Learning Outcomes

10.5 Analyze the process used to reduce carbon dioxide sugars

-3PGA produced after CO2 fixation by rubisco is phosphorylated by ATP and reduced by NADPH to produce G3P -some G3P used to synthesize other organic molecules (glucose); ATP phosphorylates the rest in series of reactions to regenerate RuBP so cycle can continue -photosynthesis stimulated by presence of light and reduced when sugar supplies high/CO2 availability low -G3P mostly converted into sucrose for distribution throughout plant when photosynthetic activity is low, or into starch for storage when activity is high

15.5 Explain some of the ways that damage to DNA is repaired

-DNA replication is accurate because DNA polymerase selectively adds deoxyribonucleotide that correctly base-pairs with template strand, proofreads each added deoxyribonucleotide, and mismatch repair proteins remove deoxyribonucleotides with incorrect bases that escape proofreading/replace them with correct deoxyribonucleotide -other types of DNA repair occur after DNA has been damaged by chemicals/radiation -nucleotide excision repair cuts out damaged portions of DNA/replaces them with correct sequences -if DNA repair proteins are defective, mutation rate increases; defects in genes responsible for DNA repair lead to several types of cancer

15.3 Analyze synthesis of the leading and lagging strands of DNA

-DNA synthesis requires different proteins/occurs in one direction (5'→3') -DNA synthesis requires template and short RNA primer; takes place at replication fork where double helix is opened -synthesis of leading strand is continuous, but synthesis of lagging strand is discontinuous (on that strand, DNA polymerase moves away from replication fork) -on lagging strand, short DNA fragments called Okazaki fragments form/are joined together. -synthesis of leading + lagging strands coordinated by replisome (large enzyme/protein complex involved in DNA synthesis that synchronously produces both leading + lagging strands of DNA

16.2 Explain the link between genotype and phenotype

-DNA transcribed to mRNA by RNA polymerase, then mRNA translated to proteins by ribosomes; genetic information converted from DNA to RNA to protein -information flow from DNA to RNA to protein called central dogma of molecular biology -central dogma extended to account for RNAs that do not code for proteins and perform other important functions in the cell

9.5 Analyze the relationship between the electron transport chain and oxidative phosphorylation

-ETC resides in inner membrane of mitochondria (plasma membrane of prokaryotes); consists of series of electron acceptors that vary in redox potential starting with oxidation of NADH and FADH2/ending with reduction of terminal electron acceptor (ex: O2) -change in energy that is produced by redox reactions in ETC transports protons across inner mitochondrial membrane, creating electrochemical gradient -ATP production coupled to ETC by oxidative phosphorylation; PE stored in proton gradient built up by ETC used to spin components of ATP synthase to produce ATP; process is responsible for ATP made by cellular respiration

3.2 Describe the four different levels of protein structure

-a protein's primary structure, or sequence of amino acids, is responsible for most of its chemical properties -interactions that take place between amino acid sequences create secondary structures (stabilized by hydrogen bonding) -tertiary structure results from interactions between R-groups that stabilize a complete polypeptide into a three-dimensional shape -the combination of polypeptides represents the protein's quaternary structure

8.3 Analyze the process of energetic coupling to drive non-spontaneous reactions

-activation energy is amount of KE required to reach transition state of a reaction -enzymes speed reaction rates but do not affect the change in free energy of the reaction -enzymes have active sites that bring substrates together and change shape to stabilize transition state -enzymes catalyze reaction by lowering activation energy with cofactors, coenzymes, prosthetic groups

20.3 Describe how genomes are studied

-advances in DNA sequencing technologies allowed investigators to sequence DNA more rapidly/cheaply -thousands of genomes sequenced for many purposes -bioinformatics is application of computer science to genome analysis/is essential for genome research -researchers annotate genome sequences using sequence data to find genes/provide clues about their function -2 common approaches to finding genes in genome sequence are to search for open reading frames/to match sequences of expressed sequence tag cDNAs to regions of genome -genome-wide association studies find genes by association between phenotypes they cause + genetic markers (SNPs) that live at known positions in genome

3.1 Analyze the characteristics of amino acids and the bonds that link them together in polypeptides

-amino acids have a central carbon bonded to an amino group, a hydrogen atom, a carboxyl group, and an R-group -the structure of the R-group affects the chemical reactivity and solubility of the amino acid -in proteins, amino acids are joined by a peptide bond between the carboxyl group of one amino acid and the amino group of another amino acid

