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Animal Diversity Week Six Notes (TEST)

by: Alivia Hunt

Animal Diversity Week Six Notes (TEST) BIOS 1000

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Summary of Notes Main Points for Notes (TEST UPLOAD)
Animal Diversity
Patrick Hassett
Class Notes
animals, diversity, test
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This 29 page Class Notes was uploaded by Alivia Hunt on Wednesday September 28, 2016. The Class Notes belongs to BIOS 1000 at Ohio University taught by Patrick Hassett in Fall 2016. Since its upload, it has received 3 views.


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Date Created: 09/28/16
Unit 1 Notes Tuesday, September 6, 2016 3:53 PM Chapter 1: Chemical, Cellular, and Evolutionary Foundation  Scientific method: Observations-->Hypothesis-->Predictions-->Experiments or new observations (must be objective and repeatable)-->Theory  Hypothesis: 1. Makes predictions about experiments not yet run 2. Are testable in an objective manner  1 observation can lead to reject/support hypothesis, not prove  Test group has variable, control group doesn't 1.3: The Cell Cell: simplest self-replicating entity that exists as independent unit of life   Essential cell features: 1 Store and transmit info, reproduce by copying DNA  DNA-->RNA-->Protein = central dogma (flow of info in cell)  The gene is a DNA sequence that corresponds to a specific protein product  DNA double-helical structure and complementary pairing secure the accuracy of replication and transmission of genetic info 1 Plasma membrane separates living materials in cell from nonliving materials outside the cell 2 Get energy from environment, metabolism converts energy into other form (ATP)  Example: Sun-->plants-->cows (beef)-->humans  Viruses can't harness energy from environment, need cell to reproduce  Redi's experiment: tested if living organisms can arise from nonliving matter o Maggots appeared in the open jar o No maggots in gauze-covered jar o No maggots in closed jar o Conclusion: Supported hypothesis that maggots come from flies and allowed Redi to reject hypothesis that maggots are spontaneously generated  Pasteur's experiment: Can microscopic life arise from nonliving matter? o Put broth in a straight-necked and swan-necked flask o Boiling killed the microbes and sterilized the broth o Dust particles w/microbes entered straight-necked flask, and not the swan-neck flask o Swan-neck flask remained clean and sterile o Conclusion: Supported hypothesis that microbes come from other microbes and aren't spontaneously generated  2 cell types are prokaryotic and eukaryotic o Common to both: enclosed by plasma membrane o Eukaryotic cells: nucleus, organelles in cytoplasm o Prokaryotic cells are always single-celled organisms, eukaryotic can be either Chapter 2: The Molecules of Life 2.4: Carbon: Life's Chemical Backbone  Carbon-containing molecules are organic  Carbon atoms form 4 covalent bonds  Carbon atoms can link w/each other to form long chains, or share 2 pairs of electrons to forma double bond  Molecules with the same chemical formula and different structures are isomers o Ex: Isoleucine and leucine  Silicon is also abundant and has 4 atomic orbitals with one electron each (like carbon), but is bound to oxygen and not as diverse as carbon 2.5: Organic Molecules  Polymers: complex molecules made of repeated simpler units connected by covalent bonds o Ex: proteins (amino acids), nucleic acids (nucleotides), carbs sugars), lipids (made of fatty acids)  Functional groups: 1 or more atoms w/particular chemical properties no matter what is attached to them o Many functional groups are more electronegative than carbon, making functional groups polar and reactive Proteins are made of amino acids  Some are catalysts or enzymes  Structure: Alpha carbon, covalent bond with amino group, hydrogen atom, carboxyl group, and R group (side chain) o Identity of the protein determined by side chain structure o Amino group gains a proton, while the carboxyl group loses a proton and the N and C form a peptide bond, while H2O is given off Nucleic acids encode genetic info in their nucleotide sequence  5-carbon sugar, phosphate group, and nitrogen-containing base-- >nucleotides-->DNA and RNA  Pyrimidine bases: Single ring, include C, U, T  Purine bases: Double-ring, include G and A  Double-helix nucleotides are complimentary and base pair through H-bonds Complex carbs are made of simple sugars  Carbs are made of C, H, and O  Simple carbs (saccharides) that are 6-carbon have same C6H12O6 formula  6-carbon sugars can have linear and cyclic configurations o Saccharides/monosaccharides combine to form polysaccharides or complex carbs  Monosaccharides are carbon chain with aldehyde or ketone group  Monosaccharides attach w/glyosidic covalent bond, giving off H2O  Polymer of glucose in plants: starch  Polymer of glucose in humans: glycogen o Glycogen is not a pure substance of glucose Lipids are hydrophobic 3 main types: 1 Triacylglycerol: used for energy storage, fat that comes from diet  Structure: 3 fatty acids joined to glycerol o Fatty acid made of hydrocarbon chain and carboxyl group o OH group in glycerol and OH groups in fatty acids make covalent bond, giving off 3 H2Os  With double bonds is unsaturated, without double bonds is saturated  No electron distribution, so triacylglycerols are uncharged and hydrophobic  Temporarily polarized by weak attraction to close atoms (van der Waals force, which stabilizes molecules)  Longer hydrocarbon means more interactions and more energy to break bonds (higher melting temperature)  Kinks reduce tightness of molecular packing, so unsaturated fatty acids have a lower melting point  Animal fat (high melting temperature, triacylglycerol w/saturated fatty acids) vs. plant fat (low melting temperature, triacylglycerol with unsaturated fatty acids) 1 Steroids: Cholesterol, hydrophobic, form animal cell membranes, precursor for synthesis of steroid hormones 2 Phospholipids: Component of cell membranes Chapter 2 Lecture Notes  Atom: basic unit of matter  Elements: smallest pure substances in chemistry = atoms o Building unit of molecules  Chemical bonds: covalent, ionic  Shell: energy level of orbital  Atoms in same colun share similar chemical properties  Bond w/shared electrons makes atoms stable by filling the shell with electrons o Covalent bond is the strongest bond, can be polar or nonpolar  Ionic bond: extreme case of polar covalent bonds, not quite sharing electrons  Bonds w/o shared electrons: bonds via charges (positive and negative) are between molecules o Ex: H-bond and van der Waals forces  Number of missing electrons in Shell 2 is the number of electrons to be shared with other atoms o Ex: Oxygen can make 3 bonds (missing 3 valence electrons) o Ex: Hydrogen can only make 1 Polar Covalent Bond and Electronegativity  Atoms on right side of periodic table have more power to pull in electrons  What happens when 2 atoms on opposite sides of periodic table forms covalent bond? o Ex: H2O is polar (bonds linking H and O are polar)  H-bonds among polar molecules: positive attracts negative charge o Other ex: bonds b/t nitrogenous bases of DNA