Thermodynamics and Enzymes Enthalpy - total energy in a molecule (H) vs. Entropy - degree of disorder (S); not efficient, given off as heat ● ΔG = ΔH - (T x ΔS); When ΔG is positive, the free energy of your product is higher than the free energy started with; to get to higher free energy, you have to put in energy; When ΔG is negative, it is an energy-releasing reaction; you do not have to put in energy ● Endergonic: energy input is required (positive ΔG) vs. Exergonic: energy is released (spontaneous, negative ΔG) ● ● ● A = Ea B = ΔG (neg. b/c product energy is lower) The transition state is very unstable; ΔG of an unstable molecule is high b/c it has a higher free energy Enzymes lower the energy of the transition state so that it is more stable and requires less energy input Between glucose, CO2, and water, glucose has the greatest potential energy Competitive Inhibition - a regulatory molecule binds to the active site, preventing the substrate from binding Allosteric ACTIVATION - the active site becomes available to the substrates when a regulatory molecule binds to a different site on the enzyme, changing the shape; allows substrate to bind when they couldn’t without the regulatory molecule Allosteric INHIBITION - the active site becomes unavailable to the substrate when a regulatory molecule binds to a different site and changes the active site to a different shape than the substrate Aerobic Cell Respiration (all yields per pyruvate) ● Glucose is oxidized to CO2, Oxygen is reduced to water (follow the hydrogens if unsure to see where the electrons are going) 1. Glycolysis - cytoplasm - NO oxygen req. - makes 4 ATP per pyruvate (net 2 per pyruvate) - NAD+ reduced to NADH, 1 NADH per pyruvate 2. Pyruvate Processing - matrix - pyruvate oxidized by losing neg. charged CO2 (exhaled) - NAD+ reduced to NADH - Acetyl CoA left ● Pyruvate + NAD+ + coenzyme A → CO2 + NADH + acetyl-CoA 3. Citric Acid Cycle - matrix - requires oxygen - Acetyl CoA oxidized - NAD+ and FAD reduced - 2 CO2, 1 ATP, 3 NADH, and 1 FADH2 4. ETC - inner mitochondrial membrane - requires oxygen - I: oxidizes NADH to NAD+ & electron transferred to CoQ and brings protons into intermembrane space, II: oxidizes FADH2 to FAD+, CoQ reduced to CoQH2, III: CoQH2 diffuses through membrane to complex III and reduces cytochrome C, moves protons through IV: Reduced cytochrome C diffuses through membrane to IV and reduces O2 (F.E.A.), protons move thru ATP synthase: protons move down conc. gradient back into matrix, potential → kinetic, spins ATP synthase → 28 ATP Anaerobic Respiration - produces 2 ATP and generates NAD+ for glycolysis Glycolysis occurs normally first, producing 2 ATP, 2 NADH, and 2 pyruvate molecules ● Lactic Acid: animals and bacteria - pyruvate accepts two electrons from NADH to become lactic acid → generates NAD+ to continue glycolysis - in humans, occurs due to inadequate muscle supply in humans ● Ethanol: plants and fungi - pyruvate oxidized by releasing CO2 and converts to acetaldehyde - acetaldehyde is reduced from 2 molecules of NADH to become ethanol Photosynthesis Light Reactions: produce H2O and ATP Photosystem II (thylakoid mem.): oxidation of the reaction center, splits H2O to produce O2, electrons given to a donor (in cytochrome comp) Photosystem I (thylakoid): energy from light allows transfer of electrons from NADP+ to NADPH (2 NADPH are produced) Exciting electrons converts the potential energy of light into chemical energy || proton build-up leads to spinning of ATP synthase = ATP Dark Reactions: take the energy from ATP and NADPH to produce glucose Carbon fixation: CO2 taken from the atmosphere is added to RuBP (catalyzed by rubisco) to make 3 PGA Reduction: 3 PGA is reduced to G3P (energy comes from ATP from light reactions) and electrons come from NADPH Regeneration: 1 G3P molecule is used to build glucose and the other five are used to regenerate RuBP Unit 1 Cell Structure and Membranes Nucleic acids, proteins, carbohydrates, lipids - nucleotides, amino acids, sugars Saturated fatty acids = less permeable, Unsaturated = more permeable || Cholesterol’s effect on fluidity depends on temp.; percent cholesterol and permeability are inversely proportional; decreases permeability even with changing temperature Cholera: water wants to follow the solutes when they move out, causing the cell to shrink → drink lots of water with a little salt Water Intoxication: cell expands, have salt foods and high solute IV Nucleotides and RNA Replication ● C and G have 3 bonds, A U and G have 2 hydrogen bonds - CUT are purines, GA are pyrimidines ● RNA transcript is synthesized 5’ to 3’ and read 3’ to 5’ → If given DNA template in 5’ to 3’, read backwards if writing 5’ to 3’ ● DNA transcript is synthesized 5’ to 3’ → If given DNA template 5’ to 3’, write the complementary