autosomes - Mammals: Female has two X chromosomes. Male has one X and one Y - Birds: Females have one Z and one W. Males have two Z chromosomes.- Nondisjunction: XO—the individual has only one sex chromosome — Turner syndrome. XXY — Klinefelter syndrome.- The SRY gene: — (sex-determining region on the Y chromosome) encodes a protein involved in primary sex determination. If SRY protein is present, the embryo develops testes. If there is no SRY, the embryo develops ovaries. A gene on the X chromosome, DAX1, produces an anti-testis factor. SRY in males inhibits the DAX1 maleness inhibitor.

- Secondary sex determination results in outward characteristics of each sex—not determined directly by presence or absence of Y chromosome. Determined by genes scattered on all the chromosomes that control hormones.- Sex-linked inheritance — governed by loci on the sex chromosomes.- X-linked recessive phenotypes: Appear much more often in males than females, Daughters who are heterozygous are carriers, Mutant phenotype can skip a generation if it passes from a male to his daughter

Chapter 11: DNA and Its Role In Heredity: 11.1 – What is the evidence that the gene is DNA:

- By the 1920s, it was known that chromosomes consisted of DNA and proteins.A new dye was capable of staining DNA and provided circumstantial evidence that DNA was the genetic material: It was in the right place, It varied among species, It was present in the right amount- Frederick Griffith, working with two strains of Streptococcus pneumoniae, determined that a “transforming principle” from dead cells of one strain produced a heritable change in the other strain. Treated pathogenic strain with heat (non-lethal) but when mixed with non-pathogenic strain – becomes lethal- Oswald Avery: Identifying the transforming principle. Treated samples to destroy different molecules; if DNA was destroyed, the transforming principle was lost. The transforming principle is DNA because when it was destroyed, no pathogen was evident- Hershey-Chase experiment: Determined whether DNA or protein is the genetic material using bacteriophage T2 virus. Bacteriophage: proteins were labeled with 35S, the DNA was labeled with 32P. The 32P proves that DNA enters bacterial cells and directs the assembly of new viruses - Transfection: Next, genetic transformation of eukaryotic cells was demonstrated. Use a genetic marker—a gene that confers an observable phenotype. Any cell can be transfected, even an egg cell—results in a transgenic organism. - Growth media = contains thymidine, marker = functional copy of thymidine kinase

11.2 – What is the structure of DNA: - The structure of DNA: was determined using many lines of evidence- Rosalind Franklin & Maurice Wilkins: One crucial piece came from X-ray crystallography, A purified substance can be made to form crystals; position of atoms is inferred by the pattern of diffraction of X-rays passed through it- Chemical composition also provided clues: DNA is a polymer of nucleotides: deoxyribose, a phosphate group, and a nitrogen-containing base. The bases: Purines: adenine (A), guanine (G), Pyrimidines: cytosine (C), thymine (T)- Erwin Chargaff found that: amount of A = amount of T & amount of C = amount of G Or, the abundance of purines = the abundance of pyrimidines — Chargaff’s rule.- Model building started by Linus Pauling: building 3-D models of possible molecular structures.- Francis Crick and James Watson used model building and combined all the knowledge of DNA to determine its structure.- Structure: X-ray crystallography convinced them the molecule was helical. Other

evidence suggested there were two polynucleotide chains that ran in opposite directions—antiparallel 1953—Watson & Crick established the general structure of DNA.- Key features of DNA: A double-stranded helix, uniform diameter, It is right-handed, It is antiparallel, Outer edges of nitrogenous bases are exposed in the major and minor grooves- Complementary base pairing: Adenine pairs with thymine by two hydrogen bonds. Cytosine pairs with guanine by three hydrogen bonds. Every base pair consists of one purine and one pyrimidine. From 5’ carbon to 3’ carbon- Antiparallel strands: direction of strand is determined by the sugar–phosphate bonds. Phosphate groups connect to the 3′ C of one sugar, and the 5′ C of the next sugar. At one end of the chain—a free 5′ phosphate group; at the other end a free 3′ hydroxyl.- Functions/attributes of DNA: 1) Store genetic material—millions of nucleotides; base sequence stores and encodes huge amounts of information. 2) Susceptible to mutation—change in information 3) Genetic material is precisely replicated in cell division—by complementary base pairing. 4) Genetic material is expressed as the phenotype—nucleotide sequence determines sequence of amino acids in proteins.