and RNA  Ionic bonds: extreme cases of polar covalent bonds  Atom on left of periodic table has less pulling power, element on far right has more pulling power o Right atom steals electron from left atom to become stable (Cl-) and make positively charged ion (Na+)  Molecules with ionic bonds dissolve early in H2O  Molecules are often classified based on whether they mix well w/H2O o Hydrophilic = water-loving, rich in non-polar covalent bonds o Hydrophobic = water-fearing  Aqueous: watery environment Water (liquid) vs Ice  Molecules become more stable w/less movement when temperatures drop o H-bonds formed when temperatures drop b/c less movement and interaction o H2O makes 4 bonds w/low temperature, forms ionic lattice with more space pH  How many protons in water-->pH = -log[H+]  Physiological pH = 7.4 (bio processes function correctly at this pH)  Enzymes have an optimal pH  Some cellular compartments have different pH to regulate enzyme activity 2.5: Organic Molecules  Molecules w/carbon atoms (except CO2)  3 key characteristics of carbon: 1 Can form 4 covalent bonds 2 Tetrahedron shape 3 Free rotation of each single bond  Carbon can make covalent bonds w/each other o Chains, branches, rings  Carbon atoms can make double bonds (do not rotate, make molecules bend) Chapter 3: Nucleic Acids and Transcription  Structure determines function o Ex: DNA is a double helix, stores genetic info in the form of genes  Turning on a gene = gene expression, controlling whether gene expression occurs = gene regulation o DNA transmits genetic info to next generation 3.1: Major Biological Functions of DNA  Biologists b/f 1950 showed support for proteins being life's info molecule DNA can transfer biological characteristics from one organism to another  Griffith worked w/strep, concluded that molecule in debris carried genetic info for virulence (nonvirulent bacteria become virulent through transformation and acquiring new genetic info) o Virulent strain-->pneumonia and death in mice o Nonvirulent strain-->mice lived o Dead virulent strain-->mice lived o Dead virulent strain mixed w/live nonvirulent strain-->mouse dies  Avery, MacLeod, and McCarty: molecule responsible for transformation of nonvirulent cells into virulent cells is DNA 1 Kill virulent cells w/heat, purify remains-->remains carry out transformation 2 Preparation w/enzymes that destroy RNA and protein-->transforming remains 3 Preparation w/enzyme that destroys DNA-->transforming lost DNA molecules are copied in the process of replication  Replication: copying DNA, allows DNA to pass genetic info from cell to cell  Mutation: Unrepaired error in DNA replication Genetic info flows from DNA to RNA to protein  Flow of info from DNA-->RNA-->Protein = central dogma o Exceptions: o RNA-->DNA in HIV o RNA-->RNA in influenza o Protein-->protein in prions  Transcription: DNA used to generate RNA  Translation: RNA used as a code for amino acids  Transcription and translation are regulated (don't occur 24/7 in cells) o Ex: Muscle cells express genes that encode for proteins involved in muscle contraction, these genes not expressed in skin cells  Transcription and translation in cytoplasm in prokaryotes, but transcription is in nucleus and translation in cytoplasm in eukaryotes (allows for additional levels of gene regulation) 3.2: Chemical Composition and Structure of DNA  Watson and Crick described 3D structure of DNA DNA strand consists of subunits called nucleotides  Nucleotide consists of 5-carbon sugar, base, and one or more phosphate groups o 5-carbon sugar and phosphate are backbone, bases give chemical identity  Phosphate group has negative charge, making DNA mild acid  Bases: A and G (purines), C and T (pyrimidines)  Nucleoside: sugar and base (if a phosphate group is added, becomes a nucleotide) o Nucleoside triphosphate used to form DNA and RNA, carries ATP and GTP (energy) DNA is a linear polymer of nucleotides linked by phosphodiester bonds  Phosphodiester bond connects 3' carbon of one nucleotide (w/3' hydroxyl) to 5' carbon of the next (w/5' phosphate) o This gives DNA polarity Cellular DNA molecules take the form of a double helix  Sugar-phosphate backbone winds around outside, bases point inward  Outside strands form major and minor grooves that let proteins interact w/DNA  DNA strands are antiparallel: run in opposite directions (3' one strand opposite 5' of the other) o Ex: 5'ATGC3'//3'TACG5'  2 purines would cause backbone bulge, 2 pyrimidines would cause it to narrow  A and T, G and C complimentary, happens sue to H-bonds o H-bonds contribute to DNA stability  Bases are nonpolar, group away from water molecules to cause base stacking The 3D structure of DNA gave important clues about its functions  No limits to base sequence suggests genetic info in DNA could be encoded in sequence of bases along the DNA  C and G held together by 3 h-bonds, A and T held together by 2  Complimentary base sequences means %A=%T and %C=%G  For DNA replication and transcription to occur, DNA must be loosened  DNA structure also allows double helix to unwind, strands are templates for complimentary daughter strand o Complimentary pairing secures accurate transfer of info from DNA to RNA Cellular DNA is coiled and packaged w/proteins  DNA forms supercoils(circular molecule of DNA coils upon itself o Supercoiling caused by enzyme topoisomerases that cleave, partially unwind, ad reattach DNA strand  Chromosome: each individual molecule of DNA  Eukaryotic DNA packaged w/histone proteins to form combo of DNA and proteins called chromatin  Histones interact w/DNA w/o regard for sequence, b/c they are evolutionarily conserved (similar in sequence for each organism, not changed much over time) 3.3: Retrieval of Genetic Info Stored in DNA: Transcription  Proteins synthesized on ribosomes  DNA in nucleus and ribosomes in cytoplasm in eukaryotes, so there must be molecule that carries DNA to ribosomes  Brenner, Jacob, and Meselson used virus T2 which infects Escherichia coli, to see that infected cells produce RNA after infection-->RNA retrieves genetic info stored in DNA What was 1st nucleic acid molecule, and how did it arise?  