18.3 Compare global gene regulation to the regulation of single genes

-bacterial cells need to coordinate expression of large sets of genes in response to changing environments -regulons coordinate expression of different genes by using shared regulator that acts on regulatory sequence found in all genes/operons of regulon; regulons work through negative control using repressors/positive control using activators -SOS regulon contains 40+ genes needed to repair DNA damage; SOS regulon controlled by repressor coded for by lexA gene; DNA damage leads to cleavage of LexA repressor, activating expression of regulon genes; LexA repressor level returns to normal when DNA damage repaired, turning off SOS regulon genes

1.6 Explain the scientific process

-biology is a hypothesis-driven, experimental science

15.2 Interpret the results of the Meselson-Stahl experiment to argue that DNA is replicated semiconservatively

-by labeling DNA with 15N/14N, researchers validated semiconservative hypothesis of DNA replication -in semiconservative replication, each strand of parental DNA molecule provides template for synthesis of daughter strand, resulting in 2 DNA double helices

12.4 Explain how the properties of cancer are related to the breakdown of social control that regulates cell division

-cancer is characterized by (1) loss of control at G1 checkpoint, resulting in cells that divide uncontrollably and (2) metastasis (ability of tumor cells to spread throughout body) -G1 checkpoint depends on Rb protein, which prevents progression to S phase, and G1 cyclin-Cdk complexes, which trigger progression to S phase; alterations in expression of Rb/G1 cyclin are common in cancer

2.5 Differentiate between the structural and functional characteristics of organic molecules

-carbon is the foundation of organic molecules based on its valence, which allows for the construction of molecules with complex shapes -organic molecules are critical to life because they possess versatility of chemical behavior due to the presence of functional groups -functional groups promote further interactions between organic molecules to form macromolecules

7.3 Explain how diverse cellular activities are correlated with the function of organelles

-cells have tightly organized interior where organelles reflect the function of the cell -activity in a cell shows dynamic nature of life in that organelles/cytosolic proteins continually bustle about like nonstop rush hour -what is known about cellular activity is from advances in cell imaging/techniques for isolating organelles

11.1 Analyze the extracellular material produced by cells

-cells produce material that forms layer outside plasma membrane -in bacteria/plants, the extracellular material is stiff and forms cell wall; in animals, the material is flexible and is called the ECM -in eukaryotes, extracellular layers are fiber composites that consist of cross-linked filaments that provide strength and ground substance that fills space/resists compression -in plants, the extracellular filaments are cellulose microfibrils; in animals, the filaments are made of the protein collagen; in both, the ground substance is composed of gel-forming polysaccharides

9.1 Describe the four interconnected processes in cellular respiration and explain their central role in catabolism and anabolism

-cellular respiration based on redox reactions that oxidize compounds with high PE (ex: glucose)/produce molecules with low PE (ex: CO2, water) -in eukaryotes, cellular respiration has 4 stages: glycolysis, pyruvate processing, citric acid cycle, and electron transport/oxidative phosphorylation -glycolysis/pyruvate processing/citric acid cycle are central to metabolism of most cells; other catabolic pathways feed into them, and intermediates of these components of cellular respiration used in the synthesis of many key molecules

2.2 Summarize the properties of water and explain how they are necessary for life

-chemical reactions required for life take place in water -water is polar (it has partial positive and negative charges) because it is bent and has two polar covalent bonds -solutes dissolve in water (water interacts with polar molecules via hydrogen bonding and ions via similar electrical attractions) -water's ability to participate in hydrogen bonding gives it an extraordinarily high capacity to absorb heat and cohere to other water molecules -water spontaneously dissociates into hydrogen ions (H+) and hydroxide ions (OH−); the concentration of protons in a solution determines the pH, which can be altered by acids and bases or stabilized by buffers

9.4 Describe the pathway used by cells to fully oxidize the remaining two carbons from glucose that are present in acetyl CoA

-citric acid cycle is 8-step reaction cycle in matrix of mitochondria/cytosol; begins with acetyl CoA and produces FADH2/NADH/ATP or GTP; at end of the citric acid cycle, all carbons from glucose are oxidized to CO2 -certain enzymes in citric acid cycle are inhibited when NADH/ATP binds to them

7.6 Differentiate the structure and function of the three major components of the eukaryotic cytoskeleton and the roles of the three types of cytoskeletal motor proteins

-cytoskeleton is a system that provides structural support, paths for moving organelles, and cellular locomotion via cell crawling/propulsion by flagella/cilia -actin filaments/microtubules have different ends designated as plus or minus (plus ends has higher growth rate) -motor proteins move along actin filaments and microtubules using ATP -myosin move toward the plus ends, while Kinesin/dynein move toward the plus and minus ends respectively -In axonemes of eukaryotic cilia/flagella, dynein motors move microtubules to generate forces that bend the structures and enable cells to swim

7.1 Differentiate the structure and function of prokaryotic cell components

-defining characteristic that differentiates prokaryotes from eukaryotes is the absence of a nucleus -most have ribosomes, cell wall, plasma membrane, interior cytoskeleton, and nucleoid -many have flagella, fimbriae, and internal compartments