11.3 – How is DNA replicated: - Arthur Kornberg showed that DNA contains information for its own replication.In a test tube: DNA four nucleotide triphosphates (dATP, dCTP, dGTP, dTTP) DNA polymerase enzyme. The DNA is a template for synthesis of new DNA.- Three possible replication patterns: Semiconservative replication, Conservative replication, and Dispersive replication- Meselson & Stahl confirmed that Semiconservative replication was the correct. They used density labeling to distinguish parent DNA strands from new DNA strands. DNA was labeled with 15N, making it more dense. Results of their experiment can only be explained by the semiconservative model. If it were conservative, the first generation of individuals would have all been high or low density, but not intermediate. If dispersive, density in the first generation would be half, but this density would not appear in subsequent generations.- Replication: the double helix is unwound, making two template strands. New nucleotides are added to the new strand at the 3′ end; joined by phosphodiester linkages. Sequence is determined by complementary base pairing

- A large protein complex—the replication complex—catalyzes the reactions of replication- All chromosomes have a base sequence called origin of replication (ori)- Replication complex binds to ori at start- DNA replicates in both directions, forming two replication forks

- DNA Helicase uses energy from ATP hydrolysis to unwind the DNA.- Single-strand binding proteins keep the strands from getting back together.- Small, circular chromosomes have a single origin of replication.- As DNA moves through the replication complex, two interlocking circular chromosomes are formed.- DNA topoisomerase relaxes coiling tension and separates the two strands

- Origins: Large linear chromosomes have many origins of replication. DNA is replicated simultaneously at the origins.- DNA polymerases are much larger than their substrates. – DNA and Nucleotides, Shape is like a hand; the “finger” regions have precise shapes that recognize the shapes of the nucleotide bases. - A primer is required to start DNA replication— a short single strand of RNA. Primer is synthesized by primase. Then DNA polymerase begins adding nucleotides to the 3′ end of the primer. – Just a few. Cells have several DNA polymerases. One is for DNA replication; others are involved in primer removal and DNA repair. Other proteins are involved in the replication process.- At the replication fork: The leading strand is pointing in the “right” direction for replication. The lagging strand is in the “wrong” direction. Synthesis of the lagging strand occurs in small, discontinuous stretches—Okazaki fragments. Each Okazaki fragment requires a primer. The final phosphodiester linkage between fragments is catalyzed by DNA ligase.- DNA polymerases work very fast. They are processive: catalyze many polymerizations each time they bind to DNA, Newly replicated strand is stabilized by a sliding DNA clamp (a protein)- The new chromosome has a bit of single stranded DNA at each end (on the lagging strand)—this region is cut off.- Telomeres: Eukaryote chromosomes have repetitive sequences at the ends. Human chromosome telomeres (TTAGGG) are repeated about 2500 times. Chromosomes can lose 50–200 base pairs with each replication. After 20–30 divisions, the cell dies. - Some cells—bone marrow stem cells, gamete-producing cells—have telomerase that catalyzes the addition of telomeres.- 90% of human cancer cells have telomerase; normal cells do not. Some anticancer drugs target telomerase. – Reason they can replicate - DNA polymerases make mistakes in replication, and DNA can be damaged in living cells.

11.4 – How are errors in DNA repaired: - DNA polymerases make mistakes in replication, and DNA can be damaged in living cells - Repair mechanisms:

Proofreading: As DNA polymerase adds a nucleotide to a growing strand, it has a proofreading function—if bases are paired incorrectly, the nucleotide is removed.Mismatch repair: The newly replicated DNA is scanned for mistakes by other proteins. Mismatch repair mechanism detects mismatched bases—the new strand has not yet been modified (e.g. methylated in prokaryotes) so it can be recognized. If mismatch repair fails, the DNA is altered.Excision repair: DNA can be damaged by radiation, toxic chemicals, and random spontaneous chemical reactions. Excision repair: enzymes constantly scan DNA for mispaired bases, chemically modified bases, and extra bases—unpaired loops.11.5 – What are some applications of our knowledge of DNA structure and replication:

- Copies of DNA sequences can be made by the polymerase chain reaction (PCR) technique. PCR is a cyclical process: heating denatures DNA fragments. A primer, plus nucleosides and DNA polymerase are added. New DNA strands are synthesized.- Kary Mullis inventor of PCR and Nobel Prize - PCR results in many copies of the DNA fragment—referred to as amplifying the sequence. Primers are 15–20 bases, made in the laboratory. The base sequence at the 3′ end of the DNA fragment must be known.- DNA polymerase that does not denature at high temperatures (>95°C) was taken from a hot springs bacterium, Thermus aquaticus.- DNA sequencing determines the base sequence of DNA molecules. Relies on altered nucleosides with fluorescent tags that emit different colors of light. DNA fragments are then denatured and separated by electrophoresis.

