Biochem 501 Final exam, Biochem 501 Unit 4, Biochem Unit 2

3 binding sites for tRNA/mRNA interactions

A-site (amino) P-site (peptide) E-site (exit)

Fumarase (Fumarate hydratase) step of Citric Acid Cycle

Hydration reaction ( not a hydrolysis or an oxidation) Prepares substrate for final oxidation

Sequence specific contact for DNA binding

Hydrogen bonds form between specific amino acids and nucleotide bases based on the patterns of H-bond donors and acceptors in each molecule. proteins can read the bases without needing to "melt" the DNA! Sequence-specificity of binding is determined by motifs (many types) in the protein structure that make direct contacts with the nucleobases

EX of catalysis

Hydrolysis Phosphoryl transfer C-C isomerization Redox Peptide bond formation

Lipases

Hydrolysis to fatty acids which transported across the plasma membrane

Enzyme substrate complex (ES complex)

Hydrophobic packet helps form enzyme substrate ● The 1st kinetic step of enzyme rxn is the rapid and reversible formation of ES ● The ES complex gets converted to enzyme plus product through the catalysis methods ● The slow conversion of ES to enzyme and product is slow and is our rate limiting step ● So rate of reaction is proportional to [ES] ● Concentration of the product is negligible so k2 is ignored ● Steady state approximation assumes the ES complex is constant ● (k2+k-1)/(k1)=Km ● V0 = (Vmax[S])/(Km+[s]) ● When substrate concentration is very low, the closest Km concentration is going to have the fastest rate ● V0 = (kcat[Et][S])/(Km+[S]) ○ When [S]<< Km, V0 = (kcat/Km) [Et][S] ● For efficient enzymes, diffusion is rate limiting step ● Enzyme rxns are dependent on temp and pH ○ Reaction can be sped up by temperature but if temp is too high it can destroy the protein ○ Same is true for pH

retrotransposon

Copy/Paste. Transposon sequence is copied to RNA intermediate used to make a second DNA copy for insertion. Double-stranded DNA fragment is made using RNA strand as template Double stranded DNA fragment inserted into genome Duplicates transposon sequence rather than moving it

Entropy change 𝝙S

change in randomness System can decrease local entropy only if greater increase in entropy occurs in the surroundings If (+): increase in randomness favorable (negative) 𝝙G

Nonsense mutations

change mRNA sequence from codon for amino acid to stop codon, terminating translation and resulting in a truncated polypeptide EX: UUA (leucine) ot UAA (stop)

silent mutations

change mRNA sequence to a synonymous codon and has no affect on resulting polypeptide EX: UUA (leucine) to UUG (leucine)

Missense mutations

change the mRNA sequence from codon for one amino acid to codon for different amino acid, changing the polypeptide sequence EX: UUA (leucine) to UCA (serine)

FADH2

chemical energy in metabolism comes from it activated carriers of electrons for fuel oxidation have higher affinity for electrons than do carbon fuels but lower affinity for electrons than O2 Riboflavin is precursor for each beta-hydroxybutyrate, 2 FADH2 are formed

NADH/NAD+

chemical energy in metabolism comes from it high amount in mitochondria high energy molecule slow down energy producing pathways high amount in mitochondria activated carriers of electrons for fuel oxidationhave higher affinity for electrons than do carbon fuels but lower affinity for electrons than O2 (for aerobic organisms) Nicotinate (niacin) (vitamin B3) is the vitamin precursor anabolic pathways in animals use it to produce large biomolecules: Oxaloacetate (OAA) is reduced to malate and shuttled into the cytoplasm and reoxidized to oxaloacetate with NADH cytoplasmic NADH is necessary in gluconeogenesis for each beta-hydroxybutyrate, 7 NADH are formed

Path of energy flow to ATP

chemiosmotic path

diabetes

Inability to make or sense insulin type I and Type II

Heterochromatin

Inaccessible Transcription of genes cannot occur here. Marked by histone methylation and binding of heterochromatin proteins. transcriptionally silent. HP1 bind across methylated histones to promote chromatin compaction

Carbohydrates

Monosaccharides and Simple sugars like glucose fructose galactose fatty acids contain more energy per gram than carbohydrates the biosynthesis of triacylglycerols from acetate occurs mainly after ingestion of excess carbohydrates Insulin stimulates conversion of dietary carbohydrate into triacylglycerols.

Supercoiled DNA

More compact than relaxed/extended DNA getting DNA to supercoil would be one mechanism by which genomic DNA can be packed down into the cell. Supercoiling can help scrunch down a prokaryotic genome, but Eukaryote genomes are even bigger.

Synthesis of NAD+

Most of the NAD+ required by our bodies is synthesized from dietary niacin Any nicotinamide released during the breakdown of cellular NAD+ can be salvaged and recycled by these reactions.

Defects in Heme Biosynthesis

Mutations or misregulaton of enzymes in the heme biosynthesis pathway lead to porphyrias. Precursors accumulate in red blood cells, body fluids, and liver. Urine becomes discolored Skin is sensitive to UV light. - There is a 'craving' for heme.

Depurination

N-glycosidic bond between base and ribose cleaved Corrected by base-excision repair (no glycosylase needed as when nucleotide is depurinated it lacks a purine base so no glycosidic bond is present) Removes entire puring base from nucleotide repaired by base excision repair

DNA ligase

connect lagging strands together seals the gap between the 3' OH of one nucleotide with the 5' phosphate of the next nucleotide denylylated and the phosphate on AMP helps facilitate the phosphoryl-transfer reaction by creating a good leaving group

N-glycosidic linkage or glycosidic bond.

connection between the nitrogenous base and the ribose sugar occurs between the 1' position on the sugar and a nitrogen on the base. covalent bonds

reading frame

consecutive, non-overlapping codon sequences translated into a polypeptide. start is set by the initiating codon (AUG).

Genomic DNA

consists of two single strands annealed together annealed form is great for long-term storage need to separate the strands to be able to make use of base-pairing for replication, transcription,

Topological properties

constrain DNA 's conformation when deformed Cause DNA to "supercoil" if you try to unwind or overwind it

Genome

contains genes that code for proteins cell will transcribe that information into RNA using the DNA template. Instead of using DNA into directly

hinge domain

contains nuclear localization signal

Gradients

ion pumping ATPases use ATP to create gradient opposite of normal mitochondrial direction enzymes cont control direction, only increase rate of equilibrium

Aspirin

irreversible inhibitor transfers an acetyl group to a serine residue in the active site of prostaglandin synthase prevents the use of arachidonate as a substrate for the enzyme that generates prostaglandin H2 (PGH2).

eicosanoid

is An early step in the path to thromboxanes is blocked by ibuprofen derived from Phospholipids eicosanoid hormones are derived from polyunsaturated fatty acids in the plasma membrane derived from the 20-carbon long unsaturated fatty acid arachidonic acid arachidonate is its precursor

Adenine

is a hydrogen bond acceptor. a purine

glycerol

lipolysis- hydrolysis of triacylglycerol to 3 fatty acids and a glycerol activated by apoC-II (derived from triacylglycerol) Phosphatidic acid has only a glycerol backbone, a phosphate and 2 fatty acid tails can serve as starting material for gluconeogenesis can be converted into dihydroxyacetone phosphate, which can be processed by gluconeogenesis or glycolysis. GLycerol --(ATP in, ADP and H+ out) glycerol kinase--> glycerol phosphate --(NAD+ in, NADH and H+ out) glycerol phosphate dehydrogenase---> dihydroxyacetone phosphate (DHAP)

very low density lipoproteins (VLDL)

lipoprotein To transport triacylglycerols to adipose and muscle tissue. have mostly triacylglycerides Removal of TAG results in the formation of LDL.

High Density Lipoprotein (HDL)

lipoprotein carries cholesterol released into the blood back to the liver, a process called reverse cholesterol transport. has highest percentage of Protein helps remove cholesterol from tissues and foam cells to reduce risk of cardiovascular disease (CVD). is cardioprotective as it removes cholesterol from macrophages and returns it to the liver for use as bile salts or excretion through reverse cholesterol transport

chylomicrons

lipoprotein contain the highest percentage of triacylglycerols. triacylglycerol are added with cholesterol and apolipoproteins into chylomicrons moved through lymphatic system and bloodstream to tissue carry dietary fat (TAG) to tissues, thus least dense.

Low-density lipoprotein (LDL)

lipoproten contains the highest percentage of cholesteryl esters. variants in LDL receptor may result in hypercholesterolemia major carrier of cholesterol in the blood. central role in cholesterol metabolism Excess LDL is oxidized and then phagocytosed (taken up) by macrophages, forming foam cells that become trapped in blood vessels leading to plaque formation and cardiovascular disease Internalization of LDL by liver cells helps recycle and reduce plasma cholesterol 1. LDL binds to the LDL-receptor on the cell surface. 2. The receptor-LDL complex is internalized, a process called endocytosis. 3. The LDL is hydrolyzed in lysosomes interacts with ApoB-100 to stimulate endocytosis

Glucose

liver processes glucose pancreas changes blood glucose concentration energy usage or storage in anabolism: glucose to glycogen excess glucose stored for later as energy or used to generate functional biomolecules carried by Uridine diphosphate glucose predominant fuel for brain from diet (carbohydrates) most glucose units are lined by alpha-1, 4-glycosidic bonds, with branches formed by alpha-1, 6-glycosidic bonds every 10-12 glucose units. in plants, stored as starch in form of amylose insulin is stimulated by high blood glucose causes blood glucose levels to decrease glucagon is stimulated by low blood glucose causing it to increase stored as polysaccharide glycogen in animals fasting state has low blood glucose one hour after eating blood glucose is high in hyperglycemic range, and causes release of insulin gluconeogenesis synthesizes glucose for fuel

Polysaccharides

monosaccharides are joined to alcohols and amines through glycosidic bonds forming polysaccharides glycogen is a polysaccharide of glucose some cant be broken down by mammals

anti-conformation of nucleotides

more energetically favorable.

disaccharide

most of us can digest Enzymes on the outer surface of intestinal epithelium cleave common disaccharides found in the lumen of the intestine. Sucrose (glucose-fructose) Lactose (glucose-galactose) Maltose (glucose-glucose)

Glucose-6-phosphate dehydrogenase deficiency

most prevalent in areas afflicted with malaria. would provide protection against malaria mostly in areas near the equator over-whelming oxidative stress, which lyses red blood cells causing serious medical problems. NADPH is diminished and detoxification inhibited cellular damage low NADPH levels cause low GSH levels and higher reactive oxygen species

Mitochondrial transport and shuttle systems

move ATP out and phosphate or ADP in energetically favorable to move ATP out and ADP in because ATP has charge of -4 while ADP has -3 and outside is positive

translocation

moves tRNA from A-site to P-site, Psite to E-site, E-site -> gone

Eukaryote

multiple oris

Muscle

muscle cells are not responsible for replenishing low levels of glucose in the blood 3 ATP are produced in muscle during glycolysis from a monomer of sugar when muscles contract lactate is produced and released into blood no glucagon receptors in muscle muscle cells don't express glucose 6-phosphatase, the enzyme catalyzing the de-phosphorylation of glucose 6-P

Insulin

originate in beta-cells of pancreas peptide hormone designating the fed state Pancreas secretes insulin to helps maintain optimal levels of glucose when glucose is high stimulates conversion of dietary carbohydrate into triacylglycerols. lack of insulin causes increased lipolysis and fatty acid oxidation, and failure to synthesize fatty acids Activates PP1 Diabetic ketosis haooens when insulin is absent High levels of ATP stimulate release of insulin Oxidation of glucose in pancreas stimulates release of insulin Insulin signaling stimulates glucose uptake and storage in fat and muscle cells causes blood glucose levels to decrease and free fatty acid levels to decrease released by pancreas--> triggering (GLUT4) transporter activating PP1 which activates glycolysis, cholesterol synthesis, nucleotide synthesis and fatty acid synthesis allowing body to absorb and store glucose closing ATP-gated K+ causes K+ to build up in beta cell causing depolarization across membrane opening voltage-gated Ca2+ channels stimulating insulin release via exocytosis in liver: used in glycolysis, Glycogen synthesis, Fatty acid synthesis, Cholesterol synthesis for adipose: used in GLucose uptakel, Fatty acid synthesis for muscle: used in Glucose uptake, Glycogen synthesis, Amino acid synthesis Insulin signaling results in the activation of PFK-2, which catalyzes the synthesis of Fructose 2,6 BP and inhibition of gluconeogenesis and activates glycolysis

open reading frame

sequence of codons flanked by start & stop codons that specifies a gene's protein sequence.

Primary protein structure

sequence of the protein or order of amino acids

Introns

sequences removed from the RNA transcript through splicing

metabolic routes for living systems to obtain energy

there are many other than fermentation and O2-based respiration using C-C and C-H bonds all routes have common features

Nucleoside monophosphates

these are what the final nucleic acid polymer is composed of. 5'AMP

ATP, NAD, FAD, CoA contain nucleotides that dont participate in chem rxn bc

they were based on RNA that were used for both info and catalysis

untreated diabetes

tissues cannot take up glucose efficiently from the blood This acetyl-CoA can't pass through the CAC (because CAC is depleted of intermediates that are used in gluconeogenesis) so more ketone bodies are formed

DNA binding domain

towards center of primary structure characterized by zinc-finger domains that confer specific DNA binding.

bacteria cell

○ Bacterial cell: ■ Small ■ 1x10^-6 m or 1 um ■ Inside single membrane is ● DNA genome: genetic material ● Proteins ● RNA ● Small molecules ● Water molecules no nucleus

fermentation of pyruvate to ethanol

EX: in yeast Pyruvate decarboxylase clips off the carboxylic acid group and releases CO2 forming a C-H bond 2 step fermentation Oxidizing ethanol provides more energy because it has more C-H bonds NAD+ must be replenished for glycolysis to continue.

Cell surface receptor

Hormone (or ligand) binds to receptor on membrane of the cell; acts through receptor without entering/exiting the cell.

heme

Porphyrin coordinated to iron atom Flat aromatic ring Provides 4 nitrogen ligands to the iron 4 bonds to iron atom through porphyrin ring that makes heme 5th bond to histidine nitrogen Oxygen binding forms 6th bond to iron atomOxygen binds at ~120 degree angle to Fe Stabilizes the +2 state of iron over the +3 state CO binds to free heme 20000x stronger than O2

Regulation of chromatin structure.

Positioning and post-translational modifications

C2'endo conformation

Predominates in DNA nucleotides laces the phosphates farther apart than in the C3'endo associated with "B-Form" double-stranded DNA

Glutathione (GSH)

eliminates toxic peroxides which are reactive oxygen species derived from amino acids present in most cells at high amounts. Reduction of oxidized glutathione requires NADH Reducing agent/antioxidant keeps proteins, metal cations reduced keeps redox enzymes in reduced state G6-P dehydrogenase lessens oxidative stress via NADPH and glutathione NADPH generated by the pentose phosphate pathway is required to maintain adequate levels of reduced glutathione. NADPH generated by the pentose phosphate pathway is required to maintain adequate levels of reduced glutathione. Oxidized to a dimer using disulfide bond (GSSG)

ketogenic amino acids

can be converted into ketone bodies

glucogenic amino acids

can be converted to glucose

synthetic DNA

can be used to modify the biology of living systems

Oxidoreductase

causes transfer of electrons like in dehydrogenases and reductases

leading strand

(continuous synthesis) at each fork

Consider the reaction A → B. If, at equilibrium, the concentration of B is greater than the concentration of A

, if the change in standard free energy (𝝙G° of the reaction is negative

Type I diabetes

- immune system attacks pancreatic beta cells (autoimmune)- insulin-dependent- used to be called juvenile diabetes- usually develops before your 20's if untreated levels of Malonyl-CoA will decrease Ketone bodies that build up in the blood cause a decrease in pH. Autoimmune disease which leads to the destruction of beta-cells and total loss of insulin production (more often in children)- hypoglycenia common breath smells like alcohol as acetone (ketone body) is exhaled, not used for energy Patient loses weight as glucose cannot be used and fats must be used for energy. Treatment: Insulin injection

Type II diabetes

- usually develops after age 40- often develops in individuals who are overweight or obese- the disease often goes undiagnosed for a while because one can be pre-diabetic for a long time- the early stages are reversible by exercise Begins a disrupted insulin signaling (insulin resistance) often (but not always) caused by obesity and eventually leads to beta-cell dysfunction (more often in adults but also in children)-Treatments: Exercise (Increase GLUT4 expression and membrane localization), Improve insulin sensitivity (weight loss or medication)

Steps of spliceosome splicing

1. 2'OH from the ribose of a "branch point A" within the intron cleaves the backbone at the 5' splice site. 2. free 3'OH of the 5' first exon attacks the phosphate connecting the intron to the second exon, releasing an RNA "lariat" in the process 3. removal of the intron and splicing of the two exons together.

steps in urea cycle

1. Ammonia is recaptured by synthesis of carbamoyl phosphate 2. Ornithine combines with carbamoyl phosphate to form citruline in mitochondria, 2 nitrogens come together 3. citrulline is transferred to cytosol 4. ATP energizes citrulline formine citrullyl-AMP intermediate 5. aspartate and citrullyl-AMP produces argininosuccinate 6.arginosuccinate releases fumarate and forms aginine 7. urea released by arginase enzyme

Nucleotides are joined together through phosphodiester bonds

1. Base activation of 3' OH 2. Nucleophilic attack of 3' OH on the alpha phosphate of a nucleoside triphosphate. 3. Pyrophosphate acts as a leaving group to drive the reaction forward. Hydrogen bonds involving the amino and carbonyl groups are the primary mode of interaction

4 steps of Beta-oxidation

1. Dehydrogenation 2. Hydration 3. dehydrogenation again 4. thiolytic cleavage

Steps of citric acid cycle

1. Citrate synthase 2. Aconitase 3. Isocitrate dehydrogenase 4. 𝛂-Ketoglutarate Dehydrogenase Complex 5. Succinyl CoA synthetase 6. Succinate Dehydrogenase 7. Fumarase (Fumarate Hydratase) 8. Malate dehydrogenase

Pathway of Gluconeogenesis

1. Conversion of Pyruvate into Phosphoenolpyruvate (PEP) takes two steps and begins with formation of oxaloacetate (inside mitochondria) (Biotin is a required cofactor for carboxylase enzymes) 2. Oxaloacetate (OAA) is reduced to malate and shuttled into the cytoplasm and reoxidized to oxaloacetate with NADH 3. conversion of Fructose 1,6-Bisphosphate into Fructose 6-Phosphate and Orthophosphate is an irreversible step by hydrolysis 4. Glucose 6-Phosphate is hydrolyzed by Glucose 6- Phosphatase in the ER lumen of the liver for transport

3'-5' proofreading activity

1. DNA polymerase adds nucleotides via its polymerase domain 2. Removes mismatched nucleotides via its exonuclease domain

hydrophobic pocket

1. Its substrate binds in hydrophobic pocket, E+S=ES complex which is energetically favorable rxn helps form enzyme substrate complex in chymotrypsin for substrate binding and specificity

Palmitoyl-CoA is a saturated, 16-carbon long fatty acid. How many acetyl-CoA, NADH and FADH2 will be formed from the full oxidation of this molecule?

8, 7, 7

3 turns of calvin cycle

3CO2 + NADPH +ATP yields one extra glyceraldehyde-3-P via steps of glycolysis in reverse Gives net gain of 3 carbon sugars

how many reduced bonds does acetate have? in other words, how many reduced cofactors are formed when acetate is fully oxidized in the citric acid cycle?

4

Synthesis of Phosphatidic Acid

1. activation of fatty acyl group 2. transfer to glycerol-3-phosphate 3.. formation of phosphatidic acid

aminoacyl-tRNA synthetase

1. amino acid is activated by the adenylation of the carboxyl group 2. Aminoacyl-tRNA synthetase then selects the matching tRNA and "charges" it, transferring the amino acid to the tRNA 3'-OH

For every one NADH molecule oxidized at complex I, how many TOTAL hydrogen ions are pumped across all of the complexes from the mitochondrial matrix to the inner membrane space?

10

for every one NADH molecule oxidized at complex I how many hydrogen ions are pumped across all of the complexes from the mitochondrial matrix to the inner membrane

10 hydrogen ions

How many pyruvate molecules are formed from one molecule of glucose?

2

Preparatory Stage of Glycolysis

2 ATP are used Glucose is split to form 2 glucose-3-phosphate input of energy to breakdown 6 carbon sugar glucose to 2 3 carbon sugars Glucose → Glucose-6-P → Fructose-6-P → Fuctose-1,6-bisP (ATP) → (ADP) (ATP). →. (ADP) Fructose-1,6-bisP → Dihydroxyacetone-P → Glyceraldehyde-3-P 1. hexokinase rxn 2. phosphohexose isomerase 3. phosphofructokinase (PFK-1) 4. adolase 5. Triose Phosphate isomerase (TPI)

Recombinases

2 classes tyrosine recombinases serine recombinases Orientation of recombinase sequences leads to different recombination products

serine recombinases

2 double strand breaks are produced one across each double-stranded DNA fragment fragments on one side of break are rotated so they switch places double strand break is repaired by religation No holliday junction intermediate catalyze phosphoryl-transfer reactions as it has hydroxyl group to initiate nucleophilic attacks on phosphate

A/T base pairs

2 hydrogen bonds easier to break than C/G base-pairs (2 H-bonds vs. 3 H-bonds)

Replication bubble

2 replication forks within that progress away in opposite directions one "leading strand" (continuous synthesis) at each fork one "lagging strand" (discontinuous synthesis) at each fork. When the replication fork gets to ENDS of LINEAR chromosomes, removal of the RNA primers leads to overhangs that can't be filled if not filled chromosomes get shorter each round

DNA nucleotides

2' position is a hydrogen steric problems are not present. Both conformers are possible but the C2'- endo conformation predominates

RNA nucleotide

2' position of the sugar contains an OH, and so the C2'-endo conformation creates steric problems with the nucleobase the C3'endo conformer is preferred. the 2' OH make it more prone to hydrolysis

Arachidonate

20-carbon fatty acid with four double bonds major precursor of eicosanoid hormones precursor for a variety of signal molecules 20 carbons long, collectively called the eicosanoids. short-lived, local hormones that alter the activity of cells in which they are made or nearby. g roles in: reproductive function; inflammation, fever, and pain associated with injury or disease; the formation of blood clots and regulation of blood pressure; and other processes important for human health.

Triplet

3 consecutive bases (CODON) correspond to 1 amino acid. tRNA uses Watson-Crick Franklin base-pairing interactions to read triplet codons in the mRNA

Transcription termination in Eukaryotes

3 different RNA polymerases in Eukaryotes. Each had its own specific and complex initiation and termination requirements Similar to in prokaryotes but more complicated.