RNA world hypothesis: RNA stores info in nucleotides and acts as enzymes, so some think it was original info-storing molecule  Szostak experiment: 1 RNA replicated 2 RNA exposed to chemical that induced nucleotide changes 3 RNA that catalyzed a reaction were isolated 4 Best-functioning RNA picked, mutated again o Result: each generation catalyzed more efficiently, showing that RNA can evolve and act as catalysts RNA is a polymer of nucleotides in which 5-carbon sugar is ribose  Chemical differences from DNA: 1 Sugar is ribose, w/hydroxyl group on 2' carbon (hydroxyl is reactive, makes RNA less stable than DNA) 2 Base Uracil used, not Thymine 3 5' end is a triphosphate, not monophosphate  Physical differences: 1 RNA is shorter 2 RNA single-stranded, folds into 3D structures to enhance stability In transcription, DNA is used as template to make complementary RNA  RNA transcript is made w/help of enzyme RNA polymerase o Nucleotides added to template 3' end  DNA nontemplate strand not transcribed Transcription starts at promoter, ends at terminator  Promoters: Few hundred bases where RNA polymerase and proteins bind to DNA duplex  1st nucleotide transcribed is 25 base pairs from TATA box  Transcription stops at terminator  For one gene, one DNA strand is transcribed, but different genes in same double-stranded DNA molecule can be transcribed from opposite strands  Transcription is constant in housekeeping genes, but most genes are transcribed at certain times o Ex: E. Coli genes that encode proteins needed to utilize lactose only transcribed w/lactose presence  In bacteria, promoter recognition is mediated by sigma factor protein, which binds to TATA box in promoter to begin transcription  In eukaryotes: 1 6 proteins (general transcription factors) assemble at promoter 2 1-2 transcriptional activator proteins bind to DNA enhancer sequence o Transcriptional activator proteins control when and in which cell gene transcription occurs 3 Mediator complex of proteins recruits RNA polymerase complex (called Pol II in eukaryotes) to promoter 4 Transcriptional initiation begins (factors brought close to allow transcription to proceed) RNA polymerase adds successive nucleotides to 3' end of transcript  Elongation: ribonucleotides added to growing transcript  Polymerization reaction: 1 Ribonucleoside accepted if correctly base paired w/DNA template 2 RNA polymerase's O in OH group at 3' end of strand gets in position to attack phosphate in triphosphate of the ribonucleoside, competing for covalent bond 3 Phosphate-phosphate (pyrophosphate) group released 4 Phosphate-Phosphate bond cleaved by enzyme, making reaction irreversible 3.4: Fate of the RNA Primary Transcript  Primary transcript: RNA transcript that comes off the template DNA strand  mRNA: RNA molecule that combines w/ribosome to direct protein synthesis mRNA carries info for the synthesis of a specific protein In prokaryotes, primary transcript is mRNA   Prokaryotes have no nuclear envelope, so transcription and translation are coupled (both happen in cytoplasm)  Prokaryote primary transcripts have genetic info for 2 or more different proteins  Polycistronic mRNA: molecules of mRNA that code for multiple proteins Primary transcripts in eukaryotes undergo several types of chemical modification  RNA processing: converts primary transcript into finished mRNA (occurs in nucleus)  RNA processing: 1 5' end of primary transcript modified by addition of special nucleotides (5' cap w/nucleotide 7-methylguanosine) o Cap is linked to RNA transcript by bridge b/t 5' carbons of both ribose sugars o Ribosome recognizes mRNA by 5' cap 2 Splicing: o Spliceosome brings specific sequence w/in intron in proximity w/intron 5' end o RNA cut at 5' splice site o Cleaved end of intron connects to form loop called lariat o Spliceosome brings 5' splice site close to splice site at 3' end of intron o Lariat is released, exons connected  Exons are protein-coding sequence, introns are noncoding regions (removed by RNA splicing catalyzed by spliceosome protein)  Presence of many introns allows for alternative splicing (primary transcripts from same gene spliced in different ways to get different mRNAs and proteins by skipping exons) 1 Polyadenylation: addition of string of 250 A-bearing nucleotides to 3' end, making Poly(A) tail  5' cap and tail provide stabilization Some RNA transcripts are processed differently from protein-coding transcripts and have functions of their own  rRNA: genes and transcripts concentrated in nucleolus (dense, non- membrane bound, in nucleus)  tRNA: carries individual amino acids for use in translation  Small nuclear RNA: involved in splicing, polyadenylation, and other processes  Regulatory RNA inhibits translation (microRNA and small interfering RNA)  80% RNA is rRNA, 10% is tRNA b/c they are needed to synthesize proteins encoded in mRNA Chapter 4: Translation and Protein Structure  Some proteins are filaments that define cell shape and hold organelles in place, others form channels for ions and small molecules to pass through, others are catalyzing enzymes, and some are signaling proteins 4.1: Molecular Structure of Proteins  Amino acids differ in their side chains Amino acids differ in their side chains  Amino acid is alpha carbon group, R group, carboxyl group, amino group, and H o 4 covalent bonds from alpha carbon at angles form tetrahedron  3 types of amino acids: 1 Hydrophobic: nonpolar R groups, hydrophobic R groups aggregate w/each other, stabilized by weak van der Waals forces o Amino acids buries in interior of folded proteins 2 Hydrophilic: permanent charge separation (acidic and basic amino acids have polar R groups) o R groups located outside folded molecule, make ionic bonds w/each other and other molecules 3 Special types o Glycine: R group is H2 so it's not asymmetric, is nonpolar and small enough to be tucked into spaces, freer rotation around C-N bond increases backbone flexibility o Proline: R group linked back to amino group, restricts C-N bond rotation o Cysteine: When 2 cysteines join side chain, covalent S-S disulfide bond forms  Stronger than ionic interactions, forms cross-bridges that can connect different or same protein  Ex: insulin Successive amino acids connected by peptide bonds  Carboxyl group of one amino acid reacts w/amino group of another, H2O released  C-O group in peptide bond is carbonyl group, N-H group is amide group o Electrons more attracted to C-O group, peptide bond has some characteristics of double bond (shorter, not free to rotate)  Polymers of amino acids have amino end, carboxyl end, and polymer of amino acids is polypeptide (protein) o Amino acids incorporated into proteins are residues Sequence of amino acids dictates protein folding, which determines function  Primary structure: Sequence of amino acids in protein  Secondary structure: Interactions b/t stretches of amino acids in proteins  Tertiary structure: 3D shape of polypeptide  Quaternary structure: Polypeptides that interact w/each other o Protein function depends on 3D shape  Some proteins have pockets w/pos or neg charged side chains to trap molecules, some have surfaces that can bind protein or nucleotides in DNA or RNA, some form rods for structural support, some keep hydrophobic side chains away from water  Amino acids listed in order from amino (N terminus) to carboxyl end (C terminus Secondary structures result from h-bonding in polypeptide backbone  H-bonds form b/t carbonyl group of one peptide and amide group of another, allowing polypeptide to fold (secondary structure)  Pauling and Corey studied crystals of purified proteins, discovered alpha helix and beta sheet  Helix stabilized by H-bonds b/t carbonyl and amide groups o R groups project outward, determine where alpha helix is in protein and interaction w/other molecules  Beta sheet is pleated, stabilized by H-bonds b/t carbonyl group in one chain, amide group in the other o Depicted by broad arrow, direction runs from amino to carbonyl end o Polypeptide chains are antiparallel (more stable b/c groups better aligned for H-bonds) Tertiary structures result from interactions b/t amino acid side chains  Shape of protein determined by interactions b/t amino acid R groups  Tertiary structure determined by spatial distribution of hydrophobic and hydrophilic R groups, and chemical bonds b/t R groups  Ionic, H-bonds, van der Waals forces, and disulfide bonds also help make 3D structure  3D structure lets protein serve as structural support, membrane channel, enzyme, signaling molecule, etc.  