Chapter 12: From DNA to Protein: Genotype to Phenotype: 12.1 – What is the evidence that genes code for proteins:

- The molecular basis of phenotypes was known before it was known that DNA is the genetic material. Studies of many different organisms showed that major phenotypic differences were due to specific proteins.- Model Organisms: easy to grow or observe; show the phenomenon to be studiedAssume that results from one organism can be applied to others (evolutionary conservation). Examples: pea plants, Drosophila, E. coli, Neurospora crassa (bread mold)-Neurospora is haploid for most of its life cycle.- Wild-type strains have enzymes to catalyze all reactions needed to make cell constituents—prototrophs.- Beadle and Tatum used X-rays as mutagens. Mutants were auxotrophs—needed additional nutrients to grow.- For each auxotrophic strain, they found a single compound that would support growth of that strain. Suggested the one-gene, one-enzyme hypothesis – each gene specifies a particular enzyme- sequencing: Template strand runs opposite from new strand

12.2 – How does information flow from genes to proteins:- Transcription—copies information from gene to a sequence of RNA.- Translation—converts RNA sequence to amino acid sequence.- Transcription: - RNA, ribonucleic acid differs from DNA: Usually one strand, The sugar is ribose, Contains uracil (U) instead of thymine (T)- RNA can pair with a single strand of DNA, except that adenine pairs with uracil instead of thymine.- Single-strand RNA can fold into complex shapes by internal base pairing.- The central dogma of molecular biology: information flows in one direction when genes are expressed (Francis Crick). How does genetic information get from the nucleus to the cytoplasm? What is the relationship between a DNA sequence and an amino acid sequence?

- Messenger hypothesis—messenger RNA (mRNA) forms as a complementary copy of DNA and carries information to the cytoplasm.- Adapter hypothesis—an adapter molecule that can bind amino acids, and recognize a nucleotide sequence—transfer RNA (tRNA).- tRNA molecules carrying amino acids line up on mRNA in proper sequence for the polypeptide chain—translation.- Viruses: acellular particles that reproduce inside cells; many have RNA instead of DNA - Synthesis of DNA from RNA is reverse transcription. Viruses that do this are retroviruses. - Within each gene, only one strand of DNA is transcribed—the template strand. Transcription produces mRNA; the same process is used to produce tRNA and rRNA.- RNA polymerases catalyze synthesis of RNA. RNA polymerases are processive—a single enzyme-template binding results in polymerization of hundreds of RNA bases.

Initiation requires a promoter—a special sequence of DNA. RNA polymerase binds to the promoter. Promoter tells RNA polymerase where to start, which direction to go in, and which strand of DNA to transcribe. Part of each promoter is the initiation site.Elongation: RNA polymerase unwinds DNA about 10 base pairs at a time; reads template in 3′ to 5′ direction. The RNA transcript is antiparallel to the DNA template strand. RNA polymerases do not proofread and correct mistakes.Termination: specified by a specific DNA base sequence. Mechanisms of termination are complex and varied. Eukaryotes—first product is a pre-mRNA that is longer than the final mRNA and must undergo processing.12.3 – How is the information content in DNA transcribed to produce RNA:

- The genetic code: specifies which amino acids will be used to build a protein- Codon: a sequence of three bases. Each codon specifies a particular amino acid.- Start codon: AUG—initiation signal for translation- Stop codons: stops translation and polypeptide is released- For most amino acids, there is more than one codon; the genetic code is redundant.But not ambiguous—each codon specifies only one amino acid - The genetic code is nearly universal: the codons that specify amino acids are the same in all organisms. Exceptions: within mitochondria and chloroplasts, and in one group of protists.- This common genetic code is a common language for evolution. The code is ancient and has remained intact throughout evolution. The common code also facilitates genetic engineering.- 20 “code words” (amino acids) are written with only four “letters.” Triplet code seemed likely: could account for 4 × 4 × 4 = 64 codons - Nirenberg and Matthaei used artificial polynucleotides instead of mRNA as a messenger. Then they identified the polypeptide that resulted.- Transcription: T = U in same orientation

12.4 – How is RNA translated into Proteins? - tRNA, the adaptor molecule: for each amino acid, there is a specific type or “species” of tRNA.