RNA polymerase in Eukaryotes

3 forms of RNA polymerase each type has its own initiation specificity (recognizes different DNA sequences as promoters). Transcription also regulated by enhancer elements and other sequences that might be far from the transcription site (complex)

C/G base pairs

3 hydrogen bonds stronger bond

Rotational catalysis/binding change Mechanism of ATP synthase

3 symmetric active sites for ATP production, one on each dimer H+ flux drives ATP synthesis ATP synthase will cause a net breakdown of ATP if conditions are such that net ATP breakdown will move rxn toward equilibrium

Epigenetic regulation:

3 types: Regulation of chromatin structure, Chemical modification of nucleoside, microRNA-mediated regulation

in the reduction step of calvin cycle

3-Phosphoglycerate → 1,3-Bisphosphoglycerate → glyceraldehyde-3-P Glycolysis payoff stage in reverse

citric acid cycle

4 oxidation reaction steps Central energy-yielding path: point of convergence of catabolism of fats, carbohydrate, protein In mitochondria in eukaryotes Intermediates recycled, thus "cycle" Source of precursors for biosythesis final phase of aerobic path of Glucose --> Pyruvate --> Acetate --> CO2 4 dehydrogenases 4 reduced cofactors requires O2 Input: Acetate of acetyl-CoA (2C and 4 reduced bonds) Output: 3 NADH, FADH2, 2 CO2 and a GTP

Receptor Enzyme (Tyrosine-Kinase)

4 types: G protein coupled receptor, Receptor enzyme (tyrosiner kinase), Gated ion channel, Nuclear receptor ligand binding activates tyrosine kinase activity by autophosphorylation kinase activates transcription factor (T) altering gene expression

4 basic receptor types transducing signals

4 types: G-protein coupled receptor, Receptor enzyme (tyrosiner kinase), Gated ion channel, Nuclear receptor

Holliday Junction

4 way DNA structure allows two strands to be moved in coordinated fashion from each double-stranded DNA to the other.

if you have a 16 carbon long fatty acid it will form

8 acetyl-CoA, 7 NADH, and 7 FADH2

Oligonucleotides

<100nt Short dNA sequences can be synthesized chemically

Methanogens

Ancient and ongoing example of anaerobic respirationUsed abundant components of early atmosphere as both e- donor and acceptorAlso fixed CO2prevented earth from freezing

thermodynamics

How much energy is released as a reaction proceeds towards equilibrium

N-glycosidic bond

A bond formed between the anomeric carbon atom and an amine

Transamination reaction

A keto acid and amino acid react to form a new amino acid, and the reaction does not require ATP synthesizes amino acids such as glutamate, aspartate, alanine Glutamate and pyruvate are reactants in a transamination reaction that results in the formation of alanine and alpha-ketoglutarate

GLUT4

A mutation in GLUT4 changes the Kt value from 5 mM (wild type) to 3 mM (mutant). The velocity of glucose entry into a mutant cell would be higher than a cell expressing the wild type version at a blood glucose concentration of 5mM. Insulin triggers release of high affinity glucose transporter (GLUT4) into plasma membrane of cells of adipose (fat) and muscle tissues which activated phosphoprotein phosphatase 1 (PP1) 1. Glucose transporters are stored within cell in membrane vesicle 2. vesicles move to the surface and fuse with the plasma membrane, increasing # of glucose transporters 3. when insulin decreases, glucose transporters are removed by endocytosis forming small vesicles 4. small vesicles fuse with larger endosome 5. patches of endosome with glucose transporters become small vesicles to return to surface when insulin increases

Condensation reaction

A-site N-terminal amine attacks P-sites ester linkage to polypeptide's carbonyl C-terminal end. The polypeptide is transferred from the P-site tRNA to the A-site tRNA in the process. Amino acids added by condensation reaction

Hoogsteen base pairs

A/T, C/G, even G/G Hoogsteen base pairs are possible Far less common that Watson Crick base pairing. Occurs when one base is in the syn conformation. Allows 3 - 4 strands to be present in a helix as part of some nucleic acid structures. Found in damaged DNA and DNA bound by drugs, but may also be present normally to regulate gene expression.

Molecules for RNA synthesis came first

ADP --(Ribonucleotide reductase)--> dADP→ dATP GDP --(Ribonucleotide reductase)--> dGDP → dGTP CDP --(Ribonucleotide reductase)--> dCDP → dCTP UDP --(Ribonucleotide reductase)--> dUDP → dTTP

all life has these cofactors

ATP, NAD, FAD, CoA

Euchromatin

Accessible Transcription of genes can occur here. Marked by histone acetylation. transcriptionally active

acetone

Acetone, a minor ketone body, is not metabolized but is eliminated in the breath. Breath can smell like alcohol in people with Type I diabetes as acetone (ketone body) is exhaled, not used for energy

Aerobic fate of Pyruvate

Acetyl-CoA → CO2 + H2O 1. acetyl-coA production from pyruvarte through citric acid cycle a. Pyruvate Oxidation to Acetyl-CoO 2. Acetyl-CoA oxidation 3. Electron transfer and oxidative phosphorylation

Fatty acid oxidation steps

Activation Transport Beta-oxidation

Lipoic Acid

Acyl- and Redox Carrier on subunit 2; ong arm facilitates shuttling of substrate

Base pairing' interactions

Adenine forms two H bonds with thymine Guanine forms three hydrogen bonds with cytosine

Specificity of base-pairing

Affects genome integrity Hydrogen bonds dictate that A pairs with T and C pairs with G Other base-pairing possibilities are disfavored if nucleobases were chemically modified base-pairing would be disrupted and mutations would be passed down

microRNA-mediated regulation

Altered protein translation mRNA degradation

𝛂-Ketoglutarate Dehydrogenase Complex Of Citric acid cycle

Analogous to pyruvate dehydrogenase: oxidative decarboxylation → thiolester (5C → 4C) Some energy of oxidation conserved in thiolester ( and NADH) Same cofactors (thiamine, lipoate) as PDH Similar E1 and E2 enzymes (common evolutionary origin) Identical E3's

Methanogens

Ancient and ongoing example of anaerobic respiration Used abundant components of early atmosphere as both e- donor and acceptor Also fixed CO2 prevented earth from freezing because Sun was only at 70% of current energy output Higher CO2 levels than present day Methanogens CH4 blanket

DNA methylation

Another form of epigenetic gene regulation affects gene expression and is a heritable modification. 5-methylcytosine is an epigenetically inherited DNA modification. Silences gene expression New methylation marks can be added to DNA sites by de novo methyltransferases The methylation patterns on the parent strand are copied to the daughter stand by maintenance methyltransferases 5-methylcytosine leads to transcriptional silencing. Useful for silencing transposons (to prevent copy/paste) and also turning off gene expression

DNA synthesis

Base activation of 3'OH leads to nucleophilic attack on a nucleoside triphosphate occurs in 5' to 3' direction of the polymer 5' end is the phosphate group To provide a primer on which DNA polymerase can initiate DNA synthesis, the enzyme primase synthesizes a short complementary (10-12nt) RNA sequence. DNA/RNA hybrid will be Aform, allowing it to be detected and eliminated later.

Nucleotide addition

Base activation of 3'OH to allow nucleophilic attack on the 5' phosphate

relationship between 𝝙G and Keq

Bc 𝝙G is a measure of how far conditions are from equilib, they are related 𝝙G° = -6logKeq or 𝝙G° = -RlogKeq

Triacylglycerol<--> fatty acid cycling step 1.

Bile salts emulsify dietary fats in the small intestine, forming mixed micelles

Signaling cascade to activate PKA

Binding glucagon to receptor allows GTP/GDP exchange activating alpha subunits GDP and beta/gamma subunits are released. Activated alpha subunit (when GTP is bound), binds adenylate cyclase, activating cyclase, which catalyzes cyclization of ATP to cAMP. Cyclic AMP (cAMP) binds regulatory subunits of PKA, which releases catalytic subunits (which are now in the active form).

High blood glucose

Binding of glucose allows removal of phosphates and occlusion of active site to inactivate breakdown of glycogen high blood glucose and high blood sugar after eating (hyperglycemic)--> glucose enters beta cells--> oxidized to CO2 and H2O--> generate ATP-->stimulate insulin-->insulin binding activates kinase on cytosilic side--> kinase signal cascading--> GLUT4 movement--> activation of PP1-->dephosphorylation of acetyl-coA carboxylase-->lower blood glucose

Dead dCas9

Binds target DNA but doesnt cut interacts with DNA through base-pairingprogrammable DNA-binding protein makes it easy to modulate gene expression in both prokaryotes and eukaryotes.

repressors in transcription

Block coactivator recruitment Block activator binding to DNA Recruit corepressors

ketoacidosis

Breath can smell like alcohol as acetone (ketone body) is exhaled, not used for energy

acetyl-CoA

Build up of acetyl-CoA allows conversion of acetyl-CoA to ketone bodies in liver mitochondria. signals high energy state signaling gluconeogenesis 3 acetyl-CoA molecules condense to form ketone bodies. Acetyl-CoA CANNOT be converted to pyruvate because appropriate cellular conditions dont exist Fat is broken down into acetyl-coA (aerobic) acetyl-CoA goes through citric acid cycle to produce reduced electron carriers which are oxidized to generate energy acetyl-CoA generated from the breakdown of amino acids and fatty acids does not enter the citric acid cycle in the liver, but acetyl-CoA derived from ketone bodies can enter the citric acid cycle in the brain. 8 Acetyl-CoA (2C) --(ATP + NADPH in)--> palmitate in fatty acid synthesis cholesterol is derived from acetyl-CoA: 18 Acetyl-CoA--(ATP + NADPH in)--> Cholesterol Three acetyl-CoAs are condensed to form HMG-CoA. Acetyl-CoA may be used to synthesize glucose in gluconeogenesis.

The of energy production from sugar to ATP formation in mitochondria

C-C and C-H bonds → NADH and FADH2 → proton gradient → high energy phosphate bonds

signal transduction

Calls receive, process and respond to information from their environment through signaling specificity- amplification- modularity- desensitization/adaptation integration 4 types: G-Protein coupled receptor, receptor enzyme (tyrosine kinase), gated ion channel, nuclear receptor

E. coli

Can grow using glucose or lactose as primary carbon and energy source If cells are grown in glucose and shifted to media (which contains lactose but no glucose) there is a lag phase in growth Cells express genes for enzymes to use lactose that weren't being made Prefers glucose when grown in it No lactose metabolizing enzymes made Can adapt to utilize lactose Even cells grown in both glucose and lactose will weakly express lactose genes Start expressing lactose genes more strongly as they exhaust the glucose supply

Long-Term Effects of Elevated Blood Sugar

Cardiovascular disease and damage to small blood vessels Kidney disease (renal failure) Neuropathy (damage to nerves) - Amputation - ulcers on feet go undetected - Vision loss (leading cause of new case blindness among 18-64 years)

Why does the presence of O2 decrease the rate of glucose consumption?

Cells produce much more ATP per glucose molecule oxidized aerobically, so phosphofructokinase-1 is inhibited, thus slowing the rate of glucose entry into the glycolytic pathway.

Combinatorial control of gene expression

Combination use of activators and repressors

Techniques for making synthetic DNA

Chemical synthesis of short oligonucleotides Polymerase chain reaction (PCR) assembly of DNA fragments and cloning of synthetic genes

Bile acids

Cholesterol is a Precursor of steroid hormones and bile acids it has a hydrophilic region added to it which is released into intestinal lumen and emulsifies fats to make fat globules helps with lipid absorption Act as detergents that render dietary lipids more accessible for digestion by lipases. Synthesized in the liver and stored in the gall bladder until secreted into the small intestine

Triacylglycerol<--> fatty acid cycling step 5.

Chylomicrons move through the lymphatic system and bloodstream to tissues

2. Hydration of Beta-oxidation

Compare with fumarate--> malate

3. Dehydrogenation of Beta-oxidation

Compare with malate--> oxaloacetate has one oxidizable OH bond that becomes a C=O double bond Forms NADH reduced cofactor

1. Dehydrogenation of Beta-oxidation

Compare with succinate → fumarate Results in a C=C double bond and a reduced cofactor being formed (FADH2) typically catalyzes redox reactions

cytochrome c shuttles e- between which complexes

Complex III and IV

Fate of dietary glucose

Complex carbohydrates (starch) broken down to simple sugars (glucose). Transport glucose into cells of small intestine, then into blood stream. Increase of blood glucose, triggers insulin release by pancreas Insulin triggers release of high affinity glucose transporter (GLUT4) into plasma membrane of cells of adipose (fat) and muscle tissues. Insulin signaling triggers growth/synthesis pathways.

Regulation of Cholesterol Synthesis

Covalent modification (de-phosphorylation) of HMG-CoA reductase results in activation. Increase in cholesterol results in proteolytic degradation of HMG-CoA reductase

DNA transposons

Cut/Paste DNA sequence is excised and pasted elsewhere in the genome 1. Transposase binds to short DNA sequences. 2. Forms a synaptic complex on DNA and cleaves adjacent to excise the transposase and transposon DNA 3. Transposon DNA complex binds to target DNa 4. 3'OH groups of the transposon DNA attacks the target DNA, integrating the transposon DNA 5. DNA polymerase and ligase seal the gaps Transposon is cut out from one location and moved to another

complex carbohydrates

animal and plant starches Complex carbohydrates (starch) broken down to simple sugars (glucose).

succinate dehydrogenase

Desaturation is an oxidation (7 useable bonds to 6) E- acceptor FAD (an acceptor like NAD+) is covalently bound to enzyme

methylation

DNA and histones are methylated causes nucleosomes to pack tightly together Transcription factors can't bind the DNA and genes aren't expressed Methylation of histone protein is associated with turning gene expression on and off Histones can be methylated on lysines by histone methyltransferases can be removed by Histone demethylases. associated with inactive gene expression and a compacted heterochromatin state. Methylated histones interact with heterochromatin proteins that oligomerize to coat and compact methylated regions.

Chemical modification of nucleoside

DNA methylation hydroxymethylation

Transcription in Eukaryotes

DNA not accessible Ground state off DNA is wrapped in nucleosomes means it will always take extra effort to transcribe any gene Activators bind to enhancer elements to recruit "coactivators" and the basal machinery to stimulate transcription. basal transcription machinery is needed to be able to assemble Eukaryotic RNA polymerase II at promoter sites at all. The need for such complex control compared to prokaryotes may be owing to the diversity of different cell types and scenarios associated with more complex development

Transcription in prokaryotes

DNA not packaged into chromatin DNA is accessible Ground state on

Telomerase enzyme

DNA polymerase prevent ends of linear chromosomes from shrinking during replication regions of repetitive sequences at end of eukaryotic chromosomes polymerase carries RNA fragment uses RNA fragment as template for DNA synthesis at end of telomeres on parental strand of DNA leading strand is first lengthened

correcting misincorporations

DNA polymerase 3'-5' exonuclease proofreading activity protects agains misincorporation corrected by mismatch repair pathway

Lipids

Fats General term which includes membrane components, hormones, vitamins etc

Oxidation of GLyceraldehyde- 3-P for glycolysis

Dehydrogenase reaction only redox reaction in glycolysis energy of oxidation preserved in Phosphate bond and NADH

Nucleoid

Densely packed state, coiled around protein

Catabolism of lipids

Fats are used as source of energy

Linking number (LK)

Describes the topology of DNA fragment sum you get from counting two different kinds of winding in the structure: Lk = Tw + Wr Tw- twist Wr- writhe cannot be changed by simply deforming the structure. if you were to cut the structure, add or removes some twist, and reseal it, you could change the linking number. if you try to deform a structure to increase or decrease twist, you will introduce writhe into the structure to ensure that the linking number remains unchanged! if you try to introduce writhe into the structure, the number of twists will adapt to ensure the linking number remains unchanged!

Cloning synthetic genes

Designed genes can be cloned into plasmids for propagation and downstream applications

If you went back in time 2.5 billion years, you would

Die b/c there would be no O2 to breathe Find only single celled organisms Get a sunburn more rapidly

Atherosclerosis

Disease that restricts blood flow in vessels Accumulation of fibrous plaques (fatty deposits) • Correlate with specific risk factors Excess LDL becomes oxidized, and the oxidized LDL is ingested by macrophage so the detergent properties of cholesterol cause the cells to appear foamy. the foam cells become trapped in blood vessels hypertensin can cause scar tissue to develop and then atherosclerosis

Coupling

Dives unfavorable reactions via energy of ATP breakdown Preserve some of the energy of very favorable rxns by coupling to ATP synthesis or synthesis of high energy compounds like NADH, acetyl-CoA, 1,3-bisphosphoglycerate, etc Thiamine is necessary for pyruvate dehydrogenase activity so pyruvate levels are elevated in a thiamine deficient person

Lineweaver Burk plot

Double reciprocal plot Plots the inverse of initial velocity and the inverse of substrate concentration 1/V0 = (Km + [S])/(Vmax[S]) Or 1/V0 = Km/(Vmax[S]) + 1/Vmax Linear line

Wildtype Cas9

Double strand breaks

Familial Hypercholesterolemia

Due to genetic mutation in LDL receptor Impairs receptor-mediated uptake of LDL Cholesterol accumulates in the blood and in foam cells. Higher risk of forming plaques. Homozygous individuals can experience severe CVD as youths. People with hypercholesterolemia can develop lipid deposits on the hands and face.

Standard reduction potential E°

E at standard conditions Can be measured relative to hydrogen half cell and used to predict direction of reaction (ΔE) between any pair At standard conditions, higher standard reduction potential gets the e- as it has a higher affinity for e- , lower E° , gives the e-

Oxidation in Pyruvate Dehydrogenase mechanism

E2 rxn covalent intermediate is oxidized by lipoic acid group

Pyruvate Dehydrogenase mechanism

E3 rxns shuttling electrons to a carrier (NAD+) Enables PDH to go another round much of the energy of oxidation preserved in NADH and thiolester bond of acetyl-CoA Acetyl-CoA can enter citric acid cycle during set up reaction there is no oxidation and CO2 is the first byproduct 1. Decarboxylation 2. Oxidation 3. Rearrangement of electrons CO2 formed during the E1 reaction

chemiosmotic part of oath of energy flow to ATP

Electron flow coupled to formation of H+ across mitochondrial inner membrane Then used for ATP synthesis

Proton motive force of chemiosmotic path

Energy of H+ gradient Gradient of anything = chemical potential energy H+ gradient also has charge difference (electrical potential) Required to release ATP that is bound to ATP synthase Mitochondria pump out protons when e- transport active Rapidly shift to lower pH (pH gradient) ATP synthesized with only a gradient required to release the ATP that is bound to ATP synthase

globular protein

Enzyme chymotrypsin is one

HMG-CoA reductase

Enzyme used in phase 1 of cholesterol synthesis where mevalonate is synthesized from acetyl-CoA. D Statins Pharmaceuticals that attenuate the cholesterol Three acetyl-CoAs are condensed to form HMG-CoA. HMG-CoA is reduced to form mevalonate HMG-CoA reductase is a common target of cholesterol-lowering drugs. Covalent modification (de-phosphorylation) of HMG-CoA reductase results in activation of cholesterol synthesis Increase in cholesterol results in proteolytic degradation of HMG-CoA reductase

Mature RNA

Exons 5'cap polyA tail

True or false Oxygen is the only electron acceptor for cellular respiration on our planet today.

False

Fat (cytosol

Fat (TAG) breakdown and mobilization of fatty acids - active Fatty acid synthesis - inactive

lipid transport

Fats ingested in diet Bile salts emulsify dietary fats in the small intestine, forming mixed micelles Intestinal lipases degrade triacylglycerols fatty acids are taken by intestinal mucosa and converted to triacylglycerol triacylglycerol are added with cholesterol and apolipoproteins into chylomicrons these are moved through lymphatic system and bloodstream to tissue lipoprotein lipase activated by apoC-II in capillary converts triacylglycerol to fatty acids and glycerol fatty acids are oxidized as fuel or reesterified for storage

Fatty acid oxidation activation

Fatty acid joined to coenzyme A Enzymes on outer mitochondrial membrane Once inside cell Fatty acids are "activated by acyl-CoA synthetases on the outer membrane of the mitochondria

compartmentalization

Fatty acid synthesis takes place in the cytoplasm. -Fatty acid oxidation is in the mitochondrion. it regulates glucose 6-phosphatase

Triacylglycerol<--> fatty acid cycling step 3.

Fatty acids and other breakdown products are taken up by the intestinal mucosa and converted into triacylglycerols

Triacylglycerol<--> fatty acid cycling step 8.

Fatty acids are oxidized as fuel or reesterified for storage

Triacylglycerol<--> fatty acid cycling step 7.

Fatty acids enter cells

Codon

Fewer tRNA synthetases than codons first two bases in the codon create the coding specificity and form strong Watson Crick-Franklin base pairs and bond strongly to the anticodon of the tRNA. third base in the codon does not make strong interaction and need not be a canonical base-pairing interaction.

Lipolysis

Glucagon in adipose triacylglycerol breakdown via hydrolysis to produce 3 fatty acids and a glycerol fatty acid release, glycerol release fatty acids released are used as a substrate for beta-oxidation for energy production lack of insulin results in increased lipolysis

Histones

Five types of histones: H1, H2A, H2B, H3, H4. Genomic DNA wraps around the histones. DNA + histone nucleoprotein complex is called a nucleosome. Histone modification impacts chromatin compaction Acetylation and methylation

Wobble hypothesis

Flexibility in the 3rd nt of the codon first two bases in the codon create the coding specificity and form strong Watson Crick-Franklin base pairs and bond strongly to the anticodon of the tRNA. third base in the codon does not make strong interaction and need not be a canonical base-pairing interaction. Inosine can base-pair with multiple different nucleobases, making it particularly well-suited to place in the "wobble" position.

membrane

Fluid mosaic model ○ Critical for life and cell function ○ Provide compartments and allow redirection of energy flow into metabolic processes ■ The compartments are selective ■ Barriers to diffusion ■ Origin of active transport ■ Organization of complex reactions ■ Signal transduction Membrane dynamic between liquid ordered and disordered state Membrane can't be rigid or liquid ordered because nutrients need to pass through it Cant have a completely disordered membrane bc too much disorder would cause it to fall apart fluidity and bacterial cells regulated by the lipid content of the bilayer increasing temp increases membrane disorder and membrane risks rupturing favor unsaturated fats at low temp

Sterols

Fused ring system that is hydrophobic, an alkyl tail and a polar head group Important in bile acids, testosterone, estradiol, cortisol, aldosterone Ex: cholesterol

Pyrimidine synthesis (de novo)

Formation of carbamoyl phosphate the same as preparation for urea cycle, except nitrogen comes from glutamine not ammonia. pyrimidine ring is synthesized first

Which step(s) in glycolysis produces ATP?

From 1,3-bisphosphoglycerate to 3-phosphoglycerate From phosphoenolpyruvate to pyruvate.

Which steps in glycolysis require ATP?

From Glucose to Glucose-6-Phosphate From Fructose-6-Phosphate to Fructose-1,6- bisphosphate

Which step(s) in glycolysis produces NADH?

From glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate

Oxidation of which of the following molecules will produce the largest amount of energy?

Molecule with the most C-H bonds

Metabolism

GLucose + NAD+ & FAD + H2O + ADP → CO2 + NADH & FADH2 + ATP

up-regulated/down-regulated

Gene is on = up-regulated Gene is off = down-regulated pathway can be up-regulated or down-regulated leading to higher or lower levels of enzyme

Transposons

Generate phenotypic diversity movement of transposons within a genome means that different cells in the same tissue can have different genomes from each other; genetic mosaics. copy/paste and cut/paste sequences that spread themselves throughout the genome mobile DNA elements that move around genome insert into origin of replication and prevent helicase from binding so replication doest initiate from here doesnt affect rate of cell division causes changes in gene expression if in gene coding region creates genetic diversity induces DNA rearrangements at defined sites. retrotransposons DNA transposons

Combustion

Glucose + O2 → CO2 + H2O

cyclic AMP (cAMP)

Glucose inhibits the production of cyclic AMP (cAMP) As glucose levels decrease, cAMP levels increase cAMP binds to CAP (catabolite activator protein) CAP binds to promoter proximal site and stimulates RNA polymerase recruitment to promoter, making it an activator of transcription

hexokinase rxn of glycolysis

Glucose is catalyzed by a hexokinase enzyme which adds a phosphate to the glucose creating glucose-6-P GLucose phos "coupled" to ATP breakdown Greater than 10000 fold increase in [Glucose-6-P] at equilibrium starting from standard conditions by coupling

Kt value

Glucose transporters with lower Kt values can transport glucose at a higher velocity Brain has low KT so it uptakes glucose at high velocity Have half maximal velocity of transport A mutation in GLUT4 changes the Kt value from 5 mM (wild type) to 3 mM (mutant).