6.3 Predict how gradients can affect the movement of water and solutes across a membrane

-diffusion is the random movement of ions/molecules (due to thermal energy) -if a membrane separates solutions that differ in concentration/charge, passive transport makes environments on both sides more similar (increase in entropy) -diffusion of water across a membrane in response to a concentration gradient is called osmosis

11.3 Analyze how information is exchanged between distant cells in multicellular organisms

-distant cells communicate by secreting signaling molecules that bind to receptors in the cytosol/on surface of specific target cells -lipid-soluble signaling molecules pass through plasma membrane and bind to cytosolic signal receptors -non-lipid soluble signaling molecules bind to signal receptors in plasma membrane -signal receptors in plasma membrane change conformation on binding to signal, which triggers production of second messenger/activates phosphorylation cascade -cell's response to signals is regulated; intracellular signals quickly deactivated without constant signaling from receptors, and signaling pathways can interact

16.3 Describe the properties of the genetic code

-each amino acid in protein specified by codon (group of 3 bases in mRNA determined by complementary DNA sequence) -by synthesizing RNAs with different base sequences and observing results of translation, researchers were able to decipher genetic code -genetic code is redundant—most of the 20 amino acids specified by more than one codon -there are certain codons signal where translation starts and stops

13.2 Explain how independent assortment, crossing over, and random fertilization work to promote genetic variation in offspring

-each cell produced by meiosis receives different combination of maternal/paternal versions of each chromosome; genes located on chromosomes + come in different forms (alleles), so each cell produced receives different complement of alleles for its genes (resulting offspring genetically distinct from one another/parents) -when meiosis + mating between unrelated individuals occur, chromosome complements of offspring differ from one another/parents for 3 reasons -gametes receive random assortment of maternal + paternal chromosomes when homologs separate in meiosis I (independent assortment) -because of crossing over, each chromosome contains random assortment of paternal/maternal alleles; random fertilization results in combination of different chromosome sets from each parent

17.4 Analyze the structure and function of transfer RNA

-each tRNA carries amino acid specified by tRNA's 3-base-long anticodon -tRNAs have L-shaped tertiary structure; one "end" of L contains anticodon, which forms complementary base pairs with mRNA codon; other end holds amino acid specified by codon -aminoacyl-tRNA synthetases link correct amino acid to correct tRNA. -wobble pairing in 3rd position of codon and anticodon allows 40 types of tRNA to translate all 61 codons that code for amino acids

8.5 Contrast the different mechanisms used by cells to regulate enzyme activity and describe the organization, regulation, and evolution of metabolic pathways

-enzymes work together in metabolic pathways that sequentially modify a substrate to make a product -feedback inhibition regulates a pathway by controlling the activity of the first enzyme in the pathway -metabolic pathways were vital to the evolution of life and new pathways continue to evolve in cells

7.2 Differentiate the structure and function of eukaryotic cell components

-eukaryotic cells are larger and structurally complex -contain many organelles that compartmentalize the cytoplasm and enable cells to grow -nucleus holds chromosomes/serves as control center -endomembrane system consists of endoplasmic reticulum, Golgi apparatus, lysosomes/vacuoles, and endosomes (synthesize, process, sort, transport, recycle material) -peroxisomes result in the generation of toxic by-products (enzymes within peroxisomes disarm these byproducts after they are generated) -mitochondria/chloroplasts, hold enzymes responsible for ATP generation/photosynthesis reside

2.4 Describe how experiments are used to investigate chemical evolution

-experiments that attempt to mimic conditions of early Earth are used to investigate the process of chemical evolution -Stanley Miller demonstrated that external sources of energy (such as lightning) could have driven chemical reactions to form highly reactive molecules and amino acids from simple molecules that were likely present in early Earth

15.1 Explain the experimental evidence that led to the acceptance of DNA as the hereditary material

-experiments using viruses with labeled proteins/DNA showed that DNA is hereditary material -each DNA strand consists of sequence of nitrogenous bases held on sugar-phosphate backbone -DNA is a double helix with two strands of deoxyribonucleotides that run in opposite directions; strands twist into double helix and are held together by hydrogen bonding between complementary bases/stacking of base pairs within the helix

16.1 Explain the function of genes

-experiments with mutants of bread mold N. crassa led to one gene-one enzyme hypothesis -original hypothesis broadened to account for genes that code for proteins other than enzymes/genes that have RNA as final product/genes that have more than one product