- Functions of tRNA: Carries an amino acid, Associates with mRNA molecules, Interacts with ribosomes- The conformation (three-dimensional shape) of tRNA results from base pairing (H bonds) within the molecule. 3′ end is the amino acid attachment site—binds covalently. Always CCA.- Anticodon: site of base pairing with mRNA. Unique for each species of tRNA.- Example : DNA codon for arginine: GCC, Complementary mRNA: CGG, Anticodon on the tRNA: GCC, this tRNA is charged with arginine.- Charging a tRNA with the correct amino acid—amino-acyl-tRNA synthetases. Each enzyme is specific for one amino acid and its corresponding tRNA. The enzymes have three-part active sites: they bind a specific amino acid, a specific tRNA, and ATP.- Experiment by Seymour Benzer and others: Chemically changed cysteine already bound to tRNA to alanine. Resulting polypeptide had alanine in every place that cysteine should be. Protein synthesis machinery recognizes the anticodon, not the amino acid.- Ribosome: the workbench—holds mRNA and tRNA in the correct positions to allow assembly of polypeptide chain. Ribosomes are not specific, they can make any type of protein.- Ribosomes have two subunits, large and small. In eukaryotes, the large subunit has three molecules of ribosomal RNA (rRNA) and 45 different proteins in a precise pattern. The small subunit has one rRNA and 33 proteins.- Large subunit has 3 tRNA binding sites: 1) A site binds with anticodon of charged tRNA. 2) P site is where tRNA adds its amino acid to the growing chain. 3) E site is where tRNA sits before being released.

Hydrogen bonds form between the anticodon of tRNA and the codon of mRNA. Small subunit rRNA validates the match—if hydrogen bonds have not formed between all three base pairs, it must be an incorrect match, and the tRNA is rejected.

- Translation also occurs in three steps: 5’ 3’Initiation: An initiation complex forms—charged tRNA and small ribosomal subunit, both bound to mRNA.rRNA binds to recognition site on mRNA—the Shine-Dalgarno sequence, “upstream” from the start codon. tRNA in P site at start codon with appropriate anti codon to form the amini acid and consequent polypeptide•Start codon is AUG; first amino acid is always methionine, which may be removed after translation.•The large subunit joins the complex, the charged tRNA is now in the P site of the large subunit.•Initiation factors are responsible for assembly of the initiation complex.Elongation•the second charged tRNA enters the A site.•Large subunit catalyzes two reactions: Breaks bond between tRNA in P site and its amino acid. Peptide bond forms between that amino acid and the amino acid on tRNA in the A site.

•The large subunit has peptidyl transferase activity. RNA acts as the catalyst; normally proteins are catalysts. Supports the idea that catalytic RNA evolved before DNA.•When the first tRNA has released its methionine, it moves to the E site and dissociates from the ribosome—can then become charged again.•Elongation occurs as the steps are repeated, assisted by proteins called elongation factors.Termination•translation ends when a stop codon enters the A site.•Stop codon binds a protein release factor—allows hydrolysis of bond between polypeptide chain and tRNA on the P site.•Polypeptide chain—C terminus is the last amino acid added.•Several ribosomes can work together to translate the same mRNA, producing multiple copies of the polypeptide.•A strand of mRNA with associated ribosomes is called a polyribosome or polysome.12.5 – What happens to polypeptides after translation:

- Posttranslational aspects of protein synthesis: Polypeptide may be moved from synthesis site to an organelle, or out of the cell. Polypeptides are often modified with more chemical groups.

12.6 – What are mutations:- Somatic mutations occur in somatic (body) cells. Mutation is passed to daughter cells, but not to sexually produced offspring.- Germ line mutations occur in cells that produce gametes. Can be passed to next generation.- Conditional mutants: express phenotype only under restrictive conditions. Example: the allele may code for an enzyme that is unstable at certain temperatures.- All mutations are alterations of the nucleotide sequence.- Point mutations: change in a single base pair—loss, gain, or substitution of a base.

•Point mutations can result from replication and proofreading errors, or from environmental mutagens.•Silent mutations have no effect on the protein because of the redundancy of the genetic code.•Silent mutations result in genetic diversity not expressed as phenotype differences.

- Chromosomal mutations: change in segments of DNA—loss, duplication, or rearrangement.