Anaerobic

Glycogen is broken down into glucose 6-phosphate Glycolysis fermentation Energy stored → short term→ stored as glycogen

Glucose 6-Phosphate (G6-P)

Glycogen is broken down into glucose 6-phosphate (anaerobic) Rapid release of G1-P from glycogen favors the isomerization reaction to form Glucose 6-Phosphate (reversible) Phosphoglucomutase catalyzes isomerization of G1-P to G6-P Phosphatase catalyzes hydrolysis of G6-P to glucose. it is dephosphorylated in the ER lumen of the liver for transport H2O in, HPO42- out. regulated by compartmentalization Glucose + ATP--(hexokinase)--> glucose 6-phosphate + ADP in glycolysis glycogen synthesis. step 1. Glucose 6-phosphate (G6P) <--> Glucose-1-phosphate (G1P) high levels of NADPH will inhibit Glucose 6-phosphate dehydrogenase diverting G6P from the PPP to glycolysis The nonoxidative phase of PPP creates fructose 6-phosphate and glyceraldehyde-3-phosphatem which is used in gluconeogenesis to produce glucose 6-phosphate, the glucose 6-phosphate can renter oxidative phase of PPP for more NADPH If body doesnt need ATP or has enough it slows down glycolysis and uses glucose 6-phosphate to convert to glucose-1-phosphate Glucose 6-Phosphate pushed towards glycogen synthesis and not converted back to glucose bc muscle cells dont express glucose 6-phosphatase Pentose phosphate pathway: Glucose 6-phosphate --(2 NADP+ --> NADPH)--> ribulose 5-phosphate

Monosaccharides

Glycogen is directly converted to monosaccharide units by glycogen phosphorylase carbohydrates are monosaccharides and simple sugars like glucose fructose and galactose simplest carbohydrates aldehydes or ketones that contain two or more alcohol groups smallest monosaccharides are composed of three carbons. joined to alcohols and amines through glycosidic bonds forming polysaccharides

Foundation of revolution water as e- donor in photosynthesis

H2O ubiquitous e- donor and sun is free source of energy Basis of food chain for many ecosystems Life no longer dependent on existing energy rich molecules Created ozone layer Certain prokaryotes evolved ability to use waste product O2 as e- acceptor

Glycogen phosphorylase

Glycogen is directly converted to monosaccharide units by it kinase catalyzed transfer of phosphoryl groups (post-translational modification) activates it via structural changes and initiates glycogen breakdown alpha-1,4-glycosidic bonds on each branch are cleaved by glycogen phosphorylase, leaving four residues along each branch. it catalyzes a phosphorolysis reaction that yields glucose 1-phosphate. it cannot cleave near branch points (alpha-1,6 linkage) and can only cleave alpha-1,4-glycosidic bonds breakdown of glycogen through phosphorolysis instead of hydrolysis the energy of the alpha 1-4 bond is used to add phosphate to glucose forming G1P instead of using triphosphate to do so (saves energy) Phosphoprotein phosphatase (PP1) catalyzes removal of phosphates from serines in glycogen phosphorylase

pancreatic beta-cells

Glycolysis Helps them sense blood glucose Insulin secretion is stimulated by metabolism of glucose by beta cells and are secreted by β cells of the pancreas in response to high blood levels of glucose. glucose enters beta cells through GLUT2 and is metabolized to pyruvate which is oxidized to CO2 and H2O increaseed ATP closes K+ channel altering membrane charge and opens Ca2+ channels stimulating release of insulin immune system attacks pancreatic beta cells (autoimmune) in type I diabetes

Leucine

Glycolysis--> PYRUVATE--> alanine, valine, leucine cannot be glucogenic

amino acids derived from glycolysis

Glycolysis--> PYRUVATE--> alanine, valine, leucine glycolysis-->3-PHOSPHOGLYCERATE-->serine-->cysteine, glycine glycolysis and pentose phosphate pathway--> PHOSPHOENOLPYRUVATE + ERYTHROSE 4-PHOSPHATE-->Tryptophan, tyrosine, phenylalanine --> tyrosine

Chromatin

Good for storage but complicates access Packaging DNA into chromatin makes it inaccessible. Characterized by histone acetylation

evolution of pre-mRNA splicing

Group II introns are evolutionarily related to the introns that are removed by the spliceosome as part of pre-mRNA splicing. Host cells came to "tame" group II introns by making their splicing activity contingent on interaction with protein machinery. Eventually these introns became entirely dependent on host for regulated splicing.

"Watson Crick-Franklin"

H-bonding pattern occurs between bases on strands oriented anti-parallel to one another Traditional Watson-CrickFranklin base pairs are anti/anti

nuclear hormone receptor

Have Similar Domain Structures activated by agonists inhibited by antagonists bind to specific regions of the DNA called response elements. complex of receptor and ligand can recruit proteins, called coactivators, that stimulate transcription in unbound form some receptors bind to corepressors and inhibit transcription. 4 domains: 1. DNA binding domain 2. ligand binding domain, 3. activation domain 4. hinge domain

Uncoupling in plants via electron shunt

Heat from rapid metabolic flux Free from normal feedback control No proton H+ pumping, short circuit not coupling Class 20

activities needed to replicate genome

Helicases Topoisomerases DNA ligase Telomerase

Branch migration

Helicases operating on Holliday junction can translocate the position of the cross-over point

Adolase reaction of glycolysis

Hexose → 2 TRioses WHen a pathway is "operating" all actual 𝝙G are negative

A-site (amino) binding

Holds aminoacyl tRNA

E-site (exit) binding

Holds tRNA that will exit

P-site (peptide) binding

Holds tRNA with growing polypeptide attached

inner membrane contains 4 complexes

I, II, III, IV they move e- from NADH to O2 or from succinate/FADH2 to O2 NADH through I → Q → III → cyt c → IV → O2 Succinate/FADH2 through II→ Q → III → cyt c→ IV → O2

homopolymer

If all of the monosaccharides in the polysaccharide are the same, cellulose and glycogen glycogen is branches homopolymer of glucose cellulose is homopolymer of glucose units linked by Beta-1,4-glycocidic bonds.

ADP

In a cell: [ATP]/[ADP][Pi] = ~500 high ratio of ADP/ATP for phosphofructokinase to be reversible In healthy cell ADP to ATP ratio is very low Protons won't flow through ATP synthase unless other substrates (ADP and Pi) are present

Pentose Phosphate Pathway (PPP)

In cytosol required for rapid cell growth like in cancer cells coversion of 3 5 carbon sugars i Glyceraldehyde 3-phosphateFructose 6-phosphate are intermediates in this and in glycolysis NADPH is formed in oxidative phase of pentose phosphate pathway (PPP) when glucose 6-phosphate dehydrogenase reduces NADP+. nonoxidative phase of PPP creates fructose 6-phosphate and glyceraldehyde-3-phosphatem which is used in gluconeogenesis to produce glucose 6-phosphate Two molecules of NADPH are generated in conversion of a hexose phosphate to a pentose phosphate 4 modes: oxidative phase, nonoxidative phase, glycolysis, gluconeogenesis NADPH generated by the pentose phosphate pathway is required to maintain adequate levels of reduced glutathione cell gets NADPH from this pathway: Glucose 6-phosphate --(2 NADP+ --> NADPH)--> ribulose 5-phosphate CO2 is produced in oxidative phase

gene promoter

In euchromatin specifies where RNA polymerase will initiate transcription Specific sequences at defined distances from the intended transcriptional start site provide a "landing strip" for RNA polymerase to bind directly to and initiate

Advanced Glycated End products (AGE)

Increased levels of sugars in prediabetic and diabetic patients over time lead to nonspecific attachment of carbohydrate molecules onto proteins via carbohydrate-nitrogen links lysine and arginine amino acids, or amino termini, proportional to the level of glucose in the body.

Non-Steroidal Anti-Inflammatory Drugs (NSAIDs)

Inhibit Cyclooxygenase (COX) Activity Ibuprofen and naproxen are competitive inhibitors. resemble substrate and block active site

Aconitase step of citric acid cycle

Isomerization Catalyzed by addition/removal of H2O Dehydrogenases catalyze progressive oxidations in clockwise direction fo citric acid cycle

Insulin

Insulin cant be harvested from humans Use to purify insulin from pigs Use Polymerase Chain Reaction to assemble a form of insulin that can be expressed in E. coli with an "affinity tag" to facilitate purification Expression of insulin gene in E. coli will only occur if "lactose" included in media

glycogen

Insulin signaling in the liver activates Phosphoprotein Phosphatase-1 which activates glycogen synthase and glycogen synthesis kinase catalyzes the release of glucose from glycogen Branched homopolymers of glucose largest stores are in liver and muscle The liver breaks down glycogen and releases glucose to the blood to provide energy for the brain and red blood cells. Muscle glycogen stores are mobilized to provide energy for muscle contraction and are not released in response to low blood glucose levels Cellulose and glycogen are both homopolymers of glucose units Humans cannot digest cellulose, but can break down glycogen into individual glucose units Rapid release of G1-P from glycogen favors the isomerization reaction to form Glucose 6-Phosphate Glucagon signaling activates glycogen breakdown directly converted to monosaccharide units by glycogen phosphorylase After 24 hours of fasting, most of stored glycogen in the liver is broken down and released as glucose. A glycogen molecule has five branches coming off the main polysaccharide chain and 1 reducing end during fasting brain cant use fatty acids because they do not cross the blood-brain barrier

regulation of citric acid cycle

Intermediates serve as precursors for biosynthetic pathways "Anaplerotic" rxns replenish (3C + CO2 to 4C

Triacylglycerol<--> fatty acid cycling step 2.

Intestinal lipases degrade triacylglycerols

Immature RNA

Introns and exons

Reversible covalent modification (or post-translation modification)

Key enzymes in pathways can be modified resulting in a change in their activity. like phosphorylation or phosphoryl transfer

phosphorylation

Key enzymes in pathways can be modified resulting in a change in their catalytic activity by Reversible covalent modification (or post-translation modification) transfers the gamma phosphate from ATP to another molecules cellular work depends on ATP energizing other molecules by phosphorylation. proteins are phosphorylated on hydroxyl groups of Serine, threonine or tyrosine by Protein kinase A (PKA) catalyzed by kinase PKA activates lipase via phosphorylation Glucagon signaling pathway leads to the phosphorylation of the bifunctional enzyme, which inhibits the kinase and stimulates the phosphatase glycerol-3-phosphate is formed by phosphorylation of glycerol Fructose 2,6 Bisphosphatase (FBPase-2), which catalyzes the phosphorylation of Fructose 6- Phosphate (F 6-P) forming Fructose-2,6-bisphosphate (F 2,6-BP).

Malate Dehyrogenase of citric acid cycle

L-malate→ Oxaloacetate Highly endergonic Actual conditions when cycle happens must be far from standard Product removal by exergonic citrate synthase rxn Ensures [OAA} extremely low when cycle running; NADH aslo low during active ATP generation

Hypertension

Leads to damage of walls of arteries • May develop scar tissue, then atherosclerosis

Light reactions

Light energy + H2O → chemical rxn (NADPH +ATP) + O2 the ATP and NADPH products are then used in dark reactions

Triacylglycerol<--> fatty acid cycling step 6.

Lipoprotein lipase, activated by apoC-II in the capillary, converts triacylglycerols to fatty acids and glycerol

natural twist (Lk0) of relaxed B-form double-stranded DNA

Lk0 = (# of base pairs)/10.4 Ex: DNA fragment on the right has 5 turns and thus has Lk0 = 5

snowball earth

Loss of methane covered earth in sheet of ice Methane is more potent greenhouse gas than CO2

Genome DNA

Master storage ability to use Watson-Crick-Franklin base pairing to template copying - is possible with either DNA or RNA . B-form (compared to A-form for dsRNA) allows easier access information in DNA in the major groove without need to unwind helix DNA is denatured during genome replication. DNA melts at 5' end of a gene before it is expressed.

Exocytosis

Method by which cells export products for use in another location 1. Molecules are packaged in a vesicle within the cell 2. The vesicle fuses with the cells membrane 3. Vesicle contents are released for use throughout the body depolarization across membrane opening voltage gated Ca2+ channels stimulating insulin release via exocytosis

complex I of inner membrane

NADH Ubiquinone Oxidoreductase Catalyzes oxidation of NADH and reduction of UQ Pumps 4 H+ NADH + H + Q + 4H+(inside) → NADH+ + QH2 + 4H+(outside) increase pool of ubiquinol (QH2)

Oxidative phosphorylation

NADH and FADH2 are oxidized for ATP production e- from NADH aand FADH2 (reducing power) transported via e- transport chain to O2 and energy stored in ATP

are Reduced carbon or light the only sources of energy used by organisms living on earth?

NO

NAD+

Nicotinamide-Adenine-Dinucleotide reduction of NAD+ by 2e- NAD+ --> NADH (oxidized) (reduced)

Decarboxylation in Pyruvate Dehydrogenase mechanism

No oxidation yet E1 rxn releases a carbon dioxide left with substate covalently bound to active site Forms C-H bond from C-C bond

Use of minerals as electron donors

Non C-H e- donor: Fe2+

Warburg effect (1920s)

Normal cells produce lactate only when anaerobic, whereas cancer cells produce lactate under both anaerobic and aerobic conditions Citric acid cycle requires O2 Increased glycolysis enables tumor growth without good blood (O2) supply Lactate can by secreted for other tissues like liver to deal with Cancer cells need as much ATP than non-cancer cells, but glycolysis for ATP needs and use the citric acid cycle for production of starting materials for lipids, proteins, nucleic acids, etc Cancer cells use cycle for biomass

Photosystem II

O2 evolving center 2H2O → 4 H+ + 4e- + O2 Responsible for earth's oxygen e- needed to start it come from H2O

The following equation is properly balanced. 6CO2 + 6H2O → 6O2 +C6H12O6 (hexose). Why is it biochemically wrong?

O2 is derived solely from H2O 6CO2 + 12H2O → 6O2 + C6H12O6 + 6H2O is correct

syn-conformation of nucleotides

Only purine nucleotides can adopt the syn-conformation Can form base pairs called "Hoogsteen" base pairs

Ribosome Translation initiation

Occurs at START codon Different for prokaryotes and eukaryotes

green sulfur bacteria

One reaction center used to make both a gradient and NADH Instead of using water, bacteria uses H2S as source of e- H2S based thought to have evolved before H2O based Easier to remove e- from H2S, thus easier to evolve source of electrons for photosynthetic organisms water isnot the only source of electrons for photosynthetic organisms

Baby with plasma ammonia levels greater than 150 µmol/L (normally 11-32 µmol/L). Its plasma glutamine and alanine are increased above normal and citrulline and arginine are decreased below normal. which enzyme is likely to be mutant?

Ornithine transcarbamylase

Catalysis by Glutamate dehydrogenase

Oxidation rxn to deaminate it (remove amino)

Isocitrate dehyrogenase of citric acid cycle

Oxidative decarboxylation: 6C → 5C

Why does the accumulation of lactate cease after O2 is added?

Oxygen allows the tissue to convert from lactic acid fermentation to respiratory electron transfer and oxidative phosphorylation as the mechanism for NADH oxidation.

Hyperbolic function

Oxygen binding to myoglobin is hyperbolic Without BPG, the binding curve is hyperbolic enzymatic reaction is a hyperbolic function

reaction centers of Chloroplast structure (eukaryotes)

PSI and PSII Membrane embedded complexes of protein chlorophyll and other pigments Different absorption ranges of chlorophylls and pigments expands the range of these solar collectors 2 molecules absorb light energy and transfer it between the molecules until it reaches reaction center. -- Antenna chlorophylls bound to protein Carotenoids

snRNPs (small nuclear ribonucleoproteins)

Pair with RNA transcript snRNAs use base-pairing interactions to locate the intron/exon boundaries within the pre-mRNA

phospholipid synthesis

Palmitate (16C) + glycerol 3-P + Oleic acid (18C) --(ATP in)--> phosphatidate --(CTP in, polar head group)--> phospholipid requires the combination of a diacylglycerol with an alcohol Phosphatidate --(H2O in, Pi out)--> diacylglycerol + alcohol (polarhead group) → glycerophospholipid

rapid cell growth

Pentose Phosphate Pathway is required for rapid cell growth. Ribose 5-phosphate and NADPH are important resources for rapidly dividing cells, such as cancer cells. Cancer cells undergoing aerobic glycolysis divert some of the glucose 6- phosphate into the pentose phosphate pathway for the generation of ribose 5-phosphate and NADPH.

chlorophylls of Chloroplast structure (eukaryotes)

Pigment Primary light collectors Porphyrin ring with complexed Mg2+ Hydrophobic side chain anchors in membrane Absorption spectrum: Chlorophylls differ; complementary λ range

Plasmid based gene expression systems

Plasmid places gene under regulated expression Induce expression, purify protein

anabolism

Precursor molecules: pyruvate acetyl-coAglycolytic intermediates energy usage or storage: Glucose to glycogenFatty acids to fats or phospholipids pentose phosphates to nucleotidesamino acids to proteins

What are the 2 stages of glycolysis?

Preparatory Payoff

Aerobic

Process that requires oxygen Glucose → 6 CO2 30 ATP

Apolipoprotein

Protein embedded in the phospholipid monolayer of lipoproteins.

Electron Transport and ATP production are coupled

Protons won't flow through ATP synthase unless other substrates (ADP and Pi) are present enzymes can't catalyze a part of the overall rxn In coupled mitochondria, e- transport/H+ pumping doesnt occur without ATP production

Purine synthesis (de novo)

Purines are synthesized on a ribose molecule The initial committed step forms 5- phosphoribosyl-1-amine from PRPP and glutamine. Inosinate (IMP) is a common precursor of adenylate (AMP) and guanylate (GMP)

Ribozymes

RNA enzymes specific 3D structures with catalytic binding pocket

Rho-dependent termination:

RNA polymerase transcribes through a stretch of DNA that produces a binding site on the RNA for "Rho factor helicase that begins translocating from the Rho binding site towards the 3' end of the transcript. will unwind the RNA/DNA hybrid that is being used to template polymerization and terminate extension

CRISPR/CAS9 genome modification

RNA-programmable DNA endonuclease Part of the bacterial immune system (cleaves viral DNAs to protect itself) uses Watson-Crick-Franklin base pairing between the "guide RNA" and double-stranded DNA to locate the target site of base-pairing interactions. Tests double-stranded DNA for target sequence by making protein/DNA interaction with short sequence called PAM Extensive pairing leads to cleavage of both DNA strands. 1) use Cas9 to induce a break at a desired location; 2) use synthetic DNA fragment as repair template By programming where double-strand breaks occur in the genome, homology-directed repair can be used to make almost any genetic modification we can imagine

Self splicing introns

RNAs that catalyze their own splicing 2 classes: group I and Group II characterized by distinct structures/sequences and different reaction mechanisms

Formation of Phosphoenolpyruvate in Glycolysis

Rearrange the molecule so phosphate is in high energy state Redistribution of energy 2-phosphoglycerate → phosphoenolpyruvate

Phosphoglycerate Mutase reaction of glycolysis

Rearrange the molecule so phosphate is in high energy state Redistribution of energy 3-phosphoglycerate → 2-phosphoglycerate

Oxaloacetate

Reduced food intake (fasting) slows CAC as oxaloacetate is siphoned away towards making glucose and in gluconeogenesis slowing citric acid cycle. Any molecule that can be converted to either pyruvate, oxaloacetate or DiHydroxyAcetone Phosphate (DHAP) can serve as starting material for gluconeogenesis during gluconeogenesis, levels of oxaloacetate in the liver are greatly diminished because it is being used as a precursor pyruvate carboxylase converts pyruvate into oxaloacetate which is reduced to malate and shuttled to cytoplasm and reoxidized to oxaloacetate with NADH which is then converted to PEP Entry of acetyl-CoA into citric acid cycle requires oxaloacetate.

Transcription

Regulated by DNA binding proteins Make sequence specific interactions with DNA Sequences are read through side-chains that H-bond with DNA bases. DNA binding activity is often separate from regulatory activity (Modularity) DNA sequences are transcribed into RNA by RNA polymerase 1. RNA polymerase unwinds DNA template and uses one strand of DNA as a template to generate a polynucleotide. 2. start of transcription is indicated by the promoter, which is bound by RNA polymerase. 3.Prokaryotes have a single type of RNA polymerase whereas eukaryotes have three types of RNA polymerases 4. In prokaryotes, transcription is terminated either via Rho or through the formation of a hairpin (intrinsic). Eukaryotic transcription termination is complicated.

evolution of H2O photosynthesis

Removed methane from atmosphere CH4 + O2 → CO2 Caused extinction of many microbes Created "snowball earth"

DNA polymerase I

Removes RNA primer and replaces it with DNA. Has 3' to 5' exonuclease activity. Also used in several DNA repair pathways.

Exonuclease

Removes nucleotide(s) from the end of a DNA strand Exonuclease domain of DNA pol removes mismatched nucleotide(s) during DNA synthesis

Nucleotide-excision repair

Repairs UV-induced dimerization damage spans more than single base, base-excision repair won't repair this class of damage distorted DNA structure recognized by surveillance complex Fragment is ~13nt long with UV dimers in the middle Fragment is removed and gaps are filled and sealed using Pol I and Ligase E. coli consists of UvrA, UvrB, and UvrC is termed "excinuclease"

Base excision repair

Repairs deamination and depurination Cleaves off nucleobase using glycosylase to convert problematic bases into "same problem" AP nuclease recognizes abasic sites and nicks the offending backbone stretch of double-stranded DNA with a free 3'OH and a single nucleotide of single-stranded DNA provides a template for DNA polymerase to extend. polymerase can extend past abasic site (long patch); 5' dRP removed by lyase and single abasic site filled by polymerase and ligase (short patch) any process that generates abasic site can be used to trigger base excision repair. EX: Uracil-DNA glycosylase cleaves off Uracil

secondary active transport

Requires an existing gradient formed by a primary transporter transport protein simultaneously moves one molecule against its concentration gradient while letting another flow down its concentration gradient No ATP is used directly in process EX: A protein moves glucose into an intestinal cell against its concentration gradient by simultaneously allowing sodium to move down its concentration gradient

true r false rapid release of glucose can provide energy in the absence of O2

TRUE

early earth

Rich in high energy electrons Organic molecules forming on earth and raining from space No O2 in atmosphere Organic molecules could accumulate in the harsh conditions of early earth Inorganics such as H2, Fe2+ stable/ did not oxidize

B-form double-stranded DNA double-helix

Right-handed helix, 10.4 bp per turn anti-parallel strands Sugar-phosphate backbone on the outside. Nucleobases are on the inside. Better biological function allows proteins access through its wide major groove. A/T and C/G base pairs line the inside of the helix. 2 grooves which provide access to the nucleobases

Poly-A tail

Signals nuclear export Stabilizes mRNA Promotes translation

Plasmid origin of replication (ori)

Sequence that recruits cellular enzymes to initiate replication

Exons

Sequences that remain in RNA transcript EXPressed

Fates of Cholesterol

Small fraction incorporated into membranes of liver cells. most expoted in 3 forms: bile acids, steroid hormones, cholesteryl esters Small fraction converted to oxysterol by adding hydroxyl group, regulator of cholesterol synthesis In other tissues, cholesterol converted to vitamin D.

evolution of citric acid cycle

Some extant anaerobes have unjoined pathways to supply intermediate Complete the loop by evolution of a-ketoglutarate dehydrogenase Creates a cycle that generates "reducing power" when left side direction proceeds when on other side of Keq

Respiring organisms have Defense against reactive oxygen

Some reducing power used to make antioxidants like glutathione to deal with toxic byproducts that result from life with O2

Oxyanion hole in chymotrypsin

Stabilizes the transition state Has NH groups that stabilize the build up of negative charge on the oxygen when it becomes an oxyanion

phosphate translocase (symported)

Symporter that transfers phosphate groups to the matrix to combine with ATP

Z-DNA

Syn-conformation of purine Left handed every other base in a stretch of Z-DNA takes on a different orientation relative to the sugar backbone than the arrangement in B-DNA, Zig zag shape Exists transiently in short stretches of up to 100 base pairs within some right-handed DNA molecules

DNA polymerase III

Synthesizes new strands through a 3'-OH nucleophilic attack. Uses Mg2+ to stabilize the negative charges of the phosphate backbone. Only the alpha phosphate from the dNTP remains. Has 3' to 5' exonuclease activity

true or False? If a reaction has a large and negative standard free energy change (∆G°), product formation will be favored in actual conditions unless the ratio of products to reactants is high enough to drive the reaction in the reverse direction.

TRUE

fixation step of calvin cycle

Takes 5 carbon sugar and splits it into 2 3 carbon sugars

Succinyl CoA synthetase of Citric acid cycle

Takes energy of thiolester (generated by preserving energy of oxidation in previous step) by substrate-level phosphorylation: GTP formed (convertible to ATP)

Steroid-Hormone Receptors

Targets for Drugs Ligands that activate a nuclear hormone receptor are called agonists ligands that inhibit the receptor are called antagonists. Some cancers are dependent on the action of the estradiol-receptor complex, growth is slowed by antagonists EX: vitamin D receptor

Sanger sequencing (ddNTP trick)

Technique for reading out the sequence of DNAs only sequences one clonal DNA at a time exploiting nucleotide structure to read DNA sequence Without a 3'OH, the strand can no longer be extended... Separate DNA fragments based on size fluorescently labeled ddNTPs (one color for each nucleotide) are used in a single reaction. identity of the terminating nucleotide is read out with a laser using fluorescence. based on including chain terminating dideoxynucleotides (ddNTPs) in a polymerization reaction.

Illumina method

Techniques for reading out the sequence of DNAs next generation/high-throughput sequencing multiple DNA fragments sequenced in parallel single DNA molecules are spotted on their "own location" on a slide, locally amplified and sequenced using microscopy to read out each base that is added.

PacBio method

Techniques for reading out the sequence of DNAs next generation/high-throughput sequencing multiple DNA fragments sequenced in parallel single molecules of DNA are trapped in tiny wells, the sequence of that DNA read out by repeatedly resequencing the same fragment over and over again.

Nanopore method

Techniques for reading out the sequence of DNAs next generation/high-throughput sequencing multiple DNA fragments sequenced in parallel the sequence of a DNA is not read out by the action of polymerase. Instead, the DNA is fed through a protein-based pore in a membrane and the changes in conductance as the DNA goes through provides the identify of different bases.

Why do Pyruvate dehydrogenase and ketoglutarate dehydrogenase have identical E3 subunits?