Proteins can be denatured (unfolded) and lose functional activity Polypeptide subunits can come together to form quaternary structures  Proteins w/2 or more polypeptide chains w/tertiary structure make quaternary structure o Polypeptide subunits can be identical or different  Homodimer = same 2 proteins  Heterodimer = 2 different proteins  Subunits can influence each other in subtle ways o Ex: One of hemoglobin subunits binds to O, slight change in structure transmitted to other subunits, making it easier for them to take up O Chaperones help some proteins fold properly  Longer polypeptides are denatured, longer their hydrophobic groups are exposed to other macromolecules o Hydrophobic groups brought together, this may prevent proper folding  Chaperone proteins help protect denatured proteins until they get proper 3D structure o Bind to hydrophobic and nonpolar R groups to prevent improper aggregation o Keep proteins folded (reverse denaturing) o Stress in cell like heat can unfold proteins 4.2: Translation: How Proteins are Synthesized  Translation: mRNA used to specify order in which amino acids are added to polypeptide chain Translation uses many molecules found in all cells  Ribosomes: structures of RNA and protein that bind w/mRNA and are site of translation o Made of small and large subunit, large has 3 binding sites for tRNA (Aminoacyl, Peptidyl, and Exit) o Ribosome makes sure mRNA sequence read in successive, non- overlapping nucleotide groups  Codon: 3 nucleotides, codes for one amino acid Reading frames: different ways of parsing string into 3-letter words   Translation of codon into amino acid carried out by tRNA  3 bases in anticodon loop make up anticodon, these are 3 nucleotides that base pair w/codon  Each tRNA has CCA at 3' end, and 3' hydroxyl of A is attachment site for amino acid  Aminoacyl tRNA synthetases: enzymes that connect specific tRNA molecules to specific amino acids (one specific enzyme for each amino acid) o tRNA w/no amino acid is uncharged, tRNAs must be charged for translation o Enzyme attaches amino acid to 3' end of tRNA to make tRNA charged Genetic code shows correspondence b/t codons and amino acids  Genetic code: codons specify amino acid according to this  Translation begins at AUG (Met) (usually most 5' AUG sequence)  At each step, ribosome binds to tRNA w/anticodon that can base pair w/codon, and amino acid becomes new carboxyl end  Stop codons: UAA, UAG, UGA  Many amino acids separated by multiple codons, resulting mostly from 3rd codon position b/c: 1 Codon is chemically modified and can pair with 2 bases at third position 2 Not perfect alignment b/t 3rd position of codon and its base pair, so pairing requirements are relaxed ("wobble")  There are 64 combos of nucleotides, but only 20 different amino acids- different sequences used for same amino acid o Called redundancy  How did scientists assign all triplets to 20 common amino acids and 3 stop codons? 1 Input: Synthesized long chain of RNA 2 Reaction: In vitro (test tube) translation system 3 Output: Determination of polypeptide (protein) sequences  Same RNA sequence-->3 different peptide sequences-->3 different reading frames  Only one frame designates correct protein sequence  Which one is correct reading frame/how to find it? o AUG = translation initiation codon Translation consists of initiation, elongation, and termination In eukaryotes: 1 Initiation: AUG codon recognized 2 Elongation: Successive amino acids added 3 Termination: Polypeptide released from ribosome 1 Initiation factors: proteins that bind to mRNA (5' cap in eukaryotes) 2 Initiation complex moves on mRNA until AUG triplet, then ribosomal subunit joins and complex is released, tRNA complimentary to next codon binds to A site 3 A reaction transfers Met to amino acid on tRNA in A site, making peptide bond 4 Ribosome moves down codon, amino acid w/polypeptide put in P site, uncharged tRNA put in E site and ejected 5 Polypeptide transfers to amino acid on tRNA in A site 6 Steps 4-5 repeated  Elongation factors: proteins bound to GTP molecules, break their bonds to get energy for polypeptide elongation  Release factor: protein that binds to A site of ribosome, causing bond connecting polypeptide to tRNA to break, making carboxyl terminus when stop codon is reached o No tRNA anticodon complementary to stop codons o Dissociation of large and small ribosomal subunits In prokaryotes:  No 5' cap on mRNA, initiation complex formed at Shine-Dalgarno sequence  Small subunit of ribosome searches for Shine-Dalgarno sequence o 3' end of rRNA in small subunit is complimentary to Shine-Dalgarno sequence  Gene structure in prokaryotes: Ability to initiate translation internally allows prokaryotic mRNAs to code for more than one protein (polycistronic mRNA)  Gene structure in eukaryotes: One mRNA corresponds to one protein  Operon: Group of functionally related genes located in tandem along DNA and transcribed as a single unit from one promoter o Genes in operons have products needed for successive steps in making molecule How did genetic code originate?  Ribosome precursors were RNA molecules that facilitated replication of other RNAs  tRNA precursors shuttled nucleotides to RNA strands  Over time, amino acids brought close together in building RNA may have polymerized, making polypeptide chains 4.3: Protein Evolution and the Origin of New Proteins  Protein families: group of structurally and functionally related proteins as a result of shared evolutionary history o Not many, b/c limited chance random sequence of amino acids would fold into stable structure Most proteins are composed of modular folding domains  Early proteins shorter than modern proteins  Folding domain: region of protein that folds in similar way independent of rest of protein o Ex: Tim barrel and beta barrel  Only 2500 folding domains b/c different protein families have different combos of folding domains  New proteins sometimes evolve by joining folding domains into new combos Amino acid sequences evolve through mutation and selection  Mutation is change in sequence of gene-some affect amino acid sequence, change level of protein expression  Selection: Random mutations retained or eliminated based on ability to survive and reproduce  Mutant gene for improved protein increases in frequency, spreads through population o Ex: Evolution of resistance of malaria parasite to pyrimethamine drug Chapter 5: Organizing Principles  Cell theory: 1 All organisms made of cells 2 Cell is fundamental unit of life 3 Cells come from preexisting cells 5.1: Structure of Cell membrane  Cell membranes separate and enclose  Lipids are main component of membranes, proteins found w/in membrane, carbs attach to lipids and proteins in membrane Cell membranes: composed of 2 lipid layers  Phospholipids are made of glycerol backbone, phosphate group, 2 fatty acids o Phosphate head is hydrophilic, fatty acid tail is hydrophobic o Phospholipids are amphipathic  Amphipathic: molecules