9.6 Differentiate cellular respiration and fermentation in terms of inputs, outputs, and ATP production

-fermentation occurs in cytosol and consists of glycolysis followed by reactions that regenerate NAD+ from NADH; oxidation of NADH via fermentation required when ETC not present/is inactive due to lack of final electron acceptor -production of NAD+ enables glycolysis to continue producing ATP, yet less ATP per glucose than produced by cellular respiration; depending on molecule acting as electron acceptor, fermentation pathways produce lactate/ethanol/organic compounds as by-product

12.1 Analyze the eukaryotic cell cycle

-for a cell to replicate, it copies chromosomes, separate the copies, and divide cytoplasm to generate daughter cells that have same complement as parent cell -eukaryotic cells divide by cycling between interphase and M phase -interphase has S phase, when chromosomes replicate, and G1/G2 phases, when cells grow/prepare for division -M phase has mitosis or meiosis, when chromosomes separate, and cytokinesis, when parent cell divides

9.2 Describe the process cells use to turn glucose into pyruvate

-glycolytic pathway is 10-step reaction sequence where glucose is broken down into 2 molecules of pyruvate (takes place in cytosol + produces ATP/NADH) -glycolysis slows when ATP binds to a regulatory site in phosphofructokinase

19.5 Explain the relationship between cancer and defects in gene regulation

-if mutations alter regulatory proteins that promote or inhibit progression through cell cycle, uncontrolled cell growth/tumor formation may result; regulatory proteins are encoded by proto-oncogenes (promote)/tumor suppressor genes (inhibit) -p53 is major tumor suppressor gene that is mutated in cancers, leading to unrestrained cell growth under conditions that normally halt cell division

13.4 Make predications about when sexual reproduction is favored over asexual reproduction

-in asexual reproduction, individuals bear offspring; asexual reproduction is more efficient, because half male offspring cannot bear offspring -there are 2 leading hypotheses to explain existence of sexual reproduction/benefits of meiosis -parents with harmful allele can produce offspring without that allele -production of genetically diverse offspring leads to populations where individuals are able to resist evolving pathogens/parasites

5.3 Analyze how structure influences the different roles of carbohydrates in cells

-in carbohydrates, structure correlates with function -cellulose, chitin, and peptidoglycan are polysaccharides that function in support (strong, flexible fibers/sheets that resist hydrolysis created through strong bonds) -oligosaccharides on cell-surface glycoproteins/glycolipids can function as identity tags -starch and glycogen function as energy-storage molecules (linkages are hydrolyzed to release glucose to produce ATP/raw materials to build new molecules)

17.2 Describe the steps needed to process primary transcripts in eukaryotic gene expression

-in eukaryotes, initial transcript processed to produce mature RNA -splicing of primary transcripts removes introns/joins together exons -spliceosomes cut introns out of pre-mRNA -"cap" added to 5′ end of pre-mRNAs/poly(A) tail added to 3′ end -cap + tail are recognition signals for starting translation and protecting mRNA from degradation -RNA processing occurs in nucleus

11.2 Analyze the interactions between adjacent cells

-in multicellular organisms, molecules in extracellular layer and plasma membrane mediate interactions between adjacent cells -adjacent cells are physically bound together by glue-like middle lamella in plants/tight junctions and desmosomes in animals -cytoplasm of adjacent cells are in direct contact through plasmodesmata in plants/gap junctions in animals; allows adjacent cells to communicate via cytosolic signals -cells respond to signals by altering expression of genes/changing activity of existing proteins; responses enable cells within tissues to coordinate activities

20.1 Describe how a gene can be cloned

-in recombinant DNA technology, DNA added to cell to modify cell's properties/clone DNA -restriction endonucleases cut DNA at certain locations; resulting DNA fragments inserted into plasmids/other vectors with help of DNA ligase -crop plants genetically engineered for traits, including pest/herbicide resistance and improved food quality

17.1 Describe the steps of transcription

-in transcription, RNA polymerase produces RNA molecule with base sequence complementary to base sequence of DNA template strand -RNA polymerase begins transcription by binding to promoter sequences in DNA with help of proteins -in bacteria, binding accomplished through sigma protein; sigma associates with RNA polymerase and recognizes sequences within promoters that are centered 10 bases + 35 bases upstream from where transcription begins -eukaryotic promoters vary more than bacterial promoters -in eukaryotes, transcription begins when general transcription factors bind to promoter, then RNA polymerase binds at promoter -in bacteria/eukaryotes, RNA elongated in 5′→3′ -transcription in bacteria ends when hairpin structure forms in transcribed RNA; in eukaryotes, transcription ends after RNA cleaved downstream of poly(A) signal

10.1 Summarize the process of photosynthesis

-light-capturing reactions of photosynthesis occur in internal membranes of chloroplast that organize into thylakoids that stack to form grana -Calvin cycle takes place in stroma (fluid in chloroplast) -CO2-reduction reactions of photosynthesis depend on products of light-capturing reactions: ATP and NADPH