The E3 subunits don't interact with pyruvate or a-ketoglutarate and the reaction that the E3 subunits catalyze have identical substrates and products in both complexes

adenylate cyclase activation

The activated G protein, termed G alphas, stimulates the integral membrane enzyme, adenylate cyclase. leads to the synthesis of the second messenger, cyclic adenosine monophosphate (cAMP). Cyclic AMP activates Protein Kinase A (PKA). Inosinate (IMP) is a common precursor of adenylate (AMP) and guanylate (GMP)

In glycolysis, the conversion of fructose-1,6-bisphosphate (6 carbons) to two trioses has a ∆G° of +23.8 kJ/mol. Why can this reaction proceed in the cell?

The concentration of fructose-1,6-bisphosphate is much higher than the trioses, driving the reaction to the right.

Rubisco

The most abundant protein on earth. Performs Carbon Fixation in the Calvin Cycle.

hydrophobic effect

The most stabilizing force in proteins spontaneous sequestering of the hydrophobic side chains into the interior of the protein in the folded state which releases ordered water Its stability is the difference in free energy between the folded and unfolded state Water soluble proteins have hydrophobic cores ■ Thermodynamic effect that comes from entropy of water and releasing ordered water molecules upon clustering hydrophobic molecules ■ Spontaneous clustering of nonpolar groups to maximize entropy ■ Hydrophobic or nonpolar molecules are insoluble in water bc ■ They interfere with the structure of water and its ability to move across and interact with one another ■ Ordering water molecules around hydrophobic molecule reduces the Entropy of water and is thermodynamically unfavorable

malate + ½ O2 → oxaloacetate + H2O ΔG=-200 kj/mol malate + NAD+ → oxaloacetate _ NADH ΔG=30 kj/mol Reduction potentials: O2 → H2O +0.82 Oxaloacetate → malate -0.17 NAD+ → NADH -0.32 Why is there an ~170 kj/mol difference depending on which e- acceptor accepts e- from malate in these rxns

The reduction potential E° of O2 is much higher than that of NAD+ The reduction of NAD+ to NADH captures the energy of malate oxidation in a biologically useful form (NADH) whereas reduction of O2 doessnt More energy is released when malate is oxidized by O2 than when malate is oxidized by NAD+

Isomerases

Transfer groups to yield isometric forms rearranges the atoms in a molecule. dont change the chemical formula of a molecule

Accessibility of substrates

Transport into or out of cell compartmentalization- oxidation of fatty acids separate from synthesis of fatty acids

Brain

Transports ions to maintain membrane potentialprocesses inputs from body and surroundingssends signals to other organsuses sugar as fuel source glucose is predominant fuel Ketone bodies can provide fuel to the skeletal and heart muscle (and brain under starvation conditions liver breaks down glycogen and releases glucose to the blood to provide energy for the brain and red blood cells. ketone bodies can enter the citric acid cycle in the brain. brain begins to use ketone bodies as a fuel during starvation Brains begins to use ketone bodies as fuel during starvation bc it cannot use fatty acids because they do not cross the blood-brain barrier Brain has low KT so it uptakes glucose at high velocity

Triacylglycerol<--> fatty acid cycling step 4.

Triacylglycerols are incorporated, with cholesterol and apolipoproteins, into chylomicrons

True or false The world's human population strongly correlates with atmospheric concentrations of carbon dioxide.

True

synonymous codons

Two codons that encode the same amino acid are said to be synonymous.

Heterodimer

Two different proteins coming togethe

Homodimer

Two of the same proteins coming together

Tarui disease

Type VII glycogen storage disease PFK-1 deficiency in muscle cells. Fatty acids and ketone bodies provide ATP

tyrosine recombinases

Tyrosine (Y) -OH attacks phosphate in DNA backbone. Forms phosphodiester bond between tyrosine and DNA catalyze phosphoryl-transfer reactions as it has hydroxyl group to initiate nucleophilic attacks on phosphate phosphodiester bond between tyrosine and DNA. Forms Holliday junction intermediate Holliday junction is resolved when tyrosine -OH in recombinase attacks phosphate in DNA backbone Phosphodiester bond between tyrosine -OH and DNA is broken when DNA -OH attacks Recombines final product is formed

ATP

Universal energy carrier Adenosine triphosphate kinetically stable little non-enzymatic breakdown allosterically inhibits phosphofructokinase Basis of large free energy change Electrostatic repulsion between O- Resonance stabilization of products Ionization stabilization and solvation (10 NADH X 2.5 ATP/NADH) + (2 FADH2 X 1.5 ATP/FADH2) + 2 ATP + 2 GTP (1GTP ~ 1ATP) = 32 ATP generated from one molecule of glucose

Adenosine Triphosphate (ATP)

Universal energy carrier kinetically stable little non-enzymatic breakdown allosterically inhibits phosphofructokinase; Basis of large free energy changeElectrostatic repulsion between O-Resonance stabilization of productsIonization stabilization and solvation; skeletal muscle uses it for mechanical work 3 net ATP molecules are produced in muscle during glycolysis from a monomer of sugar positive allosteric effector that stimulates ribonucleotide reductase activity high energy status molecule Glucose is then oxidized to CO2 and H2O to generate ATP Fatty acid synthesis requires ATP and NADPh transamination reaction doesnt require ATPsynthesizes amino acids such as glutamate, aspartate, alanine If body doesnt need ATP or has enough it slows down glycolysis and uses glucose 6-phosphate to convert to glucose-1-phosphate High levels of ATP stimulate release of insulin synthesize carbon fuels chemical energy in metabolism activated carrier of phosphoryl groups phosphoryl transfer from ATP is exergonic ligases is Coupled with the hydrolysis of ATP kinases transfers the gamma phosphate from ATP to another molecules Fasting state goal to make ATP anabolic pathways in animals use ATP and NADH/NADPH to produce large biomolecules Fatty acids and glucose are oxidized producing ATP If ATP is needed, glycolysis predominates. Glucose enters beta cell via GLUT2 and undergoes glycolysis and cellular respiration which generates ATP to bind to and causes ATP-gated K+ channels to close causing K+ to build up in beta cell causing depolarization across membrane opening voltage-gated Ca2+ channels stimulating insulin release via exocytosis in response to eating the cells lining your stomach use ATP to pump large numbers of H+ ions into the stomach no ATP is used directly in secondary active transport Stimulation of the oxidative phase to produce NADPH and the non-oxidative phase to produce glycolytic intermediates that can be used to generate ATP.

Polymerase chain reaction (PCR)

Uses oligonucleotides as primers to amplify DNA fragments by incorporating them into product Repeated cycles of denaturation, primer annealing, and polymerase extension lead to exponential amplification of a target region of DNA. Amplification depends on primer additional sequence not derived from the template itself can be added to the 5' and 3' ends of the amplicon by including it on the primers directly. assemble form of insulin that can be expressed in E. coli with affinity tag to facilitate purification Expression of insulin gene in E. coli will only occur if "lactose" included in media

Catalysis by aspartate aminotransferase

Uses oxaloacetate to transfer amino acid group from glutamate to oxaloacetate forming gaspartate and a-ketoglutarate

Voltage-gated ion channel

Voltage-gated Ca2+ channe signal: depolarization

Fermentations

Ways to anaerobically regenerate NAD+ from NADH to maintain high rate of glycolysis 1. Pyruvate to lactate 2. Pyruvate to ethanol

replication (oris)

Where DNA is melted and unwound by helicases to produce replication bubbles Provide single-stranded DNA templates for synthesis

Coupling electron Transport (ET)

With succinate alone, ET builds up proton gradient until ΔG to drive proton transport "balances" ΔG of ET With ADP + Pi, protons flowing through ATP synthase, ET proceed and O2 consumed ET creates a proton gradient that quickly reaches equilib

Post-translational modification

a regulation fo metabolic pathways Key enzymes in pathways can be modified resulting in a change in their activity. like phosphorylation or phosphoryl transfer EX: Phosphorylation of glycogen phosphorylase it is a major way liver cells activate glycogen phosphorylase as it results in a change in enzyme activity due to reversible transfer of chemical groups to the enzyme, glycogen phosphorylase b is activated by structural changes due to reversible transfer of phosphoryl group via kinase which forms glycogen phosphorylase

Ribosome

a ribonucleoprotein (RNP) that biochemically "translates" mRNAs into proteins Organizes polypeptide synthesis using mRNA/tRNA interactions site of protein synthesis and translation translocates along mRNA and tRNAs between sites to allow the elongation cycle to repeat Responsible for: initiating synthesis at START codon, forming peptide bond between amino acids to make polypeptide and terminating synthesis at STOP codon creates 3 binding sites for tRNA/mRNA interactions

Oxidation reaction

cells obtain most of their energy by this not by direct reaction with oxygen some energy of oxidations is saved as ATP

malonyl-coA

acetyl-CoA carboxylase catalyzes malonyl-coA 1. carboxylation of biotin cofactor Biotin enzyme + ATP + HCO3- <--> CO2-biotin + ADP + Pi + H+ 2. carboxylation of acetyl-coA CO2-biotin enzyme + acetyl-CoA --> malonyl-CoA + biotin enzyme enzymes extend palmitate by adding 2 carbon units using malonyl CoA as a substrate. if type I diabetes is untreated levels of Malonyl-coA will decrease

Fatty acid oxidation transport

across inner mitochondrial membrane into mitochondrial matrix Carnitine carrier system separates cytosolic and mitochondrial pool fatty acids bind to carnitine bc fatty acyl-carnitine can be transported across inner mitochondrial membrane whil fatty acyl-CoA cant once in mito, fatty acids destined for breakdown transport system keeps pools separate in cytosol fatty acid and triacylglycerol synthesis occurs when there is excess carbohydrate malonyl-CoA, product of the 1st step of fatty acid syynthesis, unhibits carnitine acyltransferase

Ketogenesis

activated by glucagon in the liver mitochondria produces ketones for fuel mobilization ketogenesis and gluconeogenesis can occur at same time during fasting

Coenzyme A (CoA-SH)

activated carrier of acyl groups, frequently 2 carbon fragments (acetyl-CoA) Acyl groups are important in catabolism and anabolism transfer of acyl group is exergonic because thioester is unstable Pantothenate (vitamin B5) is precursor

aerobic

activated carriers of electrons for fuel oxidation have higher affinity for electrons than do carbon fuels but lower affinity for electrons than O2 (for aerobic organisms) Fat is broken down into acetyl-coA Citric acid cycle Atp synthesis Energy stored → long term→ converted to fat

Phosphoprotein Phosphatase-1 (PP1)

activated kinase signals cascades--> stimulate movement of GLUT4 to plasma membrane surface, activation of phosphoprotein phosphatase 1 (PP1). activated by insulin after carb rich meal de-phosphorylates acetyl-CoA carboxylase which is inhibited when phosphorylated so the dephosphorylation of ACC by PP1 removes inhibitory activity and allows ACC to catalyze the carboxylation of acetyl-CoA into malonyl-CoA catalyzes removal of phosphates from serines in glycogen phosphorylase insulin is released by pancreas activating PP1 which activates glycolysis, cholesterol synthesis, nucleotide synthesis and fatty acid synthesis allowing body to absorb and store glucose

gluconeogenesis (glycogen breakdown)

active when glucose is scarce, elevated glucagon stimulates it regulated by Fructose 2,6-bisphosphate (inhibits it) majority of the steps in gluconeogenesis occurs in the cytosol. primarily occurs under fasting/starvation conditions. ATP, Citrate, and Acetyl-CoA signal high energy state turning on gluconeogenesis uses glucagon in liver produces glucose rapidly release glucose in the liver from glycogen to restore blood glucose glycogen---> glucose 1. Phosphorylase catalyzes release of glucose-1-phosphate (G1-P) from glycogen. 2.Debranching enzyme rearranges branched glycogen to permit continued breakdown to remove glucose from remaining branches 3. Phosphoglucomutase catalyzes isomerization of G1-P to G6-P 4.Phosphatase catalyzes hydrolysis of G6-P to glucose. not the complete reverse of glycolysis Noncarbohydrate precursors of glucose are first converted into pyruvate or enter the pathway at later intermediates. Any molecule that can be converted to either pyruvate, oxaloacetate or DiHydroxyAcetone Phosphate (DHAP) can serve as starting material for gluconeogenesis so levels of oxaoacetate in liver are greatly diminished Acetyl-CoA CANNOT be converted to pyruvate. after 24 hours of fasting Gluconeogenesis becomes sole pathway of glucose production. must bypass the 3 highly exergonic steps of Glycolysis: The expenditure of six NTP molecules in gluconeogenesis renders gluconeogenesis exergonic cannot proceed unless NADH is available in the cytosol for later protein degradation is initially the source of carbons for gluconeogenesis in the liver.

triacylglycerol

adipose tissue synthesizes stores and mobilizes them primary fuel storage in humans Phosphatase and transferase required to synthesize triacylglycerol from phosphatidate and fatty acyl CoA. chylomicrons contain the highest percentage of triacylglycerols. stored in lipid droplet broken down to produce 3 fatty acids and a glycerol by lipolysis Active lipase catalyzes hydrolysis of triacylglycerols to free fatty acids. triacylglycerols in adipose tissue lipid droplets are broken down by lipase and transported to other tissue glycerol is derived from it biosynthesis of it from acetate after ingestion of excess carbohydrates VLDL particles transport triacylglycerols to adipose and muscle tissue Intestinal lipases degrade triacylglycerols Cholesterol and triacylglycerols are transported in the blood in the form of lipoprotein particles. Insulin stimulates conversion of dietary carbohydrate into triacylglycerols.

C3'endo conformation

adopted in double-stranded DNA more tightly spaced backbone than in B-form DNA double helix adopts what is called the "A-form" DNA structure.

"sugar pucker"

affects nucleic acid tertiary structure determines the distances between phosphates in the phosphodiester backbone,

reduction potential (E)

affinity for e- to become reduced or oxidized

pentose (5-carbon) sugar

affords more conformational complexity to a nucleotide than a static drawing might suggest In three dimensions it is "puckered" and can exist in a C3'-endo or C2'-endo conformation For RNA, it is ribose. For DNA, it is deoxyribose because it lacks the 2' OH. 5' and 3' positions are the key positions involved in building the nucleic acid polymer presence or absence of the 2' OH is the defining difference between RNA and DNA D-ribose 2'-deoxy-D-ribose

fasting state (starvation)

after 48 hours of fasting, Glucagon mediated inactivation of Acetyl CoA carboxylase (enzyme involved in fatty acid synthesis) by phosphorylation occurs pathways ON during fasting (unfed) state low blood glucose (hypoglycemic) Goal: need fuel to make ATP brain begins to use ketone bodies as a fuel. ,Brains cannot use fatty acids because they do not cross the blood-brain barrier after 24 hours of fasting, most of stored glycogen in the liver is broken down and released as glucose. Gluconeogenesis becomes sole pathway of glucose production. Reduced food intake (fasting), slows CAC as oxaloacetate is used in gluconeogenesis. Build up of acetyl-CoA allows conversion of acetyl-CoA to ketone bodies which enter citric acid cycle in brain 3 acetyl-CoA molecules condense to form ketone bodies. Ketone bodies can provide fuel to the skeletal and heart muscle (and brain under starvation conditions liver cells break down triacylglycerols in adipose tissue lipid droplets using lipase and the fatty acids undergo beta-oxidation to generate energy water-soluble ketones, acetoacetate and beta-hydroxybutyrate, supplement glucose as an energy source for the brain during a long fast. gluconeogenesis and ketogenesis could occur at the same time during conditions of prolonged fasting

7-methyl guanosine cap

aids in forming the translation initiation complex and protects the 5' end from degradation also one of the signals for nuclear export.

nitrogenous base of nucleotides

aka "nucleobase" or simply "base" Two types: purine and pyrimidine ability of these bases to interact with one another as "base pairs" will form the basis of molecular information

Urea cycle

all steps do not occur in the cytosol prep reaction occurs in cytoplasm (cytosol in liver) Nitrogen can be delivered from the muscle via alanine one of the N atoms is donated from glutamate one of the N atoms is donated from aspartate 1st metabolic cycle worked out 2 former amino groups added to CO2 to form urea Brings 2 nitrogen together Carbamoyl phosphate and aspartate from the cytoplasm contribute nitrogen to make urea

Phosphofructokinase (PFK-1)

allosterically inhibited by ATP, fatty acids and citrate activity allosterically increased by AMP and ADP irriversible as it wuld require high ADP/ATP ratio to be reversible but in healthy cell ratio is low feedback inhibition: Small molecules bind to areas of the protein that are not the active site. This binding though does alter the conformation of the active site, rendering the molecule unable to hydrolyze ATP. As [ATP] rises, phosphofructokinase-1 is inhibited, thus slowing the rate of glucose entry into the glycolytic pathway.

7 transmembrane helical receptors (7TM)

always associated with G proteins, they're called G protein coupled receptors, GPCR Seven Transmembrane Helical Receptors (7TM) Respond to a variety of signal molecules (ligands). The binding of a ligand outside the cell induces a structural change in the receptor that can be detected inside the cell. Ligand binding to 7TM receptors leads to activation of G proteins

Proteins are synthesized

amino to carboxy terminal. The mRNA is read by the ribosome in the 5' to 3' direction and the first amino acid to be produced makes up the amino termini and will have free amino group. Last amino acid added to polypeptide will contain a free carboxylic acid, making it the carboxy termini amine from incoming amino acid attacks carbonyl of polypeptide chain

Lac Operon

an archetype for explaining gene regulation with activators and repressors to build gene regulation circuitry. if RNA polymerase only bound to promoters when lactose was present, this could produce the desired regulation

gel Electrophoresis

analytical method used on small scale just to analyze proteins and not purify them ● Separation of the basis of charge or size through electric field ● Smaller proteins move very quickly through the gel ● Gel is then stained to visually detect the proteins that have migrated

steps 1, 3 and 10 of glycolysis

are catalyzed by kinases are irreversible because cellular conditions dont exist for them to proceed in reverse direction

Proteins

are degraded in gastrointestinal tract degraded by chymotrypsin and trypsin into smaller peptides in small intestine

Bile salts

are detergents: emulsification let enzymes gain access to fats to break them up

Gibson assembly

assembly of DNA fragments use of a cocktail of enzymes to mimic a "recombination reaction" 5'3' exonuclease (T5) - High-fidelity DNA polymerase (Phusion) - Taq DNA ligase

Sequence-specific (site-directed) recombination

atalyzed by enzymes that bind specific DNA sequences and catalyze nucleophilic attack on the phosphodiester backbone.

worlds human population correlates with

atmospheric concentrations of carbon dioxide.

The 5' end of a gene corresponds to the 5' end of the mRNA and the a. 3' end of the template strand and 3' end of the coding strand. b. 5' end of the coding strand and 3' end of the template strand. c. 5' end of the template strand and 3' end of the coding strand. d. 5' end of the coding strand and 5' end of the template strand.

b. 5' end of the coding strand and 3' end of the template strand. Reason: DNA template and DNA coding strand are complimentary and anti-parallel to one another. Term template strand refers to sequence of DNA that is copied during synthesis of mRNA Opposite strand is called coding strand because sequence corresponds to mRNA that is transcribed Difference between mRNA and coding strand is that thymine from coding strand of DNA will be replaced with uracil for mRNA Direction for both will be the same (5' to 3')

nucleoside

base connected to a pentose (5-carbon) sugar

Ribosome Translation initiation in Prokaryotes

base-pairing interactions between the ribosome RNA and the mRNA at the Shine-Dalgarno sequence position ribosome at intended START codon.

ion exchange chromatography

based on charge for purification ● Uses ionic interactions to purify proteins ● First proteins to come to come through the column will have large negative charge that have been repelled by the column ● The column is negatively charged ● Positively charged ions stick to the column ● Elution removes proteins from the column by changing the salt conditions to a high concentration of salt allowing the ions to get between the protein and the column and shield the charge interactions ● This separates the positively charged proteins from all other proteins in the cell

size exclusion chromatography

based on size to separate proteins ● Porous column acts as molecular sieve ● Very small proteins take the longest path because they can fit through all the channels of the column ● Large proteins will take the fastest path ● Allows us to separate proteins based on size

Autophosphorylation

binding of insulin activates enzyme via autophosphorylation ligand binding activates tyrosine kinase activity by autophosphorylation

Oligomycin

blocks ATP formation by inhibiting ATP synthase no proton flow

Pyrimidine dimer:

bond between T (or C) nucleotides on same strand Corrected by nucleotide-excision repair or direct repair

O-glycosidic bond

bond formed between the anomeric carbon atom and a hydroxyl group of another molecule two monosaccharides linked

Beta-oxidation

bonds occur at the Beta-carbon occurs in mitochondria yields produces enormous amount of energy activation of palmitate requires breaking 2 ~P bonds (one ATP used but 2 bonds broken will count it as two ATP) Oxidation of palmitate has net yield of 106 ATP n# acetal-coAs formed from n-1 beta oxidations

asparagine

can form hydrogen bond with DNA bases R-group of asparagine has hydrogen bond donor and acceptors

Glucose 1-Phosphate (G1-P)

cant be directly added to the glycogen polymer. first converted to the activated form, UDP-glucose. in gluconeogenesis, glucogen Phosphorylase catalyzes release of glucose-1-phosphate (G1-P) from glycogen. alpha-1,4-glycosidic bonds on each branch are cleaved by glycogen phosphorylase, leaving four residues along each branch. Glycogen phosphorylase catalyzes a phosphorolysis reaction that yields glucose 1-phosphate. Glycogen phosphorylase cannot cleave near branch points (alpha-1,6 linkage) and can only cleave alpha-1,4-glycosidic bonds UTP reacts with Glucose 1-phosphate to form UDP glucose and release pyrophosphate Glycogen synthesis: Glucose 6-phosphate (G6P) <--> Glucose-1-phosphate (G1P) 2. Glucose-1-phosphate (G1P) --(UTP and H2O in, PPi--> 2Pi out)--> UDP-glucose Rapid release of G1-P from glycogen favors the isomerization reaction catalyzed by phosphoglucomutase to form Glucose 6-Phosphate

Calvin cycle

carbon fixation converts inorganic CO2 into organic one Glyceraldehyde-3-phosphate is used as a precursor in the synthesis of sucrose and starch carbon fixation reactions Chemical energy (NADPH + ATP) +CO2 → sugars 3 stages: fixation reduction regeneration

Phosphatidate

carried by Cytidine diphosphate diacylglycerol precursor of storage lipids and many membrane lipids. precursor of triacylglycerols and phospholipids Diacylglycerol is activated by reaction of phosphatidate with CTP to form CDP-diacylglycerol used in the synthesis of both glycerophospholipids and triacylglycerols

Cytidine diphosphate alcohol

carries polar head group (alcohol)

Biotin

carries CO2 biotin (vitamin B7) is precursor

Uridine diphosphate-glucose (UDP-glucose)

carries glucose UDP glucose is substrate of glycogen synthase which removes glucose from UDP glucose and adds it to the growing glycogen chain in glycogen synthesis Glucose-1-phosphate (G1P) --(UTP and H2O in, PPi--> 2Pi out)--> UDP-glucose3. UDP-glucose--(glycogen (n residues) in, UDP out)--> GLycogen (n+1 residues) glucose donor synthesis of UDP glucose by UDP-glucose pyrophosphorylase, results in release of pyrophosphate which is irreversible by hydrolysis of pyrophosphate UDP --(Ribonucleotide reductase)--> dUDP → dTTP

Nucleoside triphosphates

carries nucleotides

Tetrahydrofolate

carries one carbon unit and uses Folate (vitamin B9) as precursor

RNA polymerase

catalyze RNA synthesis from DNA templates 1. Activation of 3'OH to attack 5' alpha phosphate of a nucleotide triphosphate (NTP). 2. Magnesium ions (Mg2+) are critical to activate OH and stabilize the negative charge on the phosphates during the reaction does not require a primer to initiate synthesis does not require a separate helicase to unwind the DNA catalyzes its own helicase activity as it adds NTPs to the growing strand. does not have a separate 3'-5' exonuclease site to "proofread" mistakes that it makes Can backtrack upon misincorporation of nucleotides Transcribes subset of genome

phosphoglucomutase

catalyzes isomerization of G1-P to G6-P Rapid release of G1-P from glycogen favors the isomerization reaction to form Glucose 6-Phosphate The reaction is readily reversible and the direction of the reaction depends on the concentration of substrates

Prostaglandin synthase

catalyzes the first step in a pathway leading to prostaglandins, prostacyclins, and thromboxanes. bifunctional enzyme with cyclooxygenase and peroxidase activities held in the membrane by a set of a helices (orange) coated with hydrophobic side chains

UV induced dimerization

cause adjacent, stacked thymines and cytosines to become crosslinked into "pyrimidine dimers". Stacked pyrimidines only Pyrimidine dimers produce bulged, distorted DNA structure that is misread by DNA polymerase and results in replication errors. repaired by nucleotide-excision

lipoproteins

chylomicrons contain the highest percentage of triacylglycerols. have a phospholipid monolayer transports cholesterol to tissue Cholesterol and triacylglycerols are transported in the blood in the form of lipoprotein particles. protein(s) serve to solubilize the lipids and direct them classified acccording to density the greater proportion of lipid, the less dense the particle 4 main classes: chylomicrons, VLDL, LDL, HDL

Plasmid

circular DNA molecule that replicates separately from the host chromosome Occur naturally in bacteria - Usually short (<10kbp) Bacteria can be transformed with exogenous plasmids key components: an origin of replication (ori), a selectable genetic marker, A polylinker

amino acids feed into

citric acid cycle they are converted to acetate and citric acid intermediates

Kinase

class of enzyme kinase activates transcription factor (T) altering gene expression cause group transfer Modify substrates by phosphoryl group transfer phosphorylation transfers the gamma phosphate from ATP to another molecules catalyzes phosphorylation reaction for the release of glucose from glycogen (polysaccharide of glucose) must be phosphorylated to become active. Kinase catalyzed transfer of phosphoryl groups activates Glycogen kinase and the phosphatase are located on the same polypeptide chain. bifunctional enzyme

Drosha and Posha enzymes

cleave 5' and 3' to the hairpin to remove any 5'cap and poly-A structures to produce a pre-miRNA.