w/both hydrophobic and hydrophilic regions 3 structures: 1 Micelle: lipid w/bulky heads and single hydrophobic fatty acid tails packed into spheres 2 Bilayer: less bulky outer head group, 2 hydrophobic tails b/t head groups o Closed structure w/inner space means effective cell membrane and self-healing abilities o Forms spontaneously w/high phospholipid concentration and pH of 7.4 3 Liposomes: spherical bilayer structures that surround a central space o Liposomes can form, break, reform, and grow  Early membranes might have been leaky, evolved to allow molecular traffic  Now, proteins guide lipid synthesis w/in cell Cell membranes are dynamic  Membrane lipids are fluid: able to move in plane of membrane  What makes cell membranes fluid? o Long fatty acid tail = more van der Waals forces, tighter packing, less fluidity  Short tail = more fluidity b/c less van der Waals forces o Saturated fatty acids are straight w/no kinks and tightly packed w/little mobility, more van der Waals forces  Unsaturated: double bonds w/kinks in phospholipids reduce tightness of packing, less van der Waals forces, more fluidity  Cholesterol: amphipathic lipid that is 30% mass of cell membranes, affects fluidity of cell membrane o At cell temp, cholesterol lowers fluidity b/c ring interacts w/fatty acid tail to reduce mobility o At low temp, cholesterol increases fluidity b/c it prevents phospholipids from packing tightly o Hydroxyl group and hydrophobic 4 carbon w/attached hydrocarbon chain  Lipid rafts: specific types of lipids that assemble into defined patches  Transfer of lipid b/t bilayers is rare, b/c lipid would have to pass through hydrophobic interior Proteins associate w/cell membranes in different ways  Transporters: move ions/other molecules across membranes  Receptors: allow cell to receive signals from environment o Ex: Dr. T's dog sees treat, wags tail, receives treat, sends Dr. T message w/wagging tail  Enzymes: catalyze reactions  Anchors: Attach to other proteins to maintain cell structure 2 groups: 1 Integral membrane proteins: permanently associated w/cell membranes, cannot be separated o Most are transmembrane proteins: span entire bilayer length  2 hydrophilic regions, 1 hydrophobic region b/t  Allows for separate functions of each protein end 2 Peripheral membrane proteins: temporarily associated w/lipid bilayer or integral membrane proteins (w/weak noncovalent interactions) o Associated w/internal or external side of membrane o Transmit info from external signals or limit ability of transmembrane proteins to move  FRAP dyes proteins, then an area of membrane is bleached w/nonfluorescent spots o Fluorescence appears-->proteins move  Conclusion: membrane is fluid  Fluid mosaic model: lipid bilayer is fluid structure where molecules move laterally, and is mosaic of lipids and proteins 5.2: The Plasma Membrane and Cell Wall  Plasma membrane: phospholipids w/embedded proteins make up membrane around cells 1. Takes bilayer configuration of phospholipids 2. Separates internal contents from environment 3. Not a simple enclosure like water balloon rubber skin 4. Facilitates communication w/environment 5. Allows small molecules to flow in/out of cell  Internal cell operates w/in window of conditions (pH and salt concentration)  Cell wall: external to plasma membrane, maintains cell shape The plasma membrane maintains homeostasis  Homeostasis: active maintenance of constant environment o b/c plasma membrane is selectively permeable, lets some molecules in and out freely, others only in certain conditions, and prevents still others  Ions and charged particles cannot b/c hydrophobic bilayer interior  Macromolecules too large  Gases, lipids, small polar molecules can o Plasma membrane lets cell function Passive transport involves diffusion  Diffusion: random movement of molecules-->leads to net movement of substance from one region to another when there is concentration gradient (high to low concentration)  Facilitated diffusion: molecule moves by diffusion through membrane protein, bypasses lipid bilayer Transporter types: 1 Channel: Opening b/t inside and outside of cell where some molecules can pass 2 Carrier: binds to and transports specific molecules  Aquaporins: Specific protein channels for transporting H2O molecules, allow water to move more readily across plasma membrane o Water molecules diffuse very slowly through plasma membrane o Passive movement (diffusion) not sufficient for cell to function (or maintain homeostasis)  Osmosis: net movement of water across selectively permeable membrane o Regions of high water concentration to low water concentration o Regions of low solute concentration to high solute concentration o Membrane allows passage of water but not solute o This movement continues until opposing force  Ex: pressure from gravity/cell wall Primary active transport uses energy of ATP  Many molecules required by cell not in high concentration in environment (like glucose, which is in higher concentration outside of cell)  Active transport: "uphill" movement of substances against concentration gradient, requiring energy o Ex: sodium potassium pump. Sodium in low concentration in cells, potassium in high concentration. Both moved against concentration gradient (sodium out, potassium in), ATP required  Primary active transport: uses ATP directly, coupled w/transport of molecules o 2 things that move in opposite directions: antiporters o 2 things that move in same direction: symporters Secondary active transport is driven by a electrochemical gradient 1 Build up concentration of small ion on one side of membrane by primary active transport o Resulting concentration gradient has potential energy to drive other substances across membrane  Ex: H+ protons pumped across membrane using ATP (generated chemical gradient and difference in charge is called electrical gradient) 2 This creates Electrochemical gradient: gradient that has both charge and chemical components o Movement of protons is from high to low concentration, movement of coupled molecules low to high concentration 3 Secondary active transport: movement of coupled molecule driven by proton movement, not ATP directly o Uses potential energy of electrochemical gradient  First gradient provides energy to transport another molecule  This energy is shared by multiple transporters Many cells maintain size and composition using active transport  Hypertonic solution (higher solute conc.), hypotonic vice versa, isotonic is =  Contractile vacuoles: compartments that take up excess water from inside cell and by contraction expel it to external environment o Helps single-celled organisms in hypotonic solution stay isotonic o Water can be taken in by aquaporins, or take in protons, then water comes in through osmosis Cell wall provides another means of maintaining cell shape  Cell wall resists expansion, allowing pressure to build up in cell when it absorbs water o Algae, funcgi, and bacteria have cell wall too  Turgor pressure: force exerted by water pressing against an object o Makes plants stand  Vacuole: absorbs water, contributes to turgor pressure o Paramecium (single-celled) have contractile vacuoles b/c it lives in hypotonic environment, and needs to circulate