20.4 Compare and contrast bacterial and eukaryotic genomes

-linear relationship between prokaryotic gene number and genome size exists; similar relationship between complexity of metabolism + size of genome -large amount of genetic diversity in prokaryotic genomes, even among different strains of same species -lateral gene transfer common in prokaryotes/is an important source of new genes in many species -metagenomics allows analysis of all genes in community of prokaryotes and provides information on diversity/abundance of species -no correlation between morphological complexity and gene number in eukaryotes -because of alternative splicing, number of distinct transcripts produced in eukaryotes is larger than gene number -gene duplication is important source of new genes in eukaryotes -most of eukaryotic genome is transcribed, but function of most noncoding transcripts is unknown

6.1 Analyze the relationship between molecular structure and the properties of lipids

-lipids are hydrophobic compounds (high number of nonpolar C—H bonds) -3 types of lipids are fats (store chemical energy), steroids (components of cell membrane), and phospholipids (also components) -length and degree of saturation affect physical properties of hydrocarbon chains -amphipathic lipids exist -phospholipids have polar/charged head and nonpolar tail (fatty acids or isoprenoids)

13.1 Describe the transmission of chromosomes during meiosis

-meiosis is nuclear division resulting in cells that have one of each type of chromosome + half as many chromosomes as parent cell (in animals, meiosis leads to formation of eggs/sperm) -diploid organisms have 2 versions of each type of chromosome called homologs (one inherited from mother/one from father); haploid organisms have 1 version of each type of chromosome -chromosomes replicate during S phase (before meiosis) -at start of meiosis I, each chromosome consists of pair of sister chromatids (each with DNA molecule identical to other sister chromatid) -early in meiosis 1, homologous pairs of replicated chromosomes synapse, forming bivalent; non-sister chromatids undergo crossing over -during meiosis I, pair of homologous chromosomes connected by chiasma moves to metaphase plate -at end of meiosis I, homologous pairs of replicated chromosomes separate + distribute to 2 haploid cells (each contains one of each type of replicated chromosome) -during meiosis II, sister chromatids of replicated chromosomes separate + distribute to 2 cells -from one diploid cell with replicated chromosomes, meiosis produces 4 haploid daughter cells with unreplicated chromosomes

13.3 Explain how problems in separating chromosomes during meiosis can lead to problems in human health

-mistakes during meiosis result in egg/sperm cells that contain wrong number of chromosomes; human embryos formed from these gametes do not complete development (ex: down syndrome) -most mistakes in meiosis are failures of homologous chromosomes or sister chromatids to separate

7.5 Analyze the process of transporting molecules into and through the endomembrane system

-molecules synthesized in the ER are transported as cargo to Golgi apparatus, then to other organelles/ outside the cell -Before products leave the Golgi apparatus, they are sorted by "zip codes" that package them into certain vesicles, while other membrane/cytosolic proteins deliver vesicles to their target locations -lysosomes consist of enzymes/membranes that are made through the endomembrane system (lysosomes involved in recycling products via receptor-mediated endocytosis, phagocytosis, and autophagy)

5.1 Describe the structural variations that exist among monosaccharides

-monosaccharides are organic compounds that have a carbonyl group and several hydroxyl groups -the number of C-H groups may vary between sugars -monosaccharides have either an aldose (carbonyl group at end) or ketose (carbonyl group within carbon chain) -the spatial arrangement of monosaccharide functional groups lead to differences in structures/functions -in solution, monosaccharides can form ring structures that may differ in the orientation of a hydroxyl group

5.2 Analyze the relationship between the structure and function of polysaccharides

-monosaccharides can be covalently bonded through glycosidic linkages (join hydroxyl group) -polysaccharides do not always form a backbone structure due to numerous hydroxyls found in each monosaccharide that allow glycosidic linkages to form at different sites and new strands to branch from existing chains -types of monomers/geometries of the glycosidic linkages between monomers distinguish polysaccharides -most common polysaccharides are starch, glycogen, cellulose, and chitin (peptidoglycan is abundant as well)

8.4 Explain how enzyme structure affects the rate of a chemical reaction

-most enzymes are proteins and their activity is influenced by environmental factors (temperature, pH, modifications that alter 3D structure) -enzyme activity regulated by molecules competing with substrates to occupy active site or whose binding alters the enzyme shape -protein cleavage/phosphorylation regulate enzyme activity by modifying the primary structure of enzyme