Protein sequencing

code for specific shapes ● Used to identify protein of interest ● Used to identify mutations involved in diseases ● Understand shape and function of protein through homology

nucleotides

comprised of a base, (deoxy)ribose and PO4 sugar-phosphodiester forms polynucleotide "backbone" composed of a base, sugar, and phosphate purine and pyrimidine bases pair via hydrogen bonds base conformation affects hydrogen bonding between bases nucleosides with phosphoryl group(s) attached via ester linkage. its structure is essential to DNA-based activities Glycosidic bonds link the base to the ribose ring. Hydrogen bonds form between bases. conformation of the base (syn v. anti) determines how nucleotide bases interact Adenine Guanine Cytosine Thymine (DNA) Uracil (RNA)

energy storage

excess glucose stored for later or used to generate functional biomolecules

Splicing mechanism

contains sequential phosphoryl transfer reaction that begin with a hydroxyl initiating nucleophillic attack on the phosphate group to break the phosphodiester bond between the intron and exon another nucleophillic attack results in the release of the intron and connection of the 2 exons via a new phosphodiester bond 3' and 5' untranslated regions (UTRs) of an mRNA are not removed by splicing (the UTRs are part of the exons).

messenger RNA (mRNA)

contains the information to make a specific protein sequence via translation eukaryotes, final mRNA transcript is shorter than the DNA template from which it is transcribed and further processed in nucleus with modificetions to 5' and 3' ends 7-methyl guanosine " cap " added to the 5' end. have a 5' poly-A tail added on by Polyadenylate Polymerase (PAP) ordering of nucleotides in an mRNA specifies the order of amino acids in a peptide uses Uracil as nucleotide and not tyrosine (T->U) 5'-CCGTTAAACGCTA-3' --> 5'-CCGUUAAACGCUA-3'

Fatty acid oxidation Beta-oxidation

conversion of fatty acid into acetyl-CoA units in mitochondrial matrix 4 step proccess

Phosphohexose isomerase reaction of glycolysis

converts Glucose-6-P < -- > Fructose-6-P 68% glucose-6-P 32% Fructose-6-P

Mg2+

coordinated by DNA polymerase facilitates chemistry activates 3'-OH attack on dNTP phosphate: makes dNTP Pa more electrophilic stabilizes phosphates' negative charge

common sugars

cyclic form an aldehyde can react with an alcohol to form a hemiacetal, while a ketone can react with an alcohol to form a hemiketal. The α form means the the hydroxyl at C-1 is below the plane of the ring. The β form means that the hydroxyl at C-1 is above the plane of the ring

complex IV of inner membrane

cytrochrome oxidase O2 is consumed by respiring organisms accumulates 4e- from 4 cytC and reduces O2 to 2H2O pumps 2H+ per 2e-/4 H+ per O2 evolved to prevent release of toxic partially reduced oxygen species accounts for >99% of O2 we use natural selection favored tight mechanism form a respirasome that moves e- from QH2 to O2

Pasteur effect

decrease in rate of sugar metabolism when microbe shifted from anaerobic to aerobic conditions; occurs because aerobic process generates greater ATP per sugar molecule Yeast glucose consumption much greater under anaerobic than aerobic conditions

deoxyribonucleic acid (DNA)

deoxy- no hydroxyl Genetic molecule typically double-stranded in cells two strands form an anti-parallel, "right"-handed helix molecularly stable helical structure of DNA imparts a natural twist to the relaxed state of polymer. Must be packages to fit inside cell twisted polymer Topological properties constrain its conformation when deformed causing it to supercoil if you try to unwind or overwind it lack a hydroxyl at C2' position

𝝙G at nonstandard conditions

depends on reactant and product concentrations 𝝙G = 𝝙G° + 6log[products]/[reactants]

Prostaglandins

derivatives of membrane glycerophospholipids Complex groups of molecules that influence biological functions like inflammatory response, pain and fever, blood pressure and clotting, reproductive function, induction of labor, regulation of sleep cycle

S-Adenosylmethionine (SAM)

derived from amino acids major donor of methyl groups synthesized from methionine and ATP when the triphosphate of ATP is cleaved to pyrophosphate and phosphate.

Serine

derived from the glycolysis intermediate 3-phosphoglycerate

RNA and DNA

differ in the structure of their nucleotides and which bases they use both joined together through phosphate diester bond

ΔLk

difference between the "natural twist" of double-stranded DNA and the actual topology of the DNA polymer inside the cell ΔLk=Lk-Lk0 ΔLk<0 the DNA is underwound and negative-supercoiling will result. ΔLk>0, the DNA is overwound and positive-supercoiling will result. ΔLk=0 the DNA is relaxed.

Complex tertiary structure in functional RNAs

different regions of secondary structure in nucleic acids can interact to fold up into a more complex 3D structure. Stabilized by metal ions which neutralize electrostatic repulsion between negatively charged backbone phosphates Stabilized by unusual base pair geometries

hormone signaling

directs regulation of metabolic pathways hormones bind receptors initiating signaling cascades causing metabolic changes

Lagging strand

discontinuous synthesis at each fork synthesis of this requires addition of primer by primase extension by DNA pol III until it encounters 5' end of another Okazaki fragment and falls off Primase and Pol III make Okazaki fragments at head of replication fork. Pol I recognizes RNA primers and removes them, replacing with DNA sequence. nicks between fragments remain. Nicked DNA fragments sealed by DNA ligase.

Chemical changes to bases in a DNA molecule

disrupt base-pairing interactions Base alkylation: Deamination Depurination Pyrimidine dimer UV-induced dimerization

Frame shift mutations

disrupt the normal reading frame by inserting or deleting nucleotides that are not multiples of 3 (adding or deleting 3 nucleotides does not disrupt the reading frame) The reading frame downstream of the mutation is shifted giving an entirely different amino acid sequence; a stop codon is usually encountered as the aberrant polypeptide is synthesized.

Base alkylation

disrupts H-bonds that form Watson-Crick base pair Corrected by direct repair; e.g. methyltransferase adds methyl or ethyl groups to nucleobase Alkylated A/T --- disruption of H-bond between A and T Methylation can occur at a site not involved in base-pairing and is thus not a mutagenic repaired by methyltransferase

Nucleotide base tautomerization

disrupts base pairing by changing hydrogen bond donors to acceptors, or vice versa. since base pairing is based on identities of H-bond donor or H-bond acceptor, base pairing is disrupted

Transcription factors

do not alter sequence of DNA hydrogen bond with certain nucleotide functional groups they repress or promote transcription

glycine

doesn't have L-stereoisomer a chiral R group in it is a hydrogen so it is not chiral can occupy torsion angle space because its the smallest amino acid ■ 3 charge states ■ depend on the pH ■ low pH, protonate molecule fully from acidic conditions ■ pH above 2 it deprotonates to become COO- zwitterion with NH3+ group ■ higher pH, deprotonates and we have NH2 and COO- predominant charge state at ph of 7 is zwitterionic neutral form precursor to Porphyrins Porphyrin makes up the heme of hemoglobin, cytochromes, myoglobin porphyrin arises from reaction of glycine with succinyl-CoA.

artificially induced H+ gradient of chemiosmotic path

drives ATP synthesis without substratem redox or electron transport

Plasmid selectable genetic marker

e.g., antibiotic resistance) - Enables selection of cells with the recombinant plasmid

Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)

easy to generate guide RNA easy to program guide RNA

pre-miRNA

ecognized by the enzyme Dicer

Bile salts

emulsify dietary fats in the small intestine, forming mixed micelles

activation domain

enables the receptor to interact with other proteins

°

energy change from standard conditions to equilibrium

ΔE

energy in redox reaction difference in reduction potentials (electron-motive force) ΔG'= -nFΔE' if (+)ΔE°: proceed to the right

catabolism

energy rich molecules: Fats Carbohydrates Proteins energy depleted molecules: CO2 H2O NH3

lyase

enzyme class causes Breaking of various chemical bonds by elimination Often forming double bonds or rings Addition of groups to double bonds like in dehydratases and PEPCK

transferase

enzyme class causes group transfer like in kinases and glycogen synthase Debranching enzyme is a bifunctional enzyme: transferase and glucosidase.

hydrolase

enzyme class causes hydrolysis reactions like in phosphates

isomerase

enzyme class causes transfer of groups within molecule to yield isomeric forms like in Mutases

ligases

enzyme classification ● Catalyze joining together of 2 molecules coupled with hydrolysis of ATP for energy glass of enzyme like in carboxylases and synthetases

Molecular thermometers

enzymes that are temperature dependent As temp increases, enzymes lose their activity

DNA polymerase

enzymes that catalyze DNA synthesis Proof-reading activity adds nucleotides via polymerase domain removes mismatched nucleotides via exonuclease domain from end of DNA use metals to facilitate 3'OH attack and to stabilize the negatively charged phosphates requires a short stretch of existing double-stranded DNA to synthesize off of. Requires a short primer annealed to template strand to initiate synthesis can make mistakes (~1 evert 104-106 bases) if it is denied metal it wont be able to preform looks like a "claw" or "hand" template strand and newly synthesized strand adopt a double helical geometry Synthesis requires 3'OH in order to add the next dNTP. has leading strand and lagging strand Uses deoxyribonucleotide 5'-triphosphates (dNTPs) as substrates 3'OH is essential for reaction Synthesis can only proceed off an already existing doubles-stranded DNA fragment. Mg2+ coordinated by DNA polymerase facilitates chemistry:

in metabolizing cells

equilibrium isnt reached

Gene expression

expression of genes encoding for the enzymes and other proteins involved in the pathway can be upregulated or downregulated leading to higher or lower levels of enzyme Gene is on = upregulated Gene is off = downregulated

G-protein coupled receptor

external ligand Guanine nucleotide binding protein signaled by glucagon binds to receptor to activate intracellular GTP-binding protein regulates enzyme that generates second messenger PCR Seven Transmembrane Helical Receptors (7TM) Ligand binding to 7TM receptors leads to activation of G-proteins The unactivated G-protein (no ligand bound to receptor) is a heterotrimer consisting of an alpha subunit, bound to GDP, and Beta and γ subunits. alpha subunit dissociates from the Betaγ dimer and exchanges GDP for GTP. The activated G-protein, termed G alphas, stimulates the integral membrane enzyme, adenylate cyclase. leads to the synthesis of the second messenger, cyclic adenosine monophosphate (cAMP).

GLUCOSE TRANSPORT

family of glucose transporters, termed GLUT1-14, facilitate the movement of glucose across the cell membrane. Glucose transporters with lower Kt values can transport glucose at a higher velocity Glucose transporters are stored within cell in membrane vesicle vesicles move to the surface and fuse with the plasma membrane, increasing # of glucose transporters hen insulin decreases, glucose transporters are removed by endocytosis forming small vesicles Insulin triggers release of high affinity glucose transporter (GLUT4) into plasma membrane of cells of adipose (fat) and muscle tissues.

Chemical synthesis of short oligonucleotides (synthetic DNA)

fast, easy and cheap. first nucleoside is attached to bead and the DNA strand is extended one base at a time on this support extends the chain in the 3'->5' direction

low blood glucose

fasting state causes low blood glucose (hypoglycemic)--> glucagon stimulated--> phosphorylation of bifunctional enzyme inhibiting kinase and stimulating phosphatase--> ^ blood glucose

4. thiolytic cleavage of Beta-oxidation

fatty acid is now two carbons shorter, acetyl-CoA by itself again no. change of oxidation state in thiolase rxn catalyzed by thiolase enzyme reacts with previously oxidized C=O bond results in new Beta-carbon of the H-C-H bond that can then undergo another cycle of Beta-oxidation

Regulation of citric acid cycle in animals

fatty acids inhibit PDH

Fatty acid elongation

fatty acids longer than 16C palmitate Longer fatty acids are synthesized by enzymes attached to the endoplasmic reticulum. the enzymes extend palmitate by adding 2 carbon units using malonyl CoA as a substrate.

phosphoglycerate kinase reaction of glycolysis

first payoff coupled to substrate level phophorylation

Glutamate

formed by transamination reaction of amino acids Nitrogen enters the mitochondria from the liver cytosol in glutamate and glutamine undergoes catalysis by glutamate dehydrogenase in the liver and catalysis by aspartate aminotransferase in the liver

Glutamine

formed from glutamine synthetase travels through blood to liver once in liver it is deaminated by glutaminase and releases NH4+ group Nitrogen enters the mitochondria from the liver cytosol in glutamate and glutamine

glutamine synthetase

forms glutamine from glutamate by adding NH3 uses glutamate to mop up excess NH4+ in muscle and tissues once glutamine is in liver it is deaminated by glutaminase and releases NH4+ group

Glucagon

fuel energy mobilizing hormone elevated levels of glucagon stimulates gluconeogenesis reduces concentration of fructose 2,6-bisphosphate signals G-Protein coupled receptor stimulates glycogen breakdown through release by alpha cells of pancreas during fasting state ACC is inhibited when phosphorylated via glucagon or epinephrine signaling secreted by pancreas in response to low blood glucose to increase blood glucose and free fatty acid levels no glucagon receptors in muscle Originate in alpha-cells of pancreas in liver: used in Glycogen breakdown, Gluconeogenesis, Ketogenesis in adipose: used in lipolysis Binding glucagon to receptor allows GTP/GDP exchange activating alpha subunits GDP and beta/gamma subunits are released. Glucagon signaling activates glycogen breakdown glucagon receptor is in membrane of liver and fat cells Glucagon signaling activates PKA-->activates lipase via phosphorylation

fatty acids

fuel molecule lipolysis causes fatty acid release oxidized producing ATP for cells used to provide ATP for people with tarui disease contain more energy per gram than carbohydrates liver cells use them to generate energy during fasting transported to other tissues to provide energy via beta-oxidation and aerobic respiration. ■ are the building blocks of lipids ■ Carboxyl group (polar head, hydrophilic) and hydrocarbon chain (aliphatic tail, hydrophobic) saturated and unsaturated (has double bond in hydrocarbon chain) Brains cannot use fatty acids because they do not cross the blood-brain barrier Fatty acids are built by processing one acetate unit at a time can slow down energy producing pathways Longer fatty acids are synthesized by enzymes attached to the endoplasmic reticulum.

ketone bodies

fuel molecule ketogenesis produces them liver distributes them to other tissues Liver mitochondria are the source of ketone bodies Build up of acetyl-CoA allows conversion of acetyl-CoA to ketone bodies. 3 acetyl-CoA molecules condense to form ketone bodies. provide fuel to the skeletal and heart muscle (and brain under starvation conditions When oxaloacetate is depleted via gluconeogenesis, acetyl-CoA is converted into ketone bodies which can enter the citric acid cycle in the brain to produce reduced electron carriers and ATP and frees coenzyme A for continued beta-oxidation of fatty acids. during fasting/starvation brain uses ketone bodies as crucial fuel source level of ketone bodies, almost unmeasurable before a fast, rises dramatically after 2 to 4 days of fasting, with Beta-hydroxybutyrate as the major contributor. ater-soluble ketones, acetoacetate and beta-hydroxybutyrate, supplement glucose as an energy source for the brain during a long fast. Acetone, a minor ketone body, is not metabolized but is eliminated in the breath. provide ATP for people with Tarui disease Ketone bodies that build up in the blood cause a decrease in pH.

Nucleosomes

further compacted into chromatin in linear chromosomes further packaged into a 30nm fiber DNA wrapped around histone proteins.

DNA in eukaryotes

further packaged by wrapping the DNA around proteins called histones to form nucleosomes packaging of eukaryotic DNA has a huge impact on gene expression. must be unpackaged (unwound from histones) before a gene can be transcribed.

histidine

general acid base catalysis positively charged amino acids can deprotanate at high pH 1. Histidine acts general base activity and covalent chemistry. 1. Histidine causes the Breakage of peptide bond with acid chemistry, collapse of transition state and release of product 1 1. Water deprotonation by histidine as a base Also bonded to iron Called proximal histidine because its close to the iron Distal histidine is farther away and hydrogen bonds to the oxygen helping oxygen bind to myoglobin

3' overhang

generated from degradation of RNA primer on lagging strand useful for repair because DNA polymerase can extend off of it to copy the matching target. forms base pairing interactions with target, displacing one DNA strand in a process called strand invasion Polymerase extends off of free 3' end using the homology target as template displaced strand can base pair with the other 3' overhang and also get extended DNA nicks are sealed, cell is left with 2 crossover holliday junction cells must resolve junctions for 2 normal chromosomes by cutting horizontally or cutting vertically and sealing strands

glucagon signaling

glucagon signaling activates glycogen breakdown Liver cells are responsible for replenishing low levels of glucose in the blood NOT muscle cells. activates PKA. PKA activates lipase via phosphorylation. Active lipase catalyzes hydrolysis of triacylglycerols to free fatty acids. glucagon signaling reduces concentration of fructose 2,6-bisphosphate Low blood glucose stimulates glucagon secretion. Glucagon signaling pathway leads to the phosphorylation of the bifunctional enzyme, which inhibits the kinase and stimulates the phosphatase

glycogen synthase

group transfer from transferases UCP-Glucose substrate UTP reacts with Glucose 1-phosphate to form UDP glucose and release pyrophosphate. UDP glucose is substrate of glycogen synthase which removes glucose from UDP glucose and adds it to the growing glycogen chain takes over after end of synthesis of glycogen upregulated by insulin insulin signaling in liver activates Phosphoprotein Phosphatase-1 (PP1) which activates glycogen synthase by catalyzing the removal of phosphate catalyzes synthesis of glycogen chains can only synthesize alpha-1,4-linkages. transfers the glucose residue of UDP glucose to the non-reducing end of a glycogen branch.

NADH + 1/2O2 <--> NAD+ + H2O Reduced, oxidized, oxidized, reduced (e- donor) (e-acceptor)

half reactions: ½ O2 + 2H+ + 2e- → H2O E° = +0.82 (gets e-) NAD+ + 2H+ +2e- --< NADH + H+ E° = -0.32 (gives e-) direction: NADH + H+ + ½ O2 → NAD+ + H2O ΔE° = 0.82 - (-0.32) = 1.14 V

1. ammonia recaptured by synthesis of carbamoyl phosphate

happens in mitochondria adding one of 2 nitrogen to CO2 uses ATP to create high energy intermediates to drive rxn forward

proline

has a aliphatic chain that covalently bonds to its own amino group

yeast tRNAPhe

has the anticodon 5'-GmAA-3' and can recognize the codons 5'-UUC-3' and 5'-UUU-3'.

Km value

have half maximal velocity of the enzyme, the concentration of substrate where you had half max velocity

NAD, FAD, CoA

have one end to carry e- or chemical units and other to base pair at the active site of ribozyme

Single-stranded binding proteins (SSBs)

help keep single-stranded DNA from reannealing

Epigenetics

heritable changes in gene expression not caused by change in DNA

Nucleoside triphosphates:

high energy building blocks used by the cells to synthesize the nucleic acid polymer. 5'ATP

PEP phospho-enol pyruvate

higher energy than ATP PEP hydrolysis does not occur in glycolysis Many key reactions of metabolism involve the synthesis of high energy phosphate compounds

aminotransferase rxn

highly reversible forms glutamate by catalyzing amino acid pyriodoxal phosphate cofactor of enzyme to transfer amino from acid to a-ketoglutarate

cant have 2 RNA polymerase simultaneously transcribing

holds onto both the template and coding strand in the complex. two RNA polymerases trying to transcribe the same gene would block each others ability to continue onward.

RNA polymerase in E. coli (prokaryotes)

holoenzyme is composed of a core enzyme and an additional subunit called sigma (), which provides initiation specificity core enzyme can catalyze the elongation reaction, but it can not initiate RNA synthesis. Alternative sigma factors Each type of sigma factor gives the holoenzyme a unique transcription initiation specificity

nuclear receptor

hormone binding allows receptor to regulate expression of specific genes ligand diffuse across the plasma membrane, as opposed to binding a receptor embedded in the membrane and causing a conformational change in the receptor for steroidal hormones: bind to specific intracellular receptor proteins that subsequently regulate gene expression. steroid or thyroid hormone enters cell, hormone receptor complex acts in nucleus

Pyruvate Dehydrogenase Complex

huge, related enzyme complex multiple copies of 3 units; E1, E2, E3 larger than ribosome localized in the mitochondria NADH is a product inhibited by NADH, ATP and Acetyl-CoA stimulated by NAD+, AMP and CoA cofactors: Thiamine, Pyrophosphate , Lipoate, NAD+ , FAD

Aspartate groups in chymotrypsin

hydrogen bonds to histidine to stabilize + charge on histidine

Integral membrane proteins

hydrophobic domains to anchor them in the membrane Need detergents to remove them

beta-form

hydroxyl at C-1 is above the plane of the ring

generation of free glucose in gluconeogenesis

important control point occurs essentially only in the liver, final step in gluconeogenesis. Glucose 6-phosphate is transported into the lumen of the endoplasmic reticulum. Glucose 6- phosphatase, an integral membrane on the inner surface of the endoplasmic reticulum, catalyzes the formation of glucose from glucose 6- phosphate.

Electron transport chain

in eukaryotes, e- from NADH and FADH2 to O2 occurs in mitochondria evolve from range of e- acceptors

splicing

in eukaryotes, the process of removing introns Preformed in nucleus by spliceosome RNA can act as an enzyme and catalyze RNA splicing

debranching enzyme

in gluconeogenesis, Debranching enzyme rearranges branched glycogen to permit continued breakdown to remove glucose from remaining branches urther metabolism of glycogen requires action of Debranching Enzyme. Debranching enzyme is a bifunctional enzyme: transferase and glucosidase.