excess solute out of system  Loss of water from vacuoles reduces turgor pressure, cells cannot maintain shape  Plant vacuoles explain why plant cells>animal cells in size  Cell wall made of cellulose (polymer of glucose) 5.3: The Internal Organization of Cells Eukaryotes and prokaryotes differ in internal organization  Prokaryotes include bacteria and archaeons, lack nucleus  Eukaryotes include animals, plants, fungi, and protists, include nucleus and organelles made of phospholipid bilayers o Nucleus allows for separation of transcription and translation, complex ways to regulate gene expression  Prokaryotes don't make steroids, but make hopanoids (function is similar to steroids)  Archaeons and eukaryotes more closely related than to bacteria Prokaryotic cells lack a nucleus and extensive internal compartmentalization  Nucleoid: In prokaryotes, DNA is concentrated in this discrete region of cell  Plasmids: small circular molecules of DNA that carry a few genes and are transferred b/t bacteria through pili  Pili: extend from one cell to another to transfer plasmids b/t bacteria  Prokaryote features: 1 Small, 1/10 diameter and 1/1000 volume of eukaryotes o High SA to volume ratio allows for efficient nutrient absorption 2 Lack extensive internal organization Eukaryotic cells have a nucleus and specialized internal structure  Organelles: compartments that divide the eukaryotic cell contents into smaller spaces specialized for different functions  ER: organelle in which proteins and lipids are made  Golgi apparatus: modifies proteins and lipids produced by ER and acts as sorting station  Lysosomes: have enzymes that break down macromolecules like proteins, nucleic acids, lipids, and complex carbs  Peroxisomes: have many different en  Mitochondria: specialized organelles that harness cell energy  Cytoskeleton: protein scaffold that helps cells maintain shape and serves as track for movement of substances  Chloroplasts: in plants, convert energy of sun into chemical energy Cytoplasm: contents of cell other than nucleus   Cytosol: jelly-like internal environment of cell that surrounds organelles inside plasma membrane  Plasmodesmata: in plant cells, connect neighboring cells 5.4: The Endomembrane System  Vesicles: small membrane-enclosed sacs hat transport substances w/in cell or from interior to exterior of cell 1 Vesicles bud off organelle, taking some of its internal contents 2 Vesicles fuse w/another organelle or plasma membrane 3 Unload contents  Endomembrane systems: interconnected membranes including nuclear envelope, ER, Golgi apparatus, lysosomes, plasma membrane, and vesicles o Key features: o Functionally connected o Communicate w/cytoplasm and etracellular space o Make proteins, modify them, sort in cytoplasm, and secrete them o Intake molecules from extracellular space and digest them Endomembrane system compartmentalizes cell  Exocytosis: vesicle fuses w/plasma membrane, empties contents into extracellular space or delivers proteins to plasma membrane  Endocytosis: vesicle can bud off from plasma membrane, enclosing material from outside cell and bringing it in (w/o passing through membrane) Nucleus houses genome and is site of RNA synthesis  Nucleus: stores DNA, genetic material  Nuclear envelope: defines boundary of nucleus o Inner and outer membranes (lipid bilayers)  Nuclear pores: openings of protein complexes that allow molecules to move into and out of nucleus, make membranes continuous o Ex: transcription factors and RNA polymerase use to move in nucleus from cytoplasm, make membranes continuous  Ribosomes: sites of protein synthesis in which amino acids make polypeptides ER is involved in protein and lipid synthesis Outer membrane of nuclear envelope is continuous w/ER, ER makes up 1/2  cell membranes  Lumen: interior of ER, continuous throughout  RER: studded w/ribosomes, synthesizes transmembrane proteins, proteins that end up in organelles or are secreted o Ex: cells of gut that secrete digestive enzymes o Ex: cells of pancreas that release insulin  Smooth ER (located in cytoplasm) lacks ribosomes, site of fatty acid and phospholipid production o Predominates in cells specialized for production of lipids (steroid hormones like cholesterol) Golgi apparatus modifies and sorts proteins and lipids  Roles of Golgi: 1 Further modify proteins and lipids 2 Sorting station for protein and lipid destinations 3 Site of carb synthesis  Cisternae: stacks of flattened membrane stacks surrounded by small vesicles (what Golgi apparatus looks like)  Enzymes in Golgi apparatus modify proteins and lipids as they pass in sequence of steps in different Golgi regions o Ex: glycosylation: sugars covalently linked to lipids/amino acids, sugars are added or trimmed by enzyme o These sugars protect from enzyme digestion by blocking access to peptide chain o The shape sugars contribute allows recognition by certain molecules  Ex: blood types defined by sugars linked to proteins and lipids of surface of RBCs  Some traffic can move from GA to ER to retrieve proteins that were moved forward Lysosomes degrade macromolecules  Lysosomes: specialized vesicles derived from GA that degrade damaged macromolecules w/enzymes  GA sorts and delivers specialized proteins that become embedded in lysosomal membranes o Ex: protein pumps that keep pH at 5 o Ex: proteins that transport breakdown of products of macromolecules across membrane to cytosol Protein sorting directs proteins to proper location  Protein sorting: process by which proteins end up where they need to be to perform function  Free ribosomes: o Proteins produced on free ribosomes often have signal sequence (20 amino acids at N terminus) that allows them to be recognized and sorted o Nuclear localization signals: enable proteins to move through pores in nuclear envelope  RER: o Proteins produced on RER end up in lumen of ER, secreted out of cell, or as transmembrane proteins o Begin translation on free ribosomes, but amino-terminal signal sequence directs proteins to RER and lumen o Signal-anchor sequence: possible second sequence that causes proteins not to continue to lumen 1. Instead, they end up in membrane o Signal-recognition particle: RNA-protein complex that recognizes amino acid and binds to signal sequence and free ribosome, pausing translation 1. SRP binds to RER receptor so ribosome is associated w/RER 2. SRP dissociates, translation continues 3. Protease cleaves signal sequence, some proteins stay in ER, others go to GA  Proteins destined for cell membrane also have signal-anchor sequence 5.5: Mitochondria and Chloroplasts  Mitochondria and chloroplasts harness cell energy o Grow and multiply independently, have own genomes o Originated as bacteria, captured by eukaryotic cell and evolved Mitochondria provide eukaryotic cell w/most of usable energy  Harness energy from chemical compounds and convert to ATP to drive chemical rxns  Mitochondria have outer and inner convoluted membrane, electrochemical gradient generated across inner membrane stores energy to produce ATP o O consumed, CO2 released in cellular respiration Chloroplasts capture energy from sunlight  Photosynthesis: process by which chloroplasts capture sunlight energy to make simple sugars