18.2 Explain how negative and positive control of transcription controls the expression of the lac operon

-mutants that failed to cleave/transport lactose into cell, or regulate transcription of lac operon genes were basis for understanding how lac operon worked -transcription is constitutive or regulated; constitutive expression occurs in genes whose products are always required (ex: genes that encode glycolytic enzymes) -lac operon transcribed efficiently when lactose is present/glucose is absent -lac operon is under negative/positive control -in negative control, repressor protein binds to operator sequence in DNA near lac operon promoter to prevent transcription of lac operon genes -when lactose is present, binds to repressor/causes it to release from operator, allowing transcription to occur -glucose inhibits transcription of lac operon by preventing activator protein from binding near promoter/inhibiting lactose transport into cell -positive control of transcription occurs when activator binds to regulatory sequence in DNA -activator proteins bind to RNA polymerase/DNA; binding between activator + RNA polymerase increases rate of transcription initiation -trp operon codes for genes required in synthesis of tryptophan; operon under negative control by repressor that binds to operator; unlike lac repressor, trp repressor binds to operator only when it binds to tryptophan, which acts as co-repressor -trp operon exhibits negative feedback control (form of regulation where end product of pathway inhibits activity of pathway)

16.4 Explain the ways mutations can change genetic information

-mutations are random, permanent changes in DNA that range from alterations in single base pair to changes in structure/number of chromosomes -point mutations in protein-coding regions can have no effect on protein (silent mutation)/change single amino acid (missense mutation)/shorten protein (nonsense mutation)/shift reading frame + alter many amino acids (frameshift mutation) -mutations can occur anywhere in genome, including regions that do not code for proteins -mutations can have beneficial/neutral/harmful effects on fitness of organisms

4.1 Analyze the characteristics of nucleotides and the bonds that link them together in nucleic acids

-nucleic acids are polymers of nucleotide monomers, which consist of a sugar, a phosphate group, and a nitrogenous base -ribonucleotide monomers polymerize to form RNA; deoxyribonucleotide monomers polymerize to form DNA -ribonucleotides have a hydroxyl (—OH)(—OH) group on their 2′ carbon; deoxyribonucleotides have a hydrogen (—H)(—H) -nucleic acids polymerize when condensation reactions join nucleotides together via phosphodiester linkages -nucleic acids are directional: they have a 5′ end and a 3′ end (during polymerization, new nucleotides are added only to the 3′ end)

12.3 Explain how cells monitor and regulate the progression of the cell cycle

-onset of S/M phase determined by activity of protein complexes consisting of cyclin/Cdk -cyclin concentrations oscillate during cell cycle, regulating formation of complexes; activity of Cdk regulated by addition of phosphate in activating site and removal of one from inhibitory site -G1 checkpoint regulates progress based on nutrient availability, cell size, DNA damage, and social signals -G2 checkpoint delays progress until chromosome replication is complete and any damaged DNA present is repaired -2 M-phase checkpoints (1) delay anaphase until all chromosomes correctly attach to spindle apparatus and (2) delay onset of cytokinesis and G1 until all chromosomes have been partitioned

6.4 Analyze the different roles of membrane proteins in regulating the transport of solutes

-permeability of lipid bilayers can be altered by membrane proteins -channel proteins form pores in the membrane that close/open and facilitate diffusion of solutes in and out -carrier proteins undergo adaptation that facilitates diffusion in and out -pumps use energy to move ions/molecules against the electrical/chemical gradient -together, selective permeability of phospholipid bilayers and transport proteins create an environment inside a cell that is different from the exterior

6.2 Analyze the relationship between the structure and function of phospholipid bilayers

-phospholipids spontaneously assemble into bilayers (barrier between internal and external environment) -small nonpolar molecules move across lipid bilayers readily; ions cross rarely -permeability and fluidity of lipid bilayers depend on temperature, concentration of cholesterol, and chemical structure of lipids present (saturation and length of hydrocarbon chains) -phospholipids with saturated tails form dense/highly hydrophobic interior that lowers bilayer permeability

10.3 Explain how photosystems use light energy to produce chemical energy

-photosystem II: excited electrons transferred to PQ at start of electron transport chain; redox reactions in the ETC used to generate proton-motive force that drives synthesis of ATP; electrons taken from photosystem II replaced by splitting water, releasing oxygen/protons -photosystem I: excited electrons passed to ferredoxin; in enzyme-catalyzed reaction, reduced form of ferredoxin passes electrons to NADP+, forming NADPH -Z scheme connects photosystems II and I; electrons excited by light in photosystem II passed through ETC, picked up by PC, transferred to oxidized pigments in photosystem I reaction center; these electrons are excited by light in photosystem I and used to reduce NADP+ to NADPH -electrons from photosystem I may be passed back to PQ instead of NADP+; cyclic flow of electrons between photosystem I and the ETC boosts ATP supplies