Amylose

in plants glucose is stored as starch in the form of amylose linear polymer of glucose units linked by α-1,4-glycosidic bonds and as amylopectin, a branched polymer, with an α-1,6-glycosidic bond for every 30 α-1,4-glycosidic bonds.

fatty acid oxidation

in the mitochondrion. increased by lack of insulin

Insulin signaling cascade

increases expression of specific genes involved in growth and synthesis and decreases expression of genes in glucose production high blood glucose--> insulin --> insulin binding to receptor activates kinase subunit on cytosolic side--> activated kinase signals cascades--> stimulate movement of GLUT4 to plasma membrane surface, activation of phosphoprotein phosphatase 1 (PP1). modulate expression of genes involved in cell growth and biosynthesis--> phosphatase activates enzymes in lipid synthesis and glycogen synthesis; phosphatase inactivates enzymes involved in glucose production

overeating

induces UCPS

Recombination

insert or remove large pieces of DNA at genomic sites Occurs during meiosis Homology-directed recombination Sequence-specific (site-directed) recombination generates variety in distribution of paternal and maternal genes on chromosomes Ensures homologous chromosomes correctly pair during gamete production occurs in response to DNA strand break, during antibody formation and when catalyzed by a reconbinase

HMG-CoA Regulation

insulin activates PP1 which dephosphorylates the enzyme, activating it glucagon activates PKA which is a kinase which phosphorylates the reductase, inactivating the enzyme

glycogen synthesis

insulin in liver stimylates glycogen synthesis inactive in cytosol and lumen of ER in liver phosphatase activates enzymes in lipid synthesis and glycogen synthesis 1. Glucose 6-phosphate (G6P) <--> Glucose-1-phosphate (G1P) 2. Glucose-1-phosphate (G1P) --(UTP and H2O in, PPi--> 2Pi out)--> UDP-glucose 3. UDP-glucose--(glycogen (n residues) in, UDP out)--> GLycogen (n+1 residues) Uridine diphosphate-glucose (UDP-glucose) is the glucose donor Insulin signaling in the liver activates Phosphoprotein Phosphatase-1 which Activates glycogen synthase and glycogen synthesis

anomer

isomers that differ at a new asymmetric carbon atom formed on ring closure

cholesterol if it is converted into bile acid/salt through fat emulsification

it has a hydrophilic region added to it which is released into intestinal lumen and emulsifies fats to make fat globules helps with lipid absorption Act as detergents that render dietary lipids more accessible for digestion by lipases. Synthesized in the liver and stored in the gall bladder until secreted into the small intestine

In vivo conditions of ATP hydrolysis

it is a good energy source Direct ATP hydrolysis isnt a common reaction In a cell: [ATP]/[ADP][Pi] = ~500 ATP provides energy by group transfers, not by direct hydrolysis "Coupling" to ATP breakdown renders amine formation favorable

when universe was formed

it was all hydrogen

Thiamine Pyrophosphate (TTP)

its anion is stable it is a B vitamin

Gibbs free energy equation 𝝙G

kJ/mol value is a function of how far from equilibrium 𝝙G=𝝙H - T𝝙S doesnt predict how rapidly equilibrium is approached if (-): exergonic reaction goes left to right if (+): endergonic reaction goes right to left if =0: reaction at equilibrium

Fumarate

links urea and citric acid cycles from urea cycle can be converted to malate which is transported into mitochondria for citric acid cycle arginine and fumarate are formed in urea cycle when arginosuccinate is split into 2 molecules

Yeast cell lysates fermented

led to end of "vitalism" beginning of modern biochemistry

ATP-gated K+ channel

ligand gated ion channel signaled by ATP when glucose enters beta cell via GLUT2 and undergoes glycolysis and cellular respiration it generates ATP to bind to and causing ATP-gated K+ channels to close causing K+ to build up in beta cell causing depolarization across membrane opening voltage-gated Ca2+ channels stimulating insulin release via exocytosis

Chloroplast structure (eukaryotes)

like mitochondria (has genome, protein synthesis and divides) has triple membrane system has extensive inner thylakoid membrane (highly folded, more surface area for membrane integrated proteins and pigments of light rxn) came from cyanobacteria

A/T and C/G base pairs

line the inside of the DNA helix. A/T and C/G base-pairing interactions are completely orthogonal A will not pair with C; and G will not pair with T. the pairs form units that can be stacked perfectly on top of one another to stabilize the double helical structure C and G are closer together in the alphabet than A and T so they are stronger bond reinforced by base-stacking interactions

Phosphodiester bonds

link nucleotides in polynucleotide backbond covanlent bonds between 3' OH and 5' phosphate of next nucleotide in same polynucleotide strand

Z-scheme

links PSI and PSII in series plants and cyanobacteria Water is split and electrons are excited to higher energy states. light is absorbed so Photosystem II pushes electrons up to high energy level e- then move through proton pump creating proton gradient and ATP is released from F1 on the membrane to a lower energy Photosystem I e- are pushed up again to higher energy level by absorption of more light e-s produce cofactor to convert NADP+ to NADPH Light → electron flow + H+ gradient (inside has lower pH) NADPH and ATP supports the calvin cycle (CO2 to sugar)

cardiovascular disease

long term effect of elevated blood sugar Excess LDL can be phagocytosed (taken up) by macrophages, forming foam cells leading to plaque formation and cardiovascular disease HDL helps remove cholesterol from tissues and foam cells to reduce risk Disease of the heart or blood vessels or both. Fatty deposits develop in the arteries or heart muscle Reduces blood flow to tissues If coronary arteries are blocked, heart cells die

Spontaneous Deamination

loss of exocyclic amino groups Corrected by base-excision repair (glycosylase needed) Replaces a nucleobase amine with a carbonyl group ex : Cytisine → Uracil Adenine → hypoxanthine Guanine → Xanthine Thymine cannot undergo deamination Replaces a nucleobase amine with a carbonyl group ex : Cytisine → Uracil Adenine → hypoxanthine Guanine → Xanthine Thymine cannot undergo deamination repaired by base excision repair

t-state hemoglobin

low affinity binding ○ Stands for tense ○ Has more interaction between subunits ○ It is the predominant state of hemoglobin when theres low concentrations of oxygen ○ Has a gap in the center ○ Favores uptake of protons and release of O2 in the tissue which has lower pH during respiration ○ Histidine is influenced by neighboring carboxylate oxygen group in T state ○ BPG stabilizes the T state

3-phosphoglycerate

lycolysis-->3-PHOSPHOGLYCERATE-->serine-->cysteine, glycine

Ribosome translation in prokaryotes

mRNA are translated as they are transcribed Physical connection between transcription and translation allows for clever regulator strategies. Tryptophan synthesis genes are expressed from trp operon trppL encodes a "leader peptide that contains tryptophan residues

Ribosome Translation in Eukaryotes

mRNAs are translated after transcription and transported out of nucleus

NADP+ and NADPH

mainly for reductive biosynthesis high amount in cytoplasm extra phosphoryl in NADPH is a tag that allows enzymes to distinguish between high potential electrons to be used in anabolism and those in catabolism

Glycerol 3-Phosphate

major pathway of formation is through use of reducing power and dihydroxyacetone phosphate, an intermediate formed in glycolysis. Also is formed through the phosphorylation of glycerol

Acetylation of histones

make DNA more accessible (euchromatin)

Okazaki fragments

make up discontinuous strand "Okazaki Fragments" of the lagging strand joined by DNA ligase + ATP 1. DNA ligase uses ATP to adenylate itself on a lysine residue (forming Ligase-AMP) Ligase + ATP --> Ligase-AMP 2. AMP transferred from DNA ligase to 3. 5' phosphate of nicked DNA strand Ligase-AMP + 5'-P-DNA --> Ligase + 5'AMP-P-DNA 4. 5' end of nick is charged with good leaving group (AMP) and base catalyzed nucleophilic attack by 3'OH seals strand

Methylation of histones

makes DNA less accessible (heterochromatin

enzyme Dicer

makes additional cuts in the hairpin structure. converts the single-stranded RNA hairpin into a double-stranded RNA duplex.

Excinuclease

makes two cuts in the strand with the UV-dimers: one on each side of the lesion. Fragment is ~13nt long with UV dimers in the middle Fragment is removed and gaps are filled and sealed using Pol I and Ligase consists of UvrA, UvrB, and UvrC

porphyrin

makes up the heme of hemoglobin, cytochromes, myoglobin porphyrin arises from reaction of glycine with succinyl-CoA. derived from amino acids

Chromosomes

marked by accessible and inaccessible regions Euchromatin and Heterochromatin come as homologous pairs If a break happens in one chromosome, the other copy could be used as a guide to reassemble it. Staining of a drosophila chromosome reveals heterochromatic regions (dark bands) and euchromatic regions (light regions).

Enzyme

means in leaven or in yeast they lower the activation energy to increase rate of rxn

Natural uncoupler proteins

membrane permeable H carriers dissipate proton gradient and permits electron transport in absence of ATP synthesis cause increased formation of water from oxygen generation of heat increased B-oxidation of fatty acids ET with less energy conserved in ATP Increased metabolic flux, more heat and water than in coupled mitochondria. If mitochondria uncoupled, atp formation inhibited

Ubiquinone (Co-enzyme Q)

membrane soluble mobile carrier

Histone modification

methylation, acetylation, phosphorylation impact chromatin structure and accessibility.

PAthways to fix DNA chemical damage

methyltransferase Base excision repair Nucleotide-excision repair

wobbles

mispairings Different but nontautomeric chemical forms of bases (e.g., bases with an extra proton, which can still bind but often with a mismatched nucleotide, such as an A with a G instead of a T) between "normal" bases that nonetheless bond inappropriately (e.g., again, an A with a G instead of a T) because of a slight shift in position of the nucleotides in space. occurs because the DNA double helix is flexible enough to accommodate slightly misshaped pairings

lipolysis

mobilize fatty acids from fat storage and catalyze them through Beta-oxidation to product acetyl-coA which produces energy in form of reduced e- carriers

modularity

modify protein to make new interaction

Promotor or activator

modular proteins that can influence transcription and each other Lactose metabolite binds repressor and blocks DNA binding RNA polymerase can bind and initiate transcription at promotor In presence of lactose, repressor is converted to inactivate form which doesn't bind to operator RNA polymerase moves past operator and transcribes the lacZ, lacY and lacA genes into single mRNA ligand promotes binding of an activator to DNA resulting in gene activation

Repressor

modular proteins that can influence transcription and each other Negatively regulates RNA polymerase Repressor binds to "operator" sequence and blocks RNAP binding In absence of lactose, repressor remains bound to operator and RNA polymerase is prevented from moving down lac operon and transcribing its genes Repressor sometimes binds with Lac operon with phosphodiester backbone (not sequence-specific interaction) Repressor sometimes binds with Lac operon with specific nucleobases (sequence-specific interaction) If repressor protein is synthesized by cell and no lactose is present it binds to operator site near the promoter and blocks RNA polymerase binding

Aspartate

negatively charged R groups act as acids when protonated and are general base with neutral pH when deprotonated hydrogen bonds to histidine to stabilize + charge on histidine. donates the "second" ammonia used to form urea. used in the reaction where citrulline is converted into argininosuccinate with the aid of ATP

CRISPR/CAS9

new technology making it easy to perform these types of manipulations in complex cell types and organisms easy to generate guide RNA easy to program guide RNA

How is the incorrect base detected and corrected?

newly added base that cannot form canonical base-pairing interactions with the template strand will destabilize the dsDNA structure. end of the growing strand is more flexible, allowing it to adopt a conformation that moves the 3' end into the exonuclease site of the polymerase. Once 3'end enters the exonuclease site, the terminal nucleotide is removed Polymerase has 2nd chance to correct nucleotide improves fidelity of DNA replication by 2-3 orders of magnitude

pyrimidine

nitrogenous base of nucleotides longer word, smaller structure

purine

nitrogenous base of nucleotides shorter word, bigger structure can adopt the syn conformation syn-conformation of purines is observed in a very rare and very unusual alternative DNA structure called Z-DNA.

glucagon receptor

no glucagon receptors in muscle resides in membrane of liver and fat cells it is a g-protein coupled receptor signalled by glucagon

Current Anaerobic Respiration

non-O2 e- acceptor anaerobes dont only have fermentation, Many respire with rance of e- acceptors

Ribosomal RNA

non-coding roles in protein synthesis. make use of structure and base-pairing ability to perform their functions catalyzes the formation of a peptide bond between the amino acids bound to tRNAs at P and A sites

Transfer RNA (tRNA)

non-coding roles in protein synthesis. make use of structure and base-pairing ability to perform their functions serve as biochemical adapters that are "charged" to link "codons" to their specific amino acid Watson-Crick Franklin base-pairing interactions to read triplet codons in the mRNA Amino acids are loaded onto their associated specific tRNAs by aminoacyl-tRNA synthetase. Most organisms have fewer than 45 species of tRNA (<64)

Fructose 2,6-biphosphate

not a member of the glycolysis or gluconeogenesis pathway but is a regulator key regulator of glucose metabolism Fructose 2,6-bisphosphate stimulates phosphofructokinase-1 (PFK-1), and inhibits fructose 1,6- bisphosphatase (FBPase-1). glucagon signaling reduces concentration Fructose 6-phosphate is formed when Fructose 2,6-bisphosphatase (FBPase-2) removes a phosphate from the 2' position of fructose 2,6-bisphosphate (F2,6-bP). Insulin signaling results in the activation of PFK-2, which catalyzes the synthesis of Fructose 2,6 BP and inhibition of gluconeogenesis and activates glycolysis hydrolyzed by phosphofructokinase-2/fructose 2,6-bisphosphatase

Fructose 2,6-biphosphate (F2,6-bP)

not a member of the glycolysis or gluconeogenesis pathway, but it is a regulator of the pathways. has 2 phosphate groups key regulator of glucose metabolism Rates of glycolysis/gluconeogenesis in the liver are adjusted to maintain blood glucose. Fructose 2,6-bisphosphate stimulates phosphofructokinase-1 (PFK-1), and inhibits fructose 1,6- bisphosphatase (FBPase-1). stimulates phosphofructokinase-1 (PFK-1) and inhibits fructose 1,6-bisphosphatase (FBPase-1). activated by phosphoprotein phosphatase 1 (PP1) its levels are adjusted by liver cells by kinase and phosphatase located on same polypeptide chain glucagon signaling reduces concentration Fructose 6-phosphate is formed when Fructose 2,6-bisphosphatase (FBPase-2) removes a phosphate from the 2' position of fructose 2,6-bisphosphate (F2,6-bP).

A-form double-stranded DNA

not primary biological form RNA/DNA hybrids and double-stranded RNA adopt this structure

Writhe (Wr)

number of times each of the curves rotates around the central axis C of the double helix.

twist (Tw)

number of times each of the curves rotates around the central axis C of the double helix.

Chymotrypsin active site

o Aspartate groups - hydrogen bonds to histidine to stabilize + charge on histidine o Histidine group - general acid base catalysis o Serine - covalent catalysis (acylation) § Forms a covalent acyl bond (oxygen carbon bond) with the substrate § Lowers the activation energy of transition state stabilizing the oxyanion o Hydrophobic pocket - helps form enzyme substrate complex for substrate binding and specificity o Oxyanion hole- stabilizes the transition state § Has NH groups that stabilize the build up of negative charge on the oxygen when it becomes an oxyanion

Serine group in chymotrypsin

o covalent catalysis (acylation) § Forms a covalent acyl bond (oxygen carbon bond) with the substrate § Lowers the activation energy of transition state stabilizing the oxyanion ttacks carbonyl carbon forming acyl bond between enzyme and substrate

Lactose intolerance or hypolactasia

occurs because many adults lack the enzyme to degrade lactose. gut bacteria metabolize lactose, generating CH4 and H2, and disrupt water balance in the intestine.

Homology-directed recombination

occurs between homologous sequence Repairs DNA breaks and generates genetic diversity. enzymes are not sequence-specific. one strand must be chewed back to expose free overhang to search for homologous regions 5'->3' exonuclease generates free 3' overhang Polymerase extends off of free 3' end using the homology target as template can use arbitary homologous sequence to direct recombination.

Integration

opposite signals create integrate input from both receptors

genetic code

ordering of nucleotides in an mRNA specifies the order of amino acids in a peptide mapping between 3-nt "codons" in the mRNA and the 20 amino acids ordering of nucleotides in an mRNA specifies the order of amino acids in a peptide it is redundant and universal each amino acid is encoded by more than one codon except methionine and tryptophan Two codons that encode the same amino acid are said to be synonymous. same code is used in all organisms

Gout

painful joints due to deposits of sodium urate crystals High blood levels of urate induce gout allopurinol, a competitive inhibitor of the oxidase, relieves the symptoms Purines are then excreted as xanthine and hypoxanthine.

Blood glucose levels

pancreas secretes insulin and glucagon in result to changes in blood glucose levels determine release of certain hormones in fuel metabolism body tries to maintain optimal levels of blood glucose after and between meals in order to maintain proper functioning of tissues gluconeogenesis rapidly release glucose in the liver from glycogen to restore blood glucose pancreatic beta cells sense blood glucose

facilitated diffusion

passive transport requires participation of a protein carrier Molecules move across the plasma membrane with the help of a channel or carrier molecule

simple diffusion

passive transport of a substance through a membrane without the help of transport proteins diffusion directly across a membrane (no protein involved) Molecules pass directly through the plasma membrane without the assistance of another molecule Oxygen diffuses across membranes of lung cells, into the cells, while carbon dioxide diffuses in opposite direction oxygen moves from high concentration in blood to low concentration in muscle cells via simple diffusion

Catalysis

performed by the RNA component of the ribosome; but depends on protein for structure Termination: mediated by a protein "release factor" that is not a tRNA

Statins

pharmaceutical drugs used to lower cholesterol levels resemble HMG-CoA-->competitive inhibitors of HMG-CoA reductase

Phosphoenolpyruvate (PEP)

phosphoenolpyruvate (PEP) to pyruvate is bypassed in gluconeogenesis by using 2 enzymes as it is highly exergonic onversion of Pyruvate into Phosphoenolpyruvate (PEP) takes two steps and begins with formation of oxaloacetate (inside mitochondria) (Biotin is a required cofactor for carboxylase enzymes) in gluconeogenesis, it is metabolized by the enzymes of glycolysis in the reverse direction until the next irreversible step, the hydrolysis of fructose 1,6-bisphosphate.

Photosynthesis

photo (with light) synthesis (of sugar) carbon cycle of our planet H2O + CO2---(light energy)---> Sugar + O2 (Low energy) (high energy) Sugar + O2 ---(respiration, chemical energy)--->H2O + CO2 (high energy) (Low energy) discovered by Joseph priestly as method of restoring air which has been injured by burning of candles occurs in chloroplast in multicellular organisms evolution of it caused extinction of many microbes

non-coding RNA

play other roles in the cell besides specifying a protein.

Levels of protein structure

primary, secondary, tertiary, quaternary

Triacylglycerides

principle component of fat cells and seeds has 3 fatty acids attached used for energy storage ● Long term energy storage ● Efficient source of energy ○ Highly reduced and carry many electrons that can be used in oxidation rxn ○ Provide >2x the energy source of carbohydrates ○ They are dehydrated and take up less space and weight ■ Bc they pack together through hydrophobic effec and release water ● They are metabolized slowly

melting

process in cell that separates 2 strands of double-stranded DNA for important tasks breaks hydrogen bonds

de novo pathway

process that forms nucleotides from activated ribose, amino acids and ATP

Eukaryotic pre-mRNA

processed into mature mRNA composed of Introns and Exons Additional modification of pre-mRNAs to include a 5' cap and 3' poly-A tail occur. Before exciting the nucleus they are spliced and processed form alternative isoforms single location in genome can oriduce many mRNA variants Surveillance against invaders ensures mRNA in cell has features to provide proof to cell that RNA was made by it Many transposons and viruses produce RNAs that lack these features.

glycolysis

produces insulin in liver insulin is released by pancreas activating PP1 which activates glycolysis 3 ATP are produced in muscle during glycolysis active when glucose is abundant it helps pancreatic beta cells sense blood glucose Glyceraldehyde 3-phosphate and Fructose 6-phosphate are intermediates in both glycolysis and the pentose phosphate pathway high levels of NADPH will inhibit Glucose 6-phosphate dehydrogenase diverting G6P from the PPP to glycolysis AMP and ADP signal low energy state, activating glycolysis if ATP is needed, glycolysis predominates not the complete reverse of gluconeogenesis because gluconeogenesis is highly endergonic so gluconeogenesis must bypass the 3 highly exergonic steps of Glycolysis: Glucose + ATP--(hexokinase)--> glucose 6-phosphate + ADP Fructose 6-phosphate + ATP --(PFK-1)--> fructose 1,6 bisphosphate + ADP Phosphoenolpyruvate + ADP --(pyruvate kinase)--> pyruvate + ATP anaerobic reaction of PTP to pyruvate in glycolysis is highly exergonic Fructose 2,6-bisphosphate regulates it inactive in the cytosol and mitochondria of the liver Gluconeogenesis and glycolysis are reciprocally regulated (one is active while the other is inactive) Cancer cells undergoing aerobic glycolysis

If a reaction has a large and negative standard free energy change (∆G°

product formation will be favored in actual conditions unless the ratio of products to reactants is high enough to drive the reaction in the reverse direction.

Folic Acid Deficiency

promotes birth defects such as spina bifida folic acid plays role in fetal development Insufficient folic acid uptake during pregnancy can result in neural-tube defects

Mutations in genome

proofreading activity missed a mistake modified base will lead to incorrect base-pairing during future DNA replication disrupts ideal B-form structure cells mark parental strands of DNA with methylation marks for correction

RNA world model

proposed that the earliest life forms were mostly RNA

Edman degradation

protein sequencing method of sequencing amino acids in a peptide. In this method, the amino-terminal residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues.

Protein Kinase A (PKA)

proteins are phosphorylated on hydroxyl groups of Serine, threonine or tyrosine by Protein kinase A (PKA) activated by Cyclic AMP secondary messenger The activated C subunits of PKA continue the signal transduction pathway by phosphorylating protein targets that alter physiological functions of the cell. Active PKA (kinase) catalyzes the transfer of a phosphoryl group from ATP to a substrate (enzyme) glucagon signaling activates PKA activates lipase via phosphorylation which catalyzes hydrolysis of triacylglycerols to free fatty acids two molecules of cAMP are required to activate one PKA catalytic subunit, thus 200 à 100 cAMP phosphodiesterase converts cAMP to AMP, which stops activation of PKA

affinity chromatography

purification based on specificity. Uses what the protein has evolved to interact with in the cell Protein usually interacts with a ligand It uses a ligand to bind to and capture our protein of interest allowing all other proteins to come out elute our protein from the column using a high concentration of free ligand allowing for purified preparation of our protein bound to the ligand

Guanine

purine

Thymine (DNA)

pyrimidine

Uracil (RNA)

pyrimidine

cytosine

pyrimidine methylated resulting in 5-methylcytosine causing gene expression to decrease

Chemi-osmotic theory

radical idea Told the rest of the scientific community they were wrong Said proton gradient was used to combine phosphate and ATP

fate of fatty acids

rapid growth--> membranes - phospholipids no/slow growth; abundant fuel --> storage - triacylglycerols Both pathways (TAG synthesis and PL synthesis) begin at the same point: formation of fatty acyl esters of glycerol 3- phosphate. This molecule is called phosphatidate.

liver

rapidly release glucose in the liver from glycogen to restore blood glucose largest stores of glycogen are in liver and muscle Glucagon signaling activates glycogen breakdown Liver cells are responsible for replenishing low levels of glucose in the blood NOT muscle cells. glucagon receptor is in membrane of liver and fat cells liver cells use fatty acids for fuel liver cells activate glycogen phosphorylase through post translational modification levels of oxaloacetate in the liver are greatly diminished because it is being used as a precursor in gluconeogenesis. in cytosol and lumen of ER: Glycogen Breakdown (active), Glycogen synthesis (inactive) in cytosol and mitochondria: gluconeogenesis (active), glycolysis (inactive) in mitochondria: ketogenesis (active), cholesterol synthesis (inactive) After 24 hours of fasting, most of stored glycogen in the liver is broken down and released as glucose. Liver removes the lactate and converts it into glucose, which can be released into the blood

Acetyl-CoA carbosylase (ACC)

rate-limiting enzyme involved in fatty acid synthesis citrate activates ACC by facilitating formation of active polymers of ACC, palmitoyl-CoA inhibits ACC by causing depolymerization of enzyme 3 functional regions: Biotin carboxylase, transcarboxylase, biotin carrier protein requires biotin and catalyzes malonyl-CoA synthesis in 2 steps 1. carboxylation of biotin cofactor Biotin enzyme + ATP + HCO3- <--> CO2-biotin + ADP + Pi + H+ 2. carboxylation of acetyl-coA CO2-biotin enzyme + acetyl-CoA --> malonyl-CoA + biotin enzyme after 48 hours of fasting, Glucagon mediated inactivation of Acetyl-CoA carboxylase by phosphorylation occurs after carb rich meal, insulin stimulates PP1 pathway which de-phosphorylates acetyl-CoA carboxykase (ACC) removing inhibitory activity

Formation of Mevalonate in cholesterol synthesis

rate-limiting step Three acetyl-CoAs are condensed to form HMG-CoA. HMG-CoA is reduced to form mevalonate HMG-CoA reductase is a common target of cholesterol-lowering drugs.

Triose Phosphate isomerase (TPI) reaction of glycolysis

reaction of dihydroxyacetone phosphate with TPI to form glyceraldehyde-3-phosphate

RNA

read by the ribosome, has catalytic properties

Gated ion channel

receptor channel opens or closes in response to concentration of signal ligand or membrane potential

Ligand gated ion channel

receptor ATP-gated K+ channel signal: ATP

microRNA (miRNA)

regulates gene expression Small ~22nt long RNA fragments encoded in genome. Use base-pairing interactions to target mRNAs for regulation Base pairing used to locate micro-RNA target transcribed by RNA polymerase II miRNA containing transcript will adopt a secondary structure that is recognized a pair of enzymes called Drosha and Pasha miRNA is loaded into the RNA-induced silencing complex (RISC) to produce miRISC, which can search for matching mRNA targets in the cytoplasm.