o Release O2, capture CO2  Chloroplasts have 3 membranes, 3rd one defines internal thylakoid compartment  Thylakoid: has light-collecting molecules called pigments, chlorophyll is the most important of these Unit 2 Notes Thursday, September 22, 2016 12:00 PM Chapter 6: Making Life Work: Capturing and Using Energy  Cells get energy from the environment through ATP o Created from food (or sunlight in plants) by breaking chem bonds of polymers  Ex.: We make energy for muscle contraction by breaking chem bond in ATP (which has high PE) 6.1: An Overview of Metabolism Organisms can be classified according to energy and carbon sources According to energy: 1 Phototrophs: capture energy from sunlight (ex. Plants) 2 Chemotrophs: get energy directly from chemical compounds (ex. Animals) o Energy in chemical bonds of organic molecule converted to energy in bonds of ATP According to carbon: 1 Autotrophs: Convert CO2 into glucose (ex. plants) 2 Heterotrophs: Get carbon from organic molecules made by other organisms (ex. Animals)  Microorganisms that gain energy from sun but get carbon from preformed organic molecules are photoheterotrophs  Microorganisms that extract energy from inorganic sources but build own organic molecules are chemoautotrophs that often live in extreme environments Metabolism is set of chem rxns that sustain life  Metabolism: set of chem rxns that convert molecules into other molecules and transfer energy in living organisms 1 Catabolism: set of chem rxns that break down molecules into smaller units, producing ATP (ex. Carbs break down into sugars) 2 Anabolism: set of chem rxns that build molecules from smaller units and require energy 6.2: Kinetic and Potential Energy  Energy: capacity to do work o Ex.: In a cell, DNA, RNA, and proteins are made, substances pumped across plasma membrane KE and PE are 2 forms of energy  KE: energy of motion (ex. Bouncing ball, photon movement)  PE: stored energy, depends on structure of object or position relative to surroundings, released by change in object's structure/position o Ex.: PE of ball higher at top of stairs, electrochemical gradient of molecules across cell membrane  Energy can convert forms--ball at top of stairs has PE, rolls down and converts to KE, at bottom stores energy as PE Chem energy is form of PE  Chem energy: Form of PE held in chem bonds b/t pairs of atoms in molecule  More stable configuration is one w/lower PE, so energy is required to break covalent bond  Strong bonds have little chem energy o Ex.: CO2 and H2O  Weak covalent bonds need a lot of energy, have high chem energy o Ex.: Organic molecules ATP is readily accessible form of cellular energy  One form of chem energy is ATP-part adenosine (adenine base and 5 carbon ribose), and triphosphate  Chem energy of ATP held in bonds b/t phosphate groups (have neg charge and repel each other)  Energy released when more stable bonds formed, powering cell 6.3: The Laws of Thermo (2 essential physical laws in living organisms) 1st law: energy is conserved  1st law of thermo: conservation of energy, universe has constant amount of energy, energy never made or destroyed, o Energy only changes forms o Universe has constant amount of energy o It can be heat (nonliving things) and chem (nonliving and living organisms)  Ex.: ball in stairs: difference in PE at top and bottom = total KE associated w/movement 2nd law  When changing energy forms, energy available to do work decreases (energy transformations not 100% efficient)  2nd law of thermo: transformation of energy associated w/higher disorder in universe (entropy)  When entropy increases, so do # of positions and motions available to molecule  When energy changes form, we lose some as heat (increase in entropy) o Ex.: expansion of gas and free movement w/more positions and speeds o Ex.: thermal energy makes molecules faster (increasing disorder) o Ex.: contracting muscle powered by chem PE, converted to KE (movement) and thermal energy-muscles warm (by-product)  Catabolic rxns increase entropy as smaller molecules move more  2nd law applies to universe as whole (anabolic rxns decrease entropy, but increase entropy of surroundings)  Maintenance of fnt and organization of cells requires constant energy  In bio and chem energy source is food (chemicals)  Covalent bonds have energy 6.4: Chem Rxns Chem rxn occurs when molecules interact  During chem rxn, atoms keep identity, but bonds change o Ex.: CO2 + H2O-->H2CO3 (CO2 enters oceans, changing acidity)  Most chem rxns are reversible o Ex.: H2CO3-->H2O+CO2  Increasing concentration of reactants or decreasing concentration of products favors forward rxn Laws of thermo determine whether chem rxn requires or releases energy  Gibbs free energy (G): amount of energy available to do work o If products have more energy than reactants, delta G is pos, energy needed for rxn  Exergonic: rxn w/- delta G that release energy, proceed spontaneously  Endergonic: pos delta G, require input of energy, not spontaneous  Enthalpy (H): total amount of energy  Degree of disorder: entropy (S) x absolute temp (T)  H = G + TS; delta G = delta h -TdeltaS o Pos delta H and neg delta S make pos delta G, and vice versa Hydrolysis of ATP is exergonic (ATP + H2O --> ADP + Pi)  Rxn is exergonic b/c less free energy in products compared to reactants  Delta H b/c ATP has 3 phosphate groups, ADP has 2 (less chem energy)  Pos delta S b/c ATP broken into 2 molecules (ADP and Pi) o Delta G = delta H -TdeltaS, delta G is neg, rxn spontaneous  Spontaneous rxns need initial energy boost  Release of free energy from breaking weaker bonds, forming more stable product bonds Non-spontaneous rxns coupled to spontaneous rxns  Energetic coupling: spontaneous rxn drives non-spontaneous rxn o Requires net -delta G, 2 rxns to occur together o Ex.: ATP hydrolysis used to drive non-spontaneous rxn (phosphate group released transferred to glucose to make glucose 6-phosphate)  Net -delta G  ATP is energy acceptor, ADP is donor ATP + H2O-->ADP + Pi Exergonic Gluocse + Pi-->Glucose 6-phosphate + H2O Endergonic 6.5: Enzymes and Rate of Chem Rxns  Catalysts are substances that increase rate of rxn w/o being consumed o Normally proteins called enzymes (don't change delta G) Enzymes reduce activation energy of chem rxn  Transition state: intermediate stage b/t reactants and products, highly unstable, has a lot of free energy o Reactants must absorb energy from surroundings (energy input to transition state is activation energy)  Lower the Ae, faster the rxn (inverse relationship)  Heat is often used to overcome energy barrier, but enzymes decrease Ae by stabilizing transition state and reducing free energy, but not changing delta G Enzymes form complex w/reactants and products  Substrate: reactant in chem rxn catalyzed by enzyme S + E-->ES-->EP-->E + P  Active site: part of enzyme that binds to substrate and catalyzes conversion to product by forming covalent bonds w/enzyme (decreases Ae)  ES-complex promotes rxn b/t 2 substrates by aligning reactive chem groups and limiting motion  Enzymes large despite small active site, b/c if it was too short, 3D structure constrained Enzymes are highly specific  Enzymes catalyze one or ltd rxns  Enzyme only recognizes part of substrate structure o Ex.: B galactosidase cleaves B galactosidase but not a galactosidase when only difference is orientation of glycosidic bonds Enzyme activity can be influenced by inhibitors and activators  Inhibitors decreased enzyme activity, activators increase activity o Ex.: inhibitors used by plants for defense, drugs are inhibitors  Irreversible inhibitors form covalent bonds w/enzymes to irreversibly inactivate them, reversible inhibitors form weak bonds  Binding of inhibitor prevents binding of substrate (unless substrate concentration increases)  Some inhibitors bind to other site, changing enzyme shape  Allosteric enzymes: regulated by molecules that bind at site other than active sites Allosteric enzymes regulate key metabolic pathways  Neg feedback: Final product inhibits 1st step of rxn o Used for homeostasis/maintaining substance levels What naturally occurring elements might have spurred 1st rxns that led to life?  