10.2 Analyze how pigment structure and organization allow cells to acquire energy from light

-pigment molecules capture light energy by exciting electrons when photon is absorbed (pigments absorb photons of particular wavelengths); excitation energy is released as fluorescence/heat, heat alone, resonance energy that excites another pigment, or is transferred as excited electron to reduce electron acceptor -antenna pigments in thylakoid membrane transfer absorbed light energy via resonance to reaction center, where excited electron transfers to electron acceptor

20.2 Explain how PCR can create many copies of a DNA sequence

-polymerase chain reaction (PCR) produces many identical copies of gene by repeated rounds of DNA synthesis without using cells for cloning -PCR has many applications, such as DNA fingerprinting

4.2 Analyze the different levels of DNA structure and how they are related to DNA function

-primary structure consists of a sequence of linked deoxyribonucleotides -secondary structure consists of two DNA strands in opposite directions that are twisted into a double helix -secondary structure is stabilized by hydrogen bonds and base-stacking interactions between bases -tertiary structure forms structures by twisting double helix into supercoils/wrapping around histone proteins -DNA is extremely stable and serves as a great archive for information in the form of base sequences -DNA is readily copied via complementary base pairing (A-T and G-C bases)

4.3 Analyze the different levels of RNA structure and how they are related to RNA function

-primary structure consists of a sequence of linked ribonucleotides -complementary base pairing is A-U and C-G -secondary structure includes a variety of structures (double-helical stems and unpaired loops) -secondary structures folds into more complex shapes via complementary base pairing (tertiary structure) -RNA can function as an information-carrying molecule and a catalyst

12.2 Describe how the nuclear and cytoplasmic components of a cell are divided during M phase

-prophase: chromosomes condense, spindle apparatus begins to form, polar microtubules overlap -prometaphase: nuclear envelope disintegrates, microtubules attach to kinetochores of chromosomes, which begin moving to middle of spindle -metaphase: all chromosomes positioned in middle of spindle, spindle anchored to membrane by astral microtubules -anaphase: sister chromatids pulled apart by disassembly of kinetochore microtubules at kinetochore, chromatids are daughter chromosomes, spindle poles moved farther apart to separate replicated chromosomes -telophase: daughter chromosomes separated and clustered at opposite poles of spindle, envelope forms around each set, chromosomes decondense -mitosis followed by cytokinesis (division of the cytoplasm to form two daughter cells)

3.3 Explain the relationship between protein folding and function

-protein folding is spontaneous -a protein's folded shape is essential to its function -many proteins must first bind to other molecules before they can adopt their active arrangement -improperly folded proteins can cause infectious diseases that can be detrimental to life

3.4 Describe the different functions of proteins in living systems

-proteins function in catalysis, defense, movement, signaling, structural support, and transport of materials -proteins can have diverse functions in cells because they have such diverse structures and chemical properties -catalysis takes place at the enzyme's active site, which is specific to its substrates

9.3 Describe the process cells use to turn pyruvate into acetyl CoA

-pyruvate processing converts pyruvate to acetyl CoA in mitochondrial matrix (eukaryotes)/cytosol (prokaryotes); NADH/CO2 are produced -pyruvate dehydrogenase complex is inhibited when phosphorylated by ATP; speeds up in presence of reactants/slows down in presence of products

8.2 Describe the factors that determine the spontaneity and rate of a chemical reaction

-redox reactions transfer energy by coupling exergonic oxidation reactions to endergonic reduction reactions -bonds with high PE can form during reduction step of redox reaction (many form when electron is transferred along with proton H+) -PE in ATP drives a variety of cellular processes -when phosphate group from ATP is added to substrate, PE of substrate increases and can convert endergonic reactions into exergonic reactions

4.4 Evaluate the hypothesis that life began as an RNA molecule

-researchers have attempted to synthesize new ribozymes in the lab and have succeeded in identifying RNAs that catalyze several different reactions -one theory states that ribozymes that catalyzed reactions necessary for the production of ribonucleotides may have preceded the evolution of RNA replicases

19.6 Compare and contrast how gene expression is controlled in bacteria and eukaryotes

-review Table: Regulating Gene Expression in Bacteria and Eukaryotes

17.5 Explain the events of translation initiation, elongation, and termination

-ribosomes are large macromolecular machines made of many proteins/RNAs -in ribosomes, anticodon of tRNA binds to 3-base-long codon in mRNA to hold correct amino acid in ribosome -ribosome is a ribozyme that catalyzes peptide-bond formation using RNA, not protein-based enzyme -protein synthesis steps: (1) incoming aminoacyl tRNA occupies A site; (2) growing polypeptide chain transferred from tRNA in ribosome's P site to amino acid bound to tRNA in A site, forming peptide bond; (3) ribosome moves to next codon on mRNA, along with ejection of uncharged RNA from E site -chaperone proteins fold newly synthesized proteins -polypeptides need to be chemically modified after translation to activate/target them to specific locations