Mismatch repair pathway

recognizes mismatches cleaves daughter strand chews back wrong segment and corrects it MutL0MutS detects mutations and binds to mismatch DNA is threaded until it meets a MutH protein bound to nearby GATC sequence MutL-MutS-MutH complex stimulates cleavage of the unmodified daughter strand to create nick once nicked, nucleases and helicases degrade the unmethylated DNA from point of nick towards mismatch gap is filled by DNA pol III and nick is sealed by DNA ligase

release factor

recognizes stop codon and promotes polypeptide release and translation termination Not a tRNA Proteins that interact with stop codons and promote chain release and termination

salvage pathways

recycle pyrimidine and purine bases use preformed pyrimidine and purine bases, recovered from nucleic acid breakdown, to synthesize nucleotides from activated ribose and bases in nucleotide synthesis utilize preformed bases (pyrimidines and purines) recovered from nucleic acid breakdown, to attach to an activated PRPP.

Ribonucleotides

reduced to deoxyribonucleotides 2'-hydroxyl group of ribose is replaced by a hydrogen atom in a reaction catalyzed by ribonucleotide reductase, acts on all 4 ribonucleotides

Glucose-6-phosphate dehydrogenase (G6-PD)

reduces NADP+. lessens oxidative stress via NADPH and glutathione Glutathione (GSH) helps to prevent damage by reactive oxygen species generated in the course of metabolism high levels of NADPH will inhibit Glucose 6-phosphate dehydrogenase diverting G6P from the PPP to glycolysis The NADPH produced by glucose 6-phosphate dehydrogenase can be used to combat oxidative damage, synthesize fatty acids or synthesize cholesterol. NADPH is formed in oxidative phase of pentose phosphate pathway (PPP) when glucose 6-phosphate dehydrogenase reduces NADP+.

lactate dehydrogenase reaction

regenerates NAD+ for glycolysis.

Oxygen binding

regulated by 2,3-bisphosphoglycerate (BPG) Myoglobin and hemoglobin are oxygen binding proteins Oxygen binding to myoglobin is hyperbolic Oxygen binding forms 6th bond to iron atomOxygen binds at ~120 degree angle to Fe Oxygen binding to hemoglobin is sigmoidal - S shaped binding curve Oxygen binds more strongly to R state and stabilizes it Oxygen binding moves the proximal histidine and pulls on the helix and changes the conformation of the interface

allosteric regulation

regulated metabolic pathways binds to enzyme at distinct active site called allosteric site to change catalytic activity of enzyme Negative (inhibitor) or positive (activator) effector EX: Glucose binds an enzyme, decreasing its activity, which results in slowing down the metabolic pathway that includes this enzyme. EX: citrate activates ACC by facilitating formation of active polymers of ACC, palmitoyl CoA inhibits ACC by causing depolymerization of enzyme

Citrate synthase of citric acid cycle

regulated step driven by large negative 𝝙G of hydrolysis of high energy (coA-linked) form of acetate Uses some of the energy saved in Pyr dehydrog rxn CoA recycled

Phosphatase

remove phosphate groups by hydrolysis dephosphorylation catalyzed by protein phosphatases phosphatase catalyzes hydrolysis of G6-P to glucose

spliceosome

removes introns to produce a mature mRNA composed of only exons. complex machine composed of both proteins and non-coding RNAs called snRNAs Ribonucleoprotein Once intron/exon junctions are recognized, the spliceosome activates and splices 2 steps by nucleophillic attack of a hydroxyl on the phosphodiester backbone

exonuclease domain of DNA

removes mismatched nucleotide(s) during DNA synthesis

Methyltransferase

repairs alkylation alkyl groups can be transferred from nucleobase using an alkyltransferase alkyl group will become permanently attached to cysteine of alkyltransferase entire protein sacrificed to fix one alylated base ex: O6 Alkylguanine and O4 alkylthymine are repaired in such a manner by the sacrificial protein O6 alkylguanine-DNA alkyltransferase (AGT).

Helicases

required to unwind double stranded DNA

Ribosome Translation

requires "start" and "stop" signals that can be regulated Whether or not an mRNA gets translated or not determines if a protein gets made

Fatty acid synthesis

requires ATP and NADPH active after eating sugar cookie in animal cells occurs in cytosol Acetyl-coA carboxylase is rate-limiting enzyme high blood sugar and high blood glucose releases insulin activating PP1 which activates fatty acid synthesis allowing body to absorb and store glucose inactive in cytosol of fat. Inhibited by palmitate Stimulation of the oxidative phase to produce NADPH and the non-oxidative phase to produce glycolytic intermediates that can be used to generate ATP. for fatty acid synthesis 8 Acetyl-CoA (2C) --(ATP + NADPH in)--> palmitate (16C)4 enzyme catalyzed steps: condensation, reduction, dehydration, reduction catalyzes repeating 4 step sequence that elongates fatty acyl chain by 2 carbons each step, uses NADPH as electron donor cant generate fatty acids longer than C16 palmitate Fatty acids are built by processing one acetate unit at a time release of palmitate requires a hydrolysis reaction enzymes of fatty acid synthesis are regulated by adaptive control

Primary active transport

requires energy ion pumps

Topoisomerases

resolve supercoiling from unwinding hydroxyl in tyrosine is used as first nucleophile and 3' OH is used as the 2nd enzymes that change DNA topology by cutting, adjusting and the resealing the DNA structure also needed to resolve supercoiling that develops when the genome is locally unwound for DNA replication or transcription 1. Cut a strand 2. manipulate the DNA strands around the cut to adjust twist 3. Reseal 2 DNA strands

Cutting holliday junction

resolve the junctions Cut horizontally vertically and seal other strands together affects the "origins" of the DNA in each chromosome Leads to exchange between chromosomes

Heart attach

restriction of blood flow to heart, resulting in damage

Histone acetylation

results in loose packing of nucleosomes Transcription factors can bind the DNA and genes expressed Can be acetylated on lysine residues by histone acetyltransferases (HATs) Acetylation can be removed by histone deacetylases (HDACs) Acetylation is associated with active gene expression and open euchromatin state Acetylation reduces affinity of histones for DNA Acetylation marks can also recruit transcriptional activators.

diabetic ketosis

results when insulin is absent Glucose cannot enter cells. All energy must be derived from fats. OAA levels drop CAC slows Free fatty acids are released ketone bodies form Blood pH drops can result in coma and death

Keq is less than 1 and 𝝙G° is positive Keq is larger than 1*, 𝝙G° is negative

reverse rxn favored fwd rxn is favored,

if Tryptophan is low

ribosome will STALL waiting for trp-tRNAs to bind. allows different secondary structure to form that is does not function as a terminator hairpin. RNA polymerase continues transcribing the trp operon, and the ribosome will eventually translate the genes necessary for tryptophan synthesis.

Ribosome Translation initiation in Eukaryotes

s locate AUG start codon by scanning mechanism. Ribosome assembles an initiation complex mediated by 5'm7G cap and 3' poly-A tail interactions. Ribosome scans from 5' cap toward 3' end of mRNA searching for AUG. Multiple proteins and mRNA sequence context cooperate in poorly understood ways to define which AUG is selected. Blocking the interaction between the 5' m7G cap and cap binding protein (eIF4E) prevents initiation Alternative ways to form initiation complexes are used by structured viral mRNAs to initiate translati

Nucleotide synthesis

salvage pathways utilize preformed bases (pyrimidines and purines) recovered from nucleic acid breakdown, to attach to an activated PRPP. can be synthesized de novo (from precursors). Glutamine provides most amino groups Nucleotides can be salvaged from RNA, DNA, and cofactor degradation, then attached to an activated ribose. requires activated ribose (PRPP) PRPP is synthesized from ribose 5-phosphate (PPP) and ATP by PRPP synthetase

Backup state of RNA polymerase

same active site used for polymerization can now act as a nuclease to cleave the growing RNA strand Improves accuracy of RNA polymerase activity by giving enzyme 2nd chance at correct incorporation once initiated, extension proceeds rapidly and the polymerase is said to be in the "elongation state" not physically possible to have two RNA polymerases simultaneously transcribing each strand

cyclic adenosine monophosphate (cAMP)

secondeary messenger AMP is not an enzyme, no amplification at this step. Also, two molecules of cAMP are required to activate one PKA catalytic subunit, thus 200 à 100 stimulates Protein Kinase A (PKA) activity causing phosphorylation of target proteins Binding cAMP by regulatory subunits of PKA dissociates subunits from complex, resulting in activation of the catalytic subunits of PKA activated subunits of PKA signal transduction pathway by phosphorylating protein targets that alter physiological functions of the cell. cAMP phosphodiesterase converts cAMP to AMP, which stops activation of PKA

minor groove of B-form double helix

shallow and narrow

DNA polymerase primer

short piece of DNA annealed to the template facilitates addition of complimentary base-pairs to the growing strand by taking advantage of the energy of base-stacking. Base-pairing provides only a portion of the energy that stabilizes double-stranded DNA structure Base-stacking interactions provide steric and electronic interactions that reienforce base-pairing to stabilize the structure. Base-pairing interactions are more specific in the context of an existing double-stranded DNA structure than on their own

Feedback inhibition

shuts off a products synthesis by negatively regulating an enzyme in the synthesis pathway in phosphofructokinase (PFK-1), Small molecules bind to areas of the protein that are not the active site. This binding though does alter the conformation of the active site, rendering the molecule unable to hydrolyze ATP.

Prokaryote

single ori

bifunctional enzyme

single protein with 2 catalytic activities Debranching enzyme is a bifunctional enzyme: transferase and glucosidase. Ex: kinase and the phosphatase are located on the same polypeptide chain. they are regulated by Low blood glucose which stimulates glucagon secretion which phosphorylates it and inhibiting the kinase and stimulating the phosphatase Ex: PFK-2/FBPase-2

nucleic acid

single strand or multi-stranded polymers built from nucleotides Single-stranded nucleic acid can fold to form secondary structure (transfer RNA (tRNA))

Ligand-binding domain

sites for steroid hormone to bind, causes a structural change in the activation domain that enables the receptor to recruit other proteins to regulate transcription insulin receptor has an extracellular ligand-binding domain

Mitochondria

sites of oxidation inner membrane (ATP synthase) Outer membrane Matrix (soluble was one a free living bacteria that entered symbiosis to form modern eukaryotic cell

respiration

slow combustion of carbon and hydrogen; in photosynthesis: Sugar + O2 ---(respiration, chemical energy)--->H2O + CO2 (high energy) (Low energy) there are many other metabolic routes for living systems to obtain energy than fermentation and O2-based respiration using C-C and C-H bonds

hormone

small molecules or proteins produces by tissue and released into bloodstream act through receptors to change cellular activities bind receptors initiating signaling cascades causing metabolic changes hormone doesnt enter cell hormone binding allows receptor to regulate expression of specific genes Hormone (or ligand) binds to cell surface receptor on membrane of the cell; acts through receptor without entering/exiting the cell.

Acetaldehyde + 2e- + 2H+ → ethanol E°= -0.197 (gets e-) NAD+ + 2e- + 2H+ → NADH + H+ E°= -0.32 (gives e-)

so : Acetaldehyde + NADH → ethanol + NAD+ ΔE°= -0.197 - (-0.32) = +0.123 V

Plasmid polylinker

sometimes called a multiple cloning site Allows the vector to be cut with restriction enzymes

Shine-Dalgarno (SD) sequence

specifies initiation site. encoded in 5' UTR Access to SD provides a means of regulation. mRNA encoding a gene for metabolizing adenine contains an RNA element that can change structure when adenine is present If adenine is absent, the SD is involved in a hairpin structure and inaccessible; n adenine is present, the structure rearranges such that the SD is now available and translation can begin

Genes

specify polypeptide sequences with a genetic code

Glycogenin

starts synthesis of glycogenstops after several glucosyl residues have been added and glycogen synthase takes over.

Knoop Experiment

stepwise breakdown by 2C units, coined term beta oxidation because oxidation occurs at the beta carbon relative to the carboxylic acid fatty acids are oxidized 2 carbon units at a time

sterol

steroid nucleus: four fused rings hydroxyl group (polar head) in the A-ring various nonpolar side chains

endocytosis

stimulated by interaction between LDL receptor and apoB-100 when insulin decreases, glucose transporters are removed by endocytosis forming small vesicles

Ribosome Translation termination

stop codons signal to terminate translation

polysaccharide glycogen (animal starch)

storage form of glucose in animal cells.

lipid bilayer

structure in membrane ■ Only 3 nm thick ■ Holds together the whole cell through the hydrophobic effect ■ Lipids self aggregate to spontaneously form bilayers bc they have cylindrical shape that stack against each other ■ To increase the entropy of water, it folds around on itself forming liposome ■ Lipids are asymmetrically distributed at the inner mono layer and outer monolayer ■ Uncatalyzed transbilayer ('flip-flop") diffusion is very slow ■ Hydrophobic bi-layer is barrier to polar and charged molecules ■ Uncatalyzed lateral diffusion is fast because it is movement in one direction

Internal Ribosome Entry Sites (IRES)

structured RNA elements Use Alternative ways to form initiation complexes

Zymology

study of fermentation

UCP-glucose

substrate for glycogen synthase UTP reacts with Glucose 1-phosphate to form UDP glucose and release pyrophosphate. UDP glucose is substrate of glycogen synthase which removes glucose from UDP glucose and adds it to the growing glycogen chain

deoxyribonucleotide 5'-triphosphates (dNTPs)

substrates for polymerases dATP (adenosine) dTTP (thymidine) dCTP (cytosine) dGTP (guanine) base pair with nucleotides in original template DNA strand Only added to 3' end of last nucleotide

complex II of inner membrane

succinate dehydrogenase catalyzes oxidation of succinate with (FADH# as a bound cofactor) and reduction fo UQ no proton pumping of H+ ions to innter membrane only increases pool of ubiquinol Only membrane-inserted enzyme of citric cycle

Glycolysis

sweet splitting all life has glycolysis 2 stages: Preparatory and payoff net gain of 2 ATP and 2 NADH steps that require ATP: 1. Glucose ---> Glucose-6-P (Hexokinase Reaction)2. Fructose-6-P -----> Fructose-1,6-bisP (Phosphofructokinase PFK-1)

NADPH

synthesize carbon fuels to be stored Fatty acid synthesis requires it chemical energy in metabolism comes from activated carrier of electrons for synthesis of biomoleculeshigh potential of electrons required in most biosynthesis rxns because precursors are more oxidized Nicotinate (Niacin) (vitamin B3) is a precursor reductive biosynthesishigh amount in cytoplasm extra phosphoryl group is a tag that allows enzymes to distinguish between high potential electrons to be used in anabolism and those in catabolism high levels of NADPH will inhibit Glucose 6-phosphate dehydrogenase diverting G6P from the PPP to glycolysis Stimulation of the oxidative phase to produce NADPH and the non-oxidative phase to produce glycolytic intermediates that can be used to generate ATP. NADPH helps to combat oxidative stress by reducing glutathione which reduces reactive oxygen species. NADPH is formed in oxidative phase of pentose phosphate pathway (PPP) biosynthetic reducing power that also helps in detoxification of oxygen free radicals Two molecules of NADPH are generated in conversion of a hexose phosphate to a pentose phosphate Pathways requiring it: Fatty acid biosynthesis, Cholesterol biosynthesis, Neurotransmitter biosynthesis, Nucleotide biosynthesis, Reduction of oxidized glutathione, Cytochrome P450 monooxygenases important resources for rapidly dividing cells NADPH generated by the pentose phosphate pathway is required to maintain adequate levels of reduced glutathione.

Primase

synthesizes short RNA molecule that is used by DNA pol III to lengthen the growing strand. The 3'OH attacks the phosphate

Fuel mobilization

synthesizing fuel molecules. Specifically, glucose through gluconeogenesis and ketones through ketogenesis. breaking down energy storage molecules like fat and glycogen to release fatty acids and glucose mobilized by transporting them to tissues which need energy. Fatty acids and glucose are oxidized producing ATP (energy) for those cells.

melting temperature of double-stranded DNA

temperature at which the helix is half double-stranded, half single-stranded (50% denatured). related to stability Stable helix = high Tm Unstable helix = low Tm Relative A/T and G/C content sets the melting temperature of double-stranded DNA increasing concentration of Mg2+ stabilizes DNA, increasing melting temp Melting DNA breaks H-bonds, therefore more C/G base-pairs make it harder to separate the strands. melting temperature tells us a practical guide for the temperatures that we need to go above to cause double-stranded DNA strands to denature... decreased when # of base pair mismatches increases, when pH is increased and with addition of non-polar solvents

Parent strand of DNA

template to generate the daughter strand

Hemoglobin

tetramer 4 protein chains come together to form quaternary structure are oxygen binding proteins Oxygen transporter All oxygen is transported bound to hemoglobin in erythrocytes or red blood cells Tertiary structure Tetramer Quaternary structure Formed by 2 alpha protein and 2 Beta hemoglobin subunits to form (alpha beta)2 heterotetramer There are 4 binding sites for oxygen and hemoglobin Sigmoidal oxygen binding S shaped binding curve binding affinity is more sensitive to the pressure of oxygen two states: T state and R state the states are in equilibrium with one another Oxygen binding moves the proximal histidine and pulls on the helix and changes the conformation of the interface Hemoglobin transports CO2 and H+H+ is bound to several side chains with pkas that are altered by transition from R to T CO2 is transported by carbamylation of amino terminal amino acid CO2 concentration and pH affect saturation curve

alpha-form

the hydroxyl at C-1 is below the plane of the ring

Rho-independent termination:

transcribes through a stretch of DNA that will produce: A G/C rich region that is capable of adopting a hairpin structure. A U-rich segment downstream of the hairpin hairpin structure causes RNA polymerase to "stall" i.e. stop elongating from its current position. U-rich region downstream of the hairpin can only form weak base-pairing interaction with the template strand combination of stall and weak interaction with the template strand causes the polymerase to fall off.

ribosome

translates RNA into proteins that are light blue, dark blue and purple

if Tryptophan is abundant

translation proceeds quickly and transcription terminating hairpin forms in the mRNA as its being transcribed. This stops transcription of of the trp operon (and translation too).

Passive transport

transport across membrane diffusion along a gradient no energy required Occurs when molecules move across a membrane without energy input Molecules move down their concentration gradients 2 types: simple diffusion, facilitated diffusion

active transport

transport against a gradient of membrane requires energy Occurs when the movement of molecules into and out of a cell requires the input of energy 2 types: primary and secondary EX: in response to eating the cells lining your stomach use ATP to pump large numbers of H+ ions into the stomach primary and secondary A normal cell has a low concentration of sodium on the inside and a high concentration on the outside yet sodium is moved out of cell

adenine nucleotide translocase (antiporter)

transporter that carries ADP into and ATP out of the mitochondrial matrix to support ATP synthesis

corn cob genotypes

transposon insert themselves into pigmentation gene Bronze and inactivate it changes corn cob genotypes: different colored corn

toxic ammonia

travels to liver in the form of glutamate glutamine and alanine the ammonia is converted to glutamine which alters the osmotic balance leading to swelling and coma to get rid of this excess ammonia it is disposed of as urea by adding the amino group to CO2 Urea is excreted through urine

Transcription Termination in Prokaryotes

two primary mechanisms to terminate transcription. disrupts RNA polymerases ability to continue interacting with the template strand. Disengagement with template causes RNA polymerase to 'fall off' the DNA and transcription terminates Rho-dependent termination Rho-independent termination

double-stranded DNA

two strands annealed to each other separation of the two strands ("melting") requires hydrogen bonds break A/T base-pairs are easier to break than C/G base-pairs (2 H-bonds vs. 3 H-bonds) Can measure its stability with melting temperature Melting DNA breaks H-bonds, therefore more C/G base-pairs make it harder to separate the strands.

Triacylglycerols (triglycerides)

type of lipid used for energy storage with hydration they have 6.75X more energy per gram of fat compared to carbohydrate glycerol attached serves as nonpolar cap to molecule Without this cap,the acyl group would serve as free fatty acid which is disruptive to cells at high levels

ribonucleic acid (RNA)

typically single-stranded in cells widely variable secondary structures multi-functional molecule More susceptible to degradation than DNA The 2'OH can lead to breakdown of chain many viruses use RNA for their genomes. Lower stability base-pairing allows the genetic information to still be replicated the 2' OH make it more prone to hydrolysis

Insulin receptor

tyrosine kinase (enzyme linked) receptor signalled by insulin insulin binding to receptor activates kinase subunit on cytosolic side Insulin enters blood stream and binds to receptors on different cell types has an extracellular ligand-binding domain and an intracellular kinase domain requires auto-phosphorylation to become active

complex III of inner membrane

ubiquinone-cytochrome c oxidoreductase oxidizes ubiquinol and reduces cyt c1 Pumps 4 H+ per 2e- transferred to 2 cyt c1 Q cycle -- 1 e- transfer from 2 e- carrier UQ to 1 e- carrier cyt c1 form a respirasome that moves e- from QH2 to O2

L-stereoisomer

○ All amino acids in proteins are L-stereoisomers except glycine ■ b/c the R group in it is a hydrogen so it is not chiral All other amino acids are chiral

Rho Helicases

unwind or "melt" DNA hybrids. This activity breaks hydrogen bonds between strands but does not cleave the backbone. binds to exposed RHo site on forming RNA and move up RNA strand until it reaches RNA polymerase enzyme where it Melts RNA-DNA duplex, causing RNA polymerase to fall off

Group II introns

use 2' OH of adenosine within the intron to initiate cleavage. 3'OH of the 5' exon can then initiate a nucleophilic attack on the phosphodiester backbone at the 3' exon. released intron is a lariat structure. similar to spliceosome both use an A to do the first splice , both remove a lariat intron structure

Group I introns

use a free guanosine nucleotide (separate from the intron sequence itself) to initiate cleavage. 3'OH of the 5' exon can then initiate a nucleophilic attack on the phosphodiester backbone at the 3' exon. released intron is a linear fragment

Anabolic pathways

use small molecules, ATP and reduced cofactors like NADPH to synthesize carbon fuels to be stored uire energy and reducing power for biosynthesis of large molecules that can be used or stored

Amino acids

used as fuel every one has carboxylate group, amino group and unique R group

GLyceraldehyde-3-P

used to assemble other carbohydrates export energy to cytosol

coding RNA

used to template protein synthesis

fermentation of pyruvate to lactate

uses NADH + H+ -> NAD+ for glycolosis to continue, NAD+ must be regenerated Lactate can diffuse out of muscle cells and be converted to glucose and glycogen in liver Net gain of 2 ATP when you convert glucose to pyruvate keeps metabolism going yogurt is thick because lactate accumulates In fermentation energy is given back to substrate NADH is a reduced cofactor

arginase enzyme

uses water to hydrolyze off urea and ornithine from arginine ornithing then goes back through urea cycle

DNA replication

using a template strand to add complimentary nucleotides Semi-conservative each daughter helix gets one strand from parent and one from new strand parent strand of DNA serves as template to generate daughter strand double -stranded DNA is going to need to be unwound to copy both strands. requires energy as double helix is stable structure enzyme joins strands Incorrect base incorporation corrected by DNA polymerase

base stacking interactions

van der Waals interactions between hydrophobic nucleobase faces (steric effects) pi-stacking (electronic effects) reinforce A/T and C/G hydrogen bonding interactions to drive stabilization in larger context of the double-stranded DNA helix demands complimentary between the nucleobases in each strand provides the basis for genetic information storage, replication, and transmission within nucleic acid polymers. stabilizes polynucleotide structures

phages

viruses that infect bacteria uses approach of transposons to integrate into pecific sites in their bacterial host's genome.