Cofactor: metal ions that associate w/enzyme o Ex.: iron, magnesium, manganese, copper  Enzymes w/iron and sulfur play a role in cellular electron transport, rxns that are now carried out w/them are descendants of rxns from early earth  H2S + FeS-->pyrite catalyzes many pre-biotic chem rxns, like making pyruvate (intermediate in metabolism) Chapter 7: An Overview of Cellular Respiration  Cellular respiration: breaking down inorganic molecules to make organic molecules, releasing energy to do the work of the cell o Process of extracting energy from glucose  ATP: cellular respiration is a series of chem rxns that convert chem energy in fuel molecules into this kind of chem energy to be readily used  Plants use energy of sun to make carbs, break down carbs to make ATP in respiration 7.1: An Overview of Cellular Respiration  Cellular respiration is catabolic Cellular respiration uses chemical energy in carbs and lipids to produce ATP  Cellular respiration in presence of oxygen is aerobic, in absence of oxygen is anaerobic o C6H12O6 (Glucose) + 6O2 (Oxygen)-->6CO2 (Carbon Dioxide) + 6H2O (Water) + energy  Cellular respiration releases lots of energy b/c PE in bonds of reactants > than in products  Energy released in series of steps to let some energy be used in the form of ATP o 32 molecules ATP produced from aerobic respiration of 1 glucose molecule o 34% energy released by aerobic respiration harnessed in ATP form ATP is generated by substrate-level phosphorylation  Substrate-level phosphorylation: Making ATP when phosphate group is transferred to ADP (from an enzyme substrate-organic molecule) o Produces only 12% ATP from respiration  Electron carriers: chem energy of organic molecules is transferred to these, and they carry e- and energy from one set of rxns to another  E- transport chain: transfer e- along a series of membrane-associated proteins to a final e-acceptor and in the process harness energy released to make ATP o Generating ATP this way is called oxidative phosphorylation Redox rxns play a central role in cellular respiration  Oxidation-reduction rxns: chem rxns in which e- are transferred from one atom or molecule to another o Oxidation is e- loss, reduction is e- gain  E- carriers are nicotinamide adenine dinucleotide and flavin adenine dinucleotide  Reduction rxn: NAD+ + 2e- + H+ --> NADH and FAD + 2e- + 2H+ --> FADH2 o E- from chem rxns or from glucose  Oxidation rxn: NADH --> NAD + + 2e- + H+ and FADH2 --> FAD + 2e- + 2H+ o E- from chem rxns or from glucose  Losing H+ means losing energy (reduction)  In CO2, O- more e-neg, so carbon is oxidized (releases energy)  In H2O, O- more e-neg, so it gains e- to be reduced Cellular respiration occurs in 4 stages 1 Glyocolysis: glucose broken down to make pyruvate, energy transferred to ATP and reduced e- carriers o Occurs in cytoplasm 2 Pyruvate is oxidized to acetyl-CoA, producing reduced e- carriers, releasing CO2 o Occurs in matrix of mitochondria 3 Citric acid cycle (Krebs cycle): acetyl group oxidized to CO2, energy transferred to ATP and reduced e- carriers o Amount of energy transferred to ATP 2x that of stage 1 + stage 2 o Occurs in matrix of mitochondria 4 Oxidative phosphorylation: reduced e- carriers donate e- to ETC, making lots of ATP o Occurs in intermembrane space, inner membrane, and matrix o Majority of ATP produced this way  Glycolysis in cytoplasm, other 3 stages in mitochondria in eukaryotes  In bacteria, rxns in cytoplasm, ETC in plasma membrane  2 ways of making ATP are substrate-level phosphorylation and oxidative phosphorylation (mostly use oxidative for ATP) 7.2: Glycolysis: The Splitting of Sugar  In glycolysis, 6-carbon glucose split into 2 to get 2 3-carbon molecules o Anaerobic, evolved when O2 wasn't in Earth's atmosphere Glycolysis is partial breakdown of glucose 1 2 phosphate groups added to glucose (requires 2 ATP) o Glucose is trapped in cell, and 2 neg-charged phosphate groups destabilize the molecule so it can be broken apart 2 Cleavage phase: 6-carbon molecules split into 2 3-carbon molecules 3 Payoff phase: ATP and e- carrier NADH produced, 2 molecules pyruvate produced o Net gain of 2 ATP molecules, 2 NADH molecules, 2 pyruvate 7.3: Pyruvate Oxidation  W/O2, pyruvate can be further oxidized to release more energy  Intermembrane space: b/t inner and outer membranes of mitochondria  Mitochondrial matrix: space enclosed by inner membrane of mitochondria  Pyruvate transported to matrix and converted to acetyl-CoA 1. Pyruvate is oxidized, splits off to form CO2 2. Lost e- are donated to NAD+, becoming NADH 3. Acetyl group is transferred to coenzyme A (CoA)  Net gain: 2 CO2, 2 NADH, 2 acetyl-CoA 7.4: Citric Acid Cycle  Starts w/oxaloacetate and ends w/oxaloacetate  Fuel molecules are completely oxidized in the matrix In 1st rxn, 2-carbon acetyl group of acetyl-CoA is transferred to 4-carbon  oxaloacetate to make 6-carbon citric or tricarboxylic acid  Citric acid is oxidized, generating oxaloacetate  Carbons released as CO2  Energy released in oxidation rxns is transferred to NADH  3 NADH and 1 FADH2, 1 ATP made, and CO2(waste) per pyruvate molecule by using all energy from acetyl group  Substrate-level phosphorylation rxn generates GTP, which transfers a phosphate to ADP to make ATP  Net: 2 acetyl-CoA, 2 ATP, 6 NADH, 2 FADH What were the earliest energy-harnessing rxns?  Reverse citric acid cycle requires sun energy  Running cycle in reverse allows building organic molecules o Pyruvate is the start for sugars and alanine, acetate is the start for lipids, oxaloacetate forms amino acids and pyrimidine bases, alpha ketoglutarate makes other amino acids  Forward cycle maked energy-storing molecules and intermediates, reverse generates intermediates and incorporates carbon into organic molecules 7.5: The ETC and Oxidative Phosphorylation ETC transfers e- and pumps protons  Energy source is e-, not ATP  Membrane proteins are embedded in mitochondrial inner membrane  E- donated by NADH enter through complex I, those donated by FADH2 enter through complex II  W/chain complex movement, e- passed from donors to acceptors (making redox couples) o O- accepts e- at end of ETC, reduced to make H2O using PE: O2 + 4e- --> 2H2O  Coenzyme Q (CoQ)


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