17.3 Describe the roles of ribosomes, mRNA, and tRNAs in translation

-ribosomes translate mRNAs into proteins with adapter molecules (tRNAs) that act as chemical bridge between codons in mRNA and amino acids added to synthesized polypeptide. -in bacteria, RNA is transcribed/translated at same time -in eukaryotes, transcription occurs in nucleus and translation occurs in cytoplasm

8.1 Explain how energy is transformed in a chemical reaction

-standard free-energy change for a reaction measures change in ∆G (calculate combined effects of changes in enthalpy and entropy) -reactions with -ΔG are exergonic/occur spontaneously -reactions with +∆G are endergonic/ do not occur without input of energy

10.4 Compare the different pathways used for carbon fixation and explain why they are necessary

-stomata regulate exchange of CO2 and O2 between leaf tissue of a plant and its environment -rubisco catalyzes fixation of CO2 to RuBP as first step in the Calvin cycle; NADPH splits to form two molecules of 3PGA -rubisco catalyzes addition of oxygen + carbon dioxide to RuBP; reaction with oxygen leads to loss of fixed CO2 + ATP through photorespiration -in C4 plants/CAM plants, CO2 is fixed to four-carbon compounds, then released to be used by rubisco, which increases CO2 levels in plant tissues and reduces effect of photorespiration when stomata are closed

1.2 Explain what organisms are made of and how cells come to be

-the cell theory identified the fundamental structural unit common to all life -most cells are capable of reproducing by dividing

1.3 Explain how organisms process hereditary information and acquire and use energy

-the chromosome theory of inheritance states that genes are located on chromosomes -a chromosome consists of a molecule of DNA—the hereditary material -genes, located on chromosomes, consist of specific segments of DNA that code for products in the cell -the flow of information from DNA to RNA to protein is called the central dogma -organisms are highly diverse in how they acquire and use energy

2.3 Explain the changes in bonds, energy, and entropy that occur in a chemical reaction

-the first step in chemical evolution is the formation of small organic compounds from molecules such as molecular hydrogen (H2) and carbon dioxide (CO2) -chemical reactions involve bonds being broken, atoms being rearranged, and new bonds being formed; this process involves energy from either the potential energy within bonds of the reactants or kinetic energy of external sources (thermal energy) -energy comes in different forms (energy cannot be created or destroyed, but one form of energy can be transformed into another)

1.5 Describe the significance of the tree of life

-the theory of evolution predicts that all organisms are part of a genealogy of species, and that all species trace their ancestry back to a single common ancestor -to construct this phylogeny, biologists have analyzed the sequences in an array of genetic material found in all cells -a tree of life has three fundamental lineages, or domains: the Bacteria, the Archaea, and the Eukarya

1.4 Explain the relationships between species and how evolution occurs

-the theory of evolution states that all organisms are related by common ancestry -natural selection is a well-tested explanation for why species change through time and why they are so well adapted to their habitats

1.1 Explain what it means to say that an organism is alive

-there is no single, well-accepted definition of life -biologists point to five characteristics that organisms share -three of the greatest unifying ideas in biology are the cell theory, the chromosome theory of inheritance, and the theory of evolution

15.4 Analyze the replication of chromosome ends

-to prevent shortening at ends of linear chromosomes in eukaryotes, enzyme telomerase adds short, repeated sequences of single-stranded DNA made double-stranded by enzymes used for DNA replication -telomerase is active in reproductive cells that undergo meiosis and, therefore, the length of chromosomes in gametes is maintained -chromosomes in cells without telomerase shorten with continued cell division until telomeres reach critical length where cell division no longer occurs

7.4 Analyze the process of transporting molecules across the nuclear envelope

-traffic across nuclear envelope occurs through nuclear pore complexes that serve as gatekeepers -small molecules passively diffuse through nuclear pore complexes/larger molecules require nuclear localization signal to direct them through the complex via nuclear transport proteins

11.4 Analyze the role of intercellular signaling between unicellular organisms

-unicellular organisms use chemical signals to sense aspects of their environment, such as population density -quorum sensing allows populations of cells to coordinate changes in activities when population density is high

2.1 Analyze the relationship between atomic structure and how atoms interact in simple molecules

-when atoms participate in chemical bonds, the shared or transferred electrons often give the atoms full valence shells and thus contribute to the atoms' stability -electrons in a covalent bond may be shared equally or unequally, depending on the relative electronegativities of the two atoms involved -nonpolar covalent bonds result from equal sharing; polar covalent bonds are due to unequal sharing; ionic bonds form when an electron is completely transferred from one atom to another