Voltage-gated Ca2+ channel

voltage-gated ion channel signaled by depolarization K+ build up in beta cell causes depolarization across membrane opening voltage-gated Ca2+ channels stimulating insulin release via exocytosis

amino acid catabolism

when amino acids are broken down the ammonia ion is left behind (NH4+) produces toxic ammonia

gall bladder stones

when excess cholesterol is present in bile it precipitates these lead to inflammation of the gall bladder, a condition called cholelithiasis.

lactate dehydrogenase

when muscles contract lactate is produced and released into blood and lactate dehydrogenase catalyzes the formation of pyruvate from lactate Pyruvate can by formed from muscle-derived lactate in the liver \Lactate produced by muscle during contraction is released into the blood. Liver removes the lactate and converts it into glucose, which can be released into the blood Cori cycle

major groove of B-form double helix

wide and deep Proteins can bind to double-stranded DNA through the major groove in a sequence specific manner

in hypothetical pathway, step with the largest negative 𝝙G

would be catalyzed by an allosterically regulated enzyme dont go both directions under cellular conditions

anaerobically

yeast can only make ATP by glycolysis Glucose → 2 Ethanol 2 ATP

Pay off stage of glycolysis

yields 2 ATPs and 1 NADH for each carbon sugar 1,3-Boisphosphoglycerate and Phosphoenolpyruvate have high phosphate group transfer potential 1. Oxidation of GLyceraldehyde-3-P 2. Phosphoglycerate Kinase 3. Phosphoglycerate Mutase 4. Formation of Phophoenolpyruvate

burning glucose

yields 2840 kj/mol 50% captured in ATP formation

If you ingested a non-toxic dose of 2,4-DNP daily and didn't change your eating habits, what would happen? Why>

you would lose weight your metabolism is readjusting to burn more calories to get enough e-transport to meet ATP needs In the presence of sub-lethal doses of DNP the rate of B-oxidation of fatty acids and the formation of water increase lack of ATP is lethal

DNA polymerases make mistakes

~1 every 104 -106 bases occasionally a nucleobase will tautomerize into a rare form in which the position of the H-bond donor/acceptors are different. Base-pairing arrangements between rare tautomeric forms can lead to misincorporation into the growing DNA strand. Tautomeric forms and wobble pairs can lead to addition of a non-complimentary nucleotide. cause instabilities that cause the growing DNA strand to get passed into a 3'->5' exonuclease site on the polymerase.

NADH + H+ + ½ O2 → NAD+ + H2O ΔE°=1.14 V

ΔG°'= -(2 e-)(96.5 kJ/mol V)(1.14 V) = -220 kj.mol

SDS

○ Anionic detergent ○ Binds strongly to protein and denatures them ○ SDS polyacrylamide gel electrophoresis (PAGEe) ○ Unfolds the protein and coats it with negative charge from the sulfate group ○ It evens out the charge to mass ratio of proteins ○ Small proteins bind less SDS ○ Large proteins bind more SDS ○ They are hen separated by size ○ For protein analysis not protein purification

Glutamate

○ Aspartate and glutamate are negatively charged R groups act as acids when protonated and are general base with neutral pH when deprotonated

amino acids

■ Amino acids are building blocks of proteins 20 amino acids in the genetic code All proteins are built from 20 alpha amino acids has 4 functional groups: Amino group Carboxyl group Hydrogen R group - 20 different R groups All amino acids are L-stereoisomers except glycine You don't find D amino acids in cell walls of bacteria to prevent them from getting digested nonpolar aliphatic R groups are the largest class of amino acids mammals cannot synthesize all 20 amino acids not all amino acids can be used as precursors for gluconeogenesis. Derived from intermediates of: glycolysis, CAC, and PPP deficiency in even one essential amino acid can have severe physiological consequences.

charge based purification

■ Based on charge ● Ion exchange chromatography for purification ● Isoelectric focusing more of an analytical method (uses very small amounts of protein)

Enthalpy (H)

■ Bonding energy ■ Negative H means heat is released ■ Exothermic

irreversible inhibition

■ Covalently attach to enzyme to modify the active site ■ Also called suicide substrates ■ Basis of pharmaceutical agents ■ Ex: aspirin - irreversible inhibitor of prostaglandin

R-Stereoisomer

■ Has methyl group in R position ■ Chiral ■ We have L-alanine in proteins

alanine

■ Has methyl group in R position ■ Chiral ■ We have L-alanine in proteins delivers ammonia from the muscle to the liver. Alanine can be transaminated with alpha-ketoglutarate to form glutamate, which is one amino acid that can enter the urea cycle. in muscle pyruvate accepts amino group from amino acid catabolism via transamination forming alanine for transport carries NH4+ from skeletal muscle to liver

pka

■ Ka=[h+][A-]/[HA] ■ pKa=-log[Ka] ■ The lower the pKa the more acidic, the stronger the acid Buffering capacity, where we have plus or minus one unit from the pKa

paralell beta sheet

■ Made up of 3 beta strands oriented parallel, going in same direction ■ Slightly less stable than antiparallel bc the hydrogen bonds are not linear but at a slight diagonal making then weaker hydrogen bonds

quarternary protein structure

■ Multiple proteins come together to form functional protein structure ○ Hemoglobin is a tetramer- 4 protein chains come together to form quaternary structure

zwitterionic

■ Negative charge on the carboxylate group and a positive charge on the amino group ■ These negative and positive charges stabilize each other ■ Oxygen is electronegative and easily carries the - charge and can be destabilized by delocalization of the double bond and amino acids are better at carrying positive charges ■ The pKas of the carboxylate and amino group are opposite as acidic and basic so the carboxylate is better at donating a proton to become COO-

Gibbs free energy (G)

■ Negative is energetically favorable ■ Exergonic ■ Tells us if reaction is favorable

nucleus

■ Nucleus:membrane bound compartment, not in bacterial cell

sigmoidal

■ Oxygen binding to hemoglobin is sigmoidal - S shaped binding curve ● Its binding affinity is more sensitive to the pressure of oxygen ● Result of cooperativity between the 4 subunits of hemoglobin which coordinate to help bind oxygen

entropy

■ Randomness ■ As you increase temperature, entropy increases because you are adding in thermal energy so molecules move more quickly To increase the entropy of water, it folds around on itself forming liposome

enzymatic reaction

■ Rate of reaction is dependent on substrate concentration ■ Enzyme kinetics are measured by plotting initial velocities as function of substrate concentration ■ The plateau is the Vmax ■ It is a hyperbolic function ■ 1.5 V max is the midway point - KM

antiparallel beta sheet

■ Sheets are held together by dipole interactions between carbonyl oxygens and NH group of opposite strand

reversible inhibitors

■ Small molecules that bind in or close to active site ■ 3 types: competitive, uncompetitive and mixed

catalytic efficiency

■ Turnover number - how quickly enzyme converts substrate into product per second - catalytic efficiency ■ Catalytic efficiency of an enzyme should have high Kcat

threonine

■ Typically, proteins are phosphorylated on the hydroxyl groups of Serine (Ser), Threonine (Thr), or Tyrosine (Tyr)

Phenylalanine

■ aromatic doesnt absorb enough UV light to detect proteins b/c it is very stable conjugated system doesnt absorb or allow electron to get excited

Tryptophan

■ effectively absorbs UV light bc it is heterocyclic aromatic amino acid side chain

Myoglobin

■ found in muscles ■ Oxygen binding to myoglobin is hyperbolic ■ 153 amino acid residues ■ 8 alpha helixes ■ Is a monomer so it has tertiary structure ■ Poor oxygen transporter ■ Myoglobin is 98% bound to oxygen under normal Oxygen pressures in teh lungs space filling representation tertiary structure oxygen binding proteins

reaction coordinate diagram

■ graph s the free energy vs the reaction coordinate ■ Enzymes lower the activation energy of the transition state ■ Enzymes can increase the rate of reaction by 10^5 - 10^17 ■ Enzymes aren't complimentary to their substrates but they are to the transition state

Mitochondria

■ have their own membranes and DNA ● Formed by symbiosis when bacterial cell is engulfed by eukaryotic cell

weak acids and bases

○ Acids - proton donors or electron pair acceptors ○ Bases - proton acceptors or e- pair donors ○ Weak acids and bases are only partially ionized ○ Strong acids have tendency to release protons

post-translational modification

○ After a protein is made in a cell, it can be chemically modified by enzymes ■ Enzymes like phosphorylases or methylases ■ Transfer groups onto amino acids to modify them ■ They recognize specific sequence and bind to it

uncompetitive inhibitors

○ Binds next door to substrate and binds to ES complex ○ Binds only to ES complex ○ Inhibitor jumps on to form an inhibited ESI complex ○ Affects Vmax and Km equally so slope says the same ○ Intercepts change equally ○ As we increase amount of inhibitor our Vmax decreases and Km goes down by equal amount ○ Always slower than the uninhibited enzyme

mixed inhibitors

○ Binds right next to substrate on enzyme ○ Binds to both the free enzyme and the ES complex ○ Can bind to free enzyme to form inhibited ESI complex ○ Mixes all the michaelis-menten parameters ○ Change in the slope and change in x and y intercepts ○ As inhibitor is increased, Vmax decreases, Km is increasing ○ When Km is increasing it means the enzyme isnt binding to the substrate tightly and inhibits the Vmax

buffering capacity

○ Buffering capacity, where we have plus or minus one unit from the pKa

Cholesterol

○ Cholesterol is a sterile and its hormones are steroids ■ Sterile is a lipid steroid, steroid nucleus that has been modified It is a lipid modulate fluidity and permeability major site in liver The steroid nucleus of cholesterol is where hormones are derived derived from acetyl-CoA 18 Acetyl-CoA--(ATP + NADPH in)--> Cholesterol Soluble Early stages occur in the cytosol then in endoplasmic reticulum. Released from membrane and travel through bloodstream Vitamin D is derived from cholesterol and is a precursor to a hormone that regulates calcium uptake in the bone cholesterol synthesis is inactive in the liver NADPH is used to synthesize it hydrophobic triacylglycerol are added with cholesterol and apolipoproteins into chylomicrons

biological lipids

○ Class of organic molecules that are insoluble in water ○ Forms of energy stores in organisms ○ Biological membranes ○ Cofactors, electron carriers, pigments, hormones and messengers

cofactors

○ Cofactors, electron carriers, pigments, hormones and messengers Some enzymes require

amino acids (4 groups)

○ Everyone has 4 functional groups ■ Amino group ■ Carboxyl group ■ Hydrogen ■ R group - 20 different R groups

regulatory enzymes

○ Exhibit increased or decreased activity in response to cellular signals ○ 3 kinds: allosteric, covalently modified and zymogens

glutamine

○ Formed from glutamine synthetase ■ Uses glutamate to mop up excess NH4+ in the muscle and tissues ■ Glutamine travels through blood to liver ■ Once glutamine is in the liver it is deaminated by Glutaminase releases the NH4+ group

tandem mass spectrometry

○ Identifies fragments of unique mass that are small enough to be assigned to a sequence ○ Fragments of a protein enter a collision cell breaking them down

competetive inhibition

○ Inhibitor binds to free enzyme in active site to form EI complex (inhibited enzyme) ■ Cannot react with substrate ○ Competition between substrate and inhibitor to bind to same site ○ Binds only to free enzyme ○ Vmax doesn't change ■ Bc if we include a lot of substrate, inhibitor can't find enzyme because all enzyme will go to ES complex ○ As we increase the amount of inhibitor, Km increases ■ Only affects K, the slope and the x intercept

RNA world hypothesis

○ Life may have started with a self replicating RNA molecule ○ RNA is the only molecule that carries genetic info and is a catalyst of chem rxns ○ DNA is constrained into double helix and isn't reactive ○ RNA can form reactive centers Class 2

arginine

○ Lysine, histidine and arginine are all positively charged amino acids ■ Can deprotanate at high pH arginine proportional to the level of glucose in the body.

lysine

○ Lysine, histidine and arginine are all positively charged amino acids ■ Can deprotanate at high pH lysine proportional to the level of glucose in the body.

rate law

○ Measure of speed of reaction ○ Equilibrium constant: measurement of how far a reaction proceeds in net direction until equilibrium is reached

mass spectrometry

○ Measures protein mass by getting molecules to fly in gas phase by electrospray ionization ○ Getting proteins from liquid to gas phase ○ Then measures the mass to charge ratio ○ Lighter proteins go farther than heavier proteins ○ It is a rapid, convenient and sensitive method for finding the mass of a protein

Methionine

○ Methionine has a methylated thiol group in its side chain ■ Thio means sulfur and meth refers to methyl ■ Methionine means methylated sulfur group ■ This is the most aliphatic hydrocarbon side chain

chemical synthesis

○ Mimicking the atmosphere of prebiotic earth by mixing ammonia, methane, hydrogen gas and water ○ Heated it up and added energy through electricity and analyzed the condensed product ○ Tells us that biological molecules can readily form via chemical reactions

Enantiomers

○ Mirror images with same chemical formula

chiral center

○ Molecule that has a carbon with 4 substituents around that carbon ○ Molecule cannot be superimposed on its mirror image glycine is not chiral

enzyme specificity

○ Most efficient enzymes have high kcat and low Km ○ Enzymes with high kcat/Km like to bind and react to substrate EX: enzyme chymotrypsin

2,3-bisphosphoglycerate (BPG)

○ Only one BPG molecule binds per hemoglobin tetramer stabilizes the T state R state has no room for BPG to bind allosterically regulates Oxygen binding Regulates binding affinity of hemoglobin for oxygen Without BPG, the binding curve is hyperbolic in red blood cells at 5 mM and increases in high altitudes bc we need to deliver more oxygen to tissues binds on the cavity between the subunits of hemoglobin stabilizing the T state binds to positively charged side chains between B subunits Only one BPG molecule binds per hemoglobin tetramer Plays a big role in fetal development

condensation reaction

○ Opposite direction ○ Creating water through condensing two molecules Peptide bond formation is a condensation rxn

plasma membrane

○ Plasma membrane: outer membrane of cell, holds everything together ■ Supramolecular complex

peptide

○ Protein folding is restricted by the peptide bond ■ planar due to partial double bond character ■ Stabilized by dipole interaction between partial negative charge of oxygen and partial positive charge of nitrogen ■ Peptide always stays in planar configuration and cannot rotate peptide bond formation is condensation reaction peptide bond breakage is hydrolysis

SDS (PAGEe)

○ SDS polyacrylamide gel electrophoresis (PAGEe)

r-state hemoglobin

○ Stands for relaxed ○ Oxygen binds more strongly to it and stabilizes it ○ High oxygen concentration ○ Oxygen stabilizes the R state by pulling on the helix to linear shape ○ Has no room for BPG to bind

Electronegativity

○ Tendency of atom to attract electrons to itself Oxygen is electronegative and easily carries the - charge and can be destabilized by delocalization of the double bond and amino acids are better at carrying positive charges

valine

○ Valine has 3 carbons in its side chain

hydrolysis reaction

○ Water is added across the bond to break it and form new bonds, releasing energy Peptide bond breakage is hydrolysis rxn

achiral center

○ does not 4 different substituents but has 2 X functional groups ○ It can be superimposed onto its mirror image

Tertiary protein structure

○ multiple secondary structure elements fold upon themselves ■ Connected by loops and liners into 3D shape enzyme chymotrypsin has a tertiary protein structure

Eukaryotic cells

○ or animal cell ■ ~50 um ■ DNA surrounded by nuclear membrane ■ Nucleus:membrane bound compartment, not in bacterial cell ■ Endoplasmic reticuli ■ Mitochondria: have their own membranes and DNA ● Formed by symbiosis when bacterial cell is engulfed by eukaryotic cell

bohr effect

○ pH affects binding of oxygen

protein folding

○ restricted by the peptide bond ■ Peptide bond is planar due to partial double bond character ■ Stabilized by dipole interaction between partial negative charge of oxygen and partial positive charge of nitrogen ■ Peptide always stays in planar configuration and cannot rotate

secondary protein structure

○ sequence of the protein can fold up on itself

enzymes

○ usually proteins ■ Except catalytic RNA ○ The bind to ligands ○ Can be transporters are controlled by equilibrium constants changes the rate of reaction but cant change the equilibrium constant If substrate concentration is high, the reaction is driven to the right If substrate concentration is low, reaction wont proceed If product concentration is high and substrate concentration is low, drives equilib to the left and form enzyme product ○ Good catalysts ■ Increase rates of reaction under mild conditions in aqueous solution ○ Highly specific ○ Some provide control over metabolic processes ○ Has 3D structure for activity ○ Allow biological molecules and metabolites to be synthesized, degraded under physiological conditions ○ 6 classes of enzymes: ocidoreductase, transferase, hydrolase, lyase, isomerase, ligase Highly specific for their substrates

metal ion catalysis

● About ⅓ of all enzymes use metal ions ● Metal ions have positive charges that stabilize negatively charged transition states ● Ex: enzyme binds to 2 magnesium ions with +2 charge which coordinate the carboxyl oxygens and phosphorous oxygen to stabilize the negative charge build up ● lower s the activation energy by shielding the build up of negative charge in the transition state

lyases

● Addition of groups to double bonds or formation of double bonds by removing groups class of enzyme

specificity based purification

● Affinity chromatography

Ramachandran plot

● Allowed regions of protein folding space by mapping the phi and psi torsion angles ● Glycine can occupy torsion angle space because its the smallest amino acid

allosteric enzymes

● Bind regulatory compounds (allosteric modulators) noncovalently (reversibly) ● Help change the shape of the enzyme ● Has subunit interactions ○ Catalytic subunit and regulatory subunit ○ The regulatory subunit binds to modulator that makes the enzyme more active ● Quaternary structure ● Is a heterodimer ● Metabolic pathways are kept in balance with it ● Have sigmoidal behavior

saturated aliphatic tails

● Can be saturated- has all single bond carbons ○ Pack very closely and efficiently together through hydrophobic effect ○ Found in fats that are solids at room temp ○ Like animal fat ○ Have higher melting points

cell turnover

● Enzymes arent used up during a reaction and can convert many substrate molecules into products ● Enzyme binds to substrate, converting it to product, release that product, regenerating free enzyme which then binds to another substrate

lipids

● Fatty acids are building blocks of lipids ○ Structural components of membranes ○ 3 classes of lipids in membranesL glycerophospholipids, sphingolipids, sterols

acid based catalysis

● Glutamate and aspartate act as acids when protonated and are general base with neutral pH when deprotonated ● Histidine is a common general acid and base at neutral pH ● Tyrosine acts as a acid when protanated

transferanses

● Group transfer ● Post translational modification class of enzyme

alpha helix

● Has ~4 amino acids per turn ● Hydrogen pattern between the carbonyl oxygen of the nth amino acid and the amide N-H group of the (n+4) stabilizes the helix ● N+4 bc every 4 amino acids the alpha helix rotates upon itself and aligns a carbonyl negative dipole with NH positive dipole ○ Dipole hydrogen bonding interaction stabilizes shape of alpha helix ● Most helixes are right handed Myoglobin has 8 alpha helixes

Glycerophospholipids

● Have glycerol, 2 fatty acids and phosphate group ● Fatty acids linked via ester links to carboxylic group ● Glycerol has 3 carbons and is an alcohol bc of its hydroxyl group ○ Complex groups of molecules that influence biological functions like inflammatory response, pain and fever, blood pressure and clotting, reproductive function, induction of labor, regulation of sleep cycle

sphinogolipids

● Have sphingosine backbone ● Has 3 carbons ● One of the fatty acids is in an amide linkage with a peptide like bond ● Important immunogenic determinant ● Red blood cells have this lipid ceramide ● Oligo saccharides pact as flags on outside of red blood cells

hydrogen bonds

● Hydrogen bonds are longer and weaker than covalent bonds but you need more energy to break all of the hydrogen bonds in water ○ But since there are so many hydrogen bonds in water, it becomes a very strong force have directional preference hydrogens want to line up in a linear configuration bc of the position of the electrons on the O Weaker h bond is due to bent configuration as the partial (-) charge on the O is not aligned with the H When we add thermal energy, it breaks the hydrogen bonds and melts Liquid water Now has av. of 3.4 hydrogen bonds per water molecule In ice water forms a hexagonal hydrogen bonding pattern each hydrogen is participating in 4 h bonds Water is denser than ice b/c when we add thermal energy the crystalline lattice collapses inward on itself

hydrolases

● Hydrolysis reactions class of enzyme

covalent catalysis

● Involves an intermediate that is covalently bonded to enzyme ● The covalent bond must be broken in the catalytic cycle to release product and regenerate free enzyme serine

beta sheet

● Made of beta strands ● 2 types: parallel and antiparallel contain few amino acids (3-10) have characteristic twist

zymogens

● Made of inactive precursors that need to be cleaved to become active

Flagellum

● Molecular motor ● Uses energy of ATP to spin around and let cell swim Protein assembly

DNA

● Nucleoid: Densely packed state, coiled around protein

peptide bond formation

● Peptide bond formation is a condensation rxn Peptide bond breakage is hydrolysis rxn

macromolecules

● Polymers ● Made up by stitching together lots of monomeric units that are polymerized into larger molecule

Covalently Modified Enzymes

● Regulatory compounds are covalently attached in a reversible manner ● Attached to enzymes that are doing post translational modifications to another enzyme to covalently regulate them

size based purification

● Size exclusion chromatography ● Gel electrophoresis - more analytical method used on small scale just to analyze proteins and not purify them

Enzyme: Chymotrypsin

● Small, globular enzyme ● Tertiary structure ● Digests proteins containing aromatic amino acid residues Has 3 chains held together through covalent disulfide bond 1. Its substrate binds in hydrophobic pocket, E+S=ES complex which is energetically favorable rxn 2. Histidine acts general base activity and covalent chemistry: 3. Serine alkoxide ion attacks carbonyl carbon forming acyl bond between enzyme and substrate 4. Tetrahedral transition state stabilization by oxyanion hole 5. Histidine causes the Breakage of peptide bond with acid chemistry, collapse of transition state and release of product 1 6. Water enters active site 7. Water deprotonation by histidine as a base 8. Hydroxide attacks acyl bond between substrate and enzyme 9. Formation of 2nd transition state stabilized by oxyanion hole 10. Collapse of transition state intermediate forms product 2 11. Release of product 2

fibrous protein structure

● They are highly extended and have repeating helical or beta sheets ● Ex: keratin ● Amino acid residue is amino acid embedded in peptide that has lost dome of its atoms in condensation reaction creating free amino acids

elaidic acid

● Trans fats ● These clog arteries cause our body doesnt know how to metabolize them trans double bond

isomerases

● Transfer groups to yield isometric forms class of enzyme

Oxidoreductases

● Transfer of electrons ● Do oxidation and reduction reactions class of enzyme

Tyrosine

● Tyrosine acts as a acid when protanated

protein sequencer

● Used to identify protein of interest ● Used to identify mutations involved in diseases ● Understand shape and function of protein through homology ● Edman Degration can code for specific shapes

Van der Waals interactions

● Van der Waals interaction ○ Induced dipole when 2atoms have close contact and induced dipole ○ Very weak interaction

cysteine

● alkyl group will become permanently attached to the cysteine of the alkyltransferase

Isoelectric Focusing

● based on charge of the protein to separate ● analytical method ● Usually uses small amount of protein ● Can be done on larger scale for protein purification ● Protein sample applied to strip with immobilized pH gradient then electric field is applied ● Negative protein groups migrate to positive end and positively charged groups migrate to negative end ● move down the strip until it hits isoelectric point pH

ice

● forms a hexagonal hydrogen bonding pattern ○ each hydrogen is participating in 4 h bonds ○ When we add thermal energy, it breaks the hydrogen bonds and melts ■ Liquid water Now has av. of 3.4 hydrogen bonds per water molecule ○ Water is denser than ice b/c when we add thermal energy the crystalline lattice collapses inward on itself

Unsaturated aliphatics

● has a double bond between 2 carbons ○ Double bond kinks the fatty acid tail ■ Double bond is normally cis ○ Cant pack efficiently ○ Less dense ○ Liquids at 25 degrees ○ Ex: an oil like olive oil ○ Kinkl from double bond interferes with packing of carbons and lowers melting point ○ Hydrogenation of unsaturated fatty acids adds hydrogens across double bonds, turning them into single bonds and increases the melting point ■ Hydrogenation sometimes is imperfect and eliminates the hydrogen that were adding and creates a trans double bond

water

● most abundant molecule in cells ● molecules have a tendency to ionize hermodynamic effect that comes from entropy of water and releasing ordered water molecules upon clustering hydrophobic molecules Hydrophobic or nonpolar molecules are insoluble in water Water has high melting, high boiling point and higher heat of vaporization relative to other liquids because structure of water has strong hydrogen bond donor and acceptor capabilities

protein purification

● separates out a protein ○ Protein purification protocol separates proteins based on physical properties like size, shape, sequence composition and function ○ 1st step: choice of protein source based on convenience and quantity ○ 2nd step: disrupt cells to solubilize the proteins through grinding, sonication (high energy soundwaves) pressure or osmotic shock ○ 3rd step: purification based

feedback inhibition

● shuts off a products synthesis by negatively regulating an enzyme in the synthesis pathway ● Have sigmoidal behavior regulates biosynthesis regulating metabolic flux final product in a pathway inhibits the enzyme catalyzing the committed step build-up of products of a metabolic pathway can inhibit key enzymes, reducing their activity and slowing down the pathway dATP can inhibit ribonucleotide reductase through feedback inhibition

Enthalpy change 𝝙H

𝝙H = 𝝙E + P𝝙V Difference in bond energies between reactants and products if (-): -exothermic (heat released) -More stable bonds formed and heat released -ex : candle burning =-Contributes for favorable (negative) 𝝙G if there is strong entropy term If (+): -endothermic (heat input) -less stable bonds formed