strand backwards if writing 5’ to 3’ RNA Transcription 1) Transcription factors and RNA polymerase bind to the promoter, including the TATA box 2) RNA Polymerase separates the double-stranded DNA into two strands, creating a transcription bubble 3) Ribonucleotide triphosphates (NTP’s: RNA nucleotides that have 3 phosphates) enter the transcription bubble 4) A ribonucleotide triphosphate (NTP) that is complementary to a base on the template DNA strand is added to the growing RNA polymer and two phosphates are released 5) Elongation of the RNA transcript continues as polymerization is repeated 6) A modified guanine nucleotide is added to the 5’ end of the RNA (5 prime cap) 7) The spliceosome removes introns from the RNA 8) RNA Polymerase and the mRNA transcript dissociate from (comes off) the DNA template strand 9) A poly(A) ribonucleotide tail is added to the 3’ end (3 prime tail) 10) mRNA moves from the nucleus to the cytoplasm RNA Translation ● Recognition of 5’ cap and AUG start codon (Shine-Delgarno in prok.) || Anticodon in tRNA base pairs with a complementary codon through hydrogen bonds || Wobble Hypothesis: third codon can vary, allowing 40 tRNA anticodons to match with the 60 codons ● A-site holds an aminoacyl tRNA, peptide formation occurs between A and P site, P-site holds tRNA with growing polypeptide, E-site holds tRNA that will exit || Termination: specific stop codons, coding for a release factor, filling the E site with a tRNA Mutations Silent: no effect || Missense: change in amino acid affects folding/ structure || nonsense: stops early || frameshift: add/deletion, changing frame ** Notice start/stop codons and if it is in frame when deciding what mutation/ what amino acid Unit 2 Cell Cycle G1 Phase: Cell decides to begin replication; the cell grows and replicates its organelles. G1 Checkpoint: Ensures there is no damage to DNA and there are sufficient nutrients G2 Phase: More growth to begin Mitosis. G2 Checkpoint: Checks to ensure that DNA was replicated properly M1 Checkpoint: Checks to ensure all spindles attached to centromeres. M2: Ensure sister chromatids separated ● P53 - is a protein in the nucleus that checks for DNA damage - if it finds DNA it activates kinases that phosphorylate DNA, which acts as a transcription factor that turns on genes that inhibit the cell cycle, giving time to repair the damaged DNA → Spindle FIBERS form during prophase, Spindle apparatus forms in prometaphase || A human cell is briefly tetraploid (4) during anaphase and telophase || A chromosome has gone through S phase if it is attached at the kinetochore Mitosis & DNA Replication - DNA polymerase III replicates DNA and proofreads, nucleotides added to 3’ end ALWAYS and reads 3’ to 5, DNA polymerase I replaces RNA primer, DNA helicase separates and unwinds - dNTPs; three phosphates are removed, providing energy - Topiosomerase cuts and rejoins DNA to relieve of tightly wound DNA - SSBPs prevent strands from binding together - Primase adds RNA primer to DNA and helps DNA polymerase III recognize and know where to start - DNA ligase catalyzes bonds between Ozaki fragments to prevent lagging strand from lagging; away from fork - Eukaryotes have multiple bubbles, prokaryotes have one - Telomeres are extended back to their original length by the protein called telomerase. This protein has its own internal RNA template. Meiosis & Epigenetics Ploidy: # of complete sets of chromosomes; first #: # of chromosomes per complete set, n: # of unique chromosomes, second: total Histone Acetylation: the positive lysine residues of the histone protein are neutralized, decreasing condensation of DNA. DNA Methylation: A methyl group is added to DNA and regonized by proteins that condense DNA Pedigrees ● If a male inherits a recessive disease from two parents who do not have it, the affected male inherited it from the heterozygous mother because fathers can only have 1 X chromosome. If males inherit just one allele, they are affected by that allele. ● If there is an autosomal dominant disorder and one parent does not have it (aa), the genotype of a child who has it has to be heterozygous. ○ All daughters of an affected male have the disorder ○ No sons of an affected male and an unaffected female have the disorder ○ Affected sons always have affected mothers ○ Affected daughters can have an affected mother or father ● If a disorder affects both genders, it is likely autosomal. ● If an infected father has a son with a homozygous dominant mother, will the son have the disease? - NO ● If an infected father has a daughter with a homozygous recessive mother, will the daughter have the disease? - YES Why?: Sons inherit the X chromosome from the mother and the Y chromosome from the father. Daughters inherit one X from the mother and one X from the father.
