Quicksheet: Biochemistry

central dogma

DNA—>RNA—>proteins

degenerate code

allows multiple codons to encode for the same AA

initiation, termination, wobble

AUG

UAA, UGA, UAG

third base codon; allos mutations to occur without affecting the protein

point mutations can cause

• silent: no effect

• nonsense: premature stop codon

• missense: codon codes for diff AA

  • frameshift mutations

differences of RNA compared to DNA

• ribose sugar (vs deoxyribose)

• uracil (vs thymine)

• single stranded (vs DS)

3 major types of RNA

• mRNA: carries message from DNA via transcription (nucleus—>cytoplasm)

• tRNA: brings in AA; rec. codon on mRNA

  • rRNA: enzymatically active, makes up ribo

steps of transcirption

• helicase and topoisomerase unwind DNA double helix

• RNA polyII bind to TATA box w/in promoter region of gene (25 bp upstream)

• hnRNA synthesized from DNA template (antisense) strand

posttranscriptional modifications

• 7-methylguanylate triphosphate cap added to 5’ end

• poly-A tail added to 3’ end

• splicing remove introns and ligate exons

  • alternative: combines diff exons to acquire different gene products

three stages of translation

initiation: 30S attaches to Shine-Dalgarno sequence

elongation: adding new aminoacyl-tRNA

termination: release factor

3 sites: APE

posttranslational modification

• folding by chaperones

• forming of quaternary structure

• cleavage of proteins or signal sequences

  • covalent addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation)

operons

inducible or repressible clusters of genes transcribed as a single mRNA

transcription factors

• promoters: w/in 25 bp of transcription start site

• enhancers: more than 25 bp away from transcription start site

negative control

binding of protein to DNA stops transcription

positive control

binding of protein to DNA increases transcription

inducible system

system normally “off” but can be made to turn “on” given particular signal

repressible system

normally turned “on” but can be made to turn “off” given a particular signal

lac operon vs trp operon

negative inducible system vs negative repressible system

Hardy-Weinberg equations

p+q = 1

p² +2pq+q² = 1

• p² = homozygous dominant

• 2pq = heterozygous dominant

• q² = homozygous recessive

glycolysis

occurs in cytoplasm; yields 2 ATP/glucose

important glycolysis enzymes

• glucokinase: irreversible

• hexokinase: irreversible

• phsophofuctokinase-1 (PFK-1): irreversible

• phsophofructokinase-2 (PFK-2)

• glyceraldehyde-3-phosphate dehydrogenase: produces NADH

• 3-phsophoglycerate kinase and pyruvate kinase (irreversible)

glucokinase

present in liver and pancreatic B cells, responsive to insulin; phosphorylates glucose

hexokinase

present in all tissue; phosphorylates glucose to trap it in cells

phosphofructokinase-1 (PFK-1)

rate limiting step

phosphfructokinase-2 (PFK-2)

product activates PFK-1

3-phsophoglycerate kinase and pyruvate kinase

perform substrate leven phosphorylation

pyruvate dehydrogenase

converts pyruvate to acetyl-CoA

stimulated by insulin and inhibited by acetyl-CoA

citric acid cycle

oxidize acetyl-CoA to CO2 and make high energy electron carriers (NADH and FADH2) and GTP

• occurs in mitochondrial matrix

electron transport chain

• NADH donates electrons (glycerol 3-phosphate or malate-aspartate shuttle)

• reduction potentials inc. until e- end up on oxygen (has highest reduction potential)

• occurs in matrix-facing surface of inner mitochondrial membrane

proton motive force

electrochemical gradient generated by ETC across inner mito. membrane

• en stored and used to form ATP via chemiosmotic coupling

ATP synthase

enzyme responsible for generating ATP from ADP and an inorganic phosphate (Pi)

glycolysis yield

2 ATP and 2 NADH

pryuvate dehydrogenase yield

2 NADH/molecule of glucose

1 NADH/pyruvate molecule

citric acid cycle yield

6 NADH, 2 FADH2, 2GTP / molecule of glucose

3 NADH, 1 FADH2, 1GTP / pyruvate

NADH and FADH2 ATP yeild

2.5 ATP and 1.5 ATP

total anerobic respiration yield

30-32 ATP per molecule of glucose (optimal)

metabolic states

• postprandial/well-fed (absorptive) state

• postabsorptive (fasting) state

• starvation

absorptive state

insulin secretion is high and anabolic metabolism prevails

fasting state

insulin secretion decreased while glucagon and catecholamine secretion increases

starvation

increases glucagon and catecholamines secretion. most tissues rely of fatty acids

primary structure

linear sequence of amino acids

secondary structure

local structure stabilized by non covalent bonds; including a-helices and B-sheets

tertiary structure

3-D stabilized by hydrophobic interactions, A/B interactions (salt bridges), H-bonding and disulfide bonds

quaternary structure

interactions btwn subunits; heat and solutes can cause denaturation

enzymes

type of catalyst that lowers the activation energy necessary for rxn; change rate (kinetics) at which equilibrium is reached

ligases

joining two large biomolecules, often the same type

isomerases

catalyze interconversion of isomers, including both constitutional and stereoisomers

lyases

catalyze cleavage without addition of water/transfer of electrons; reverse rxn (synthesis) more bio important

hydrolases

catalyze cleavage with addition of water

oxidoreductases

catalyze oxidation-reduction rxn that involve transfer of electrons

transferases

move functional group from one molecule to another

competitive

active site; inc. Km; same Vmax

noncompetitive

allosteric site; same Km; dec. Vmax

uncompetitive

enzyme substrate complex; dec. Km; dec. Vmax

mixed inhibition

allosteric site; inc. or dec. Km; dec. Vmax

DNA structure

-nucleosides—>5-C sugar + nitrogenous base

-nucleotide—>5-C sugar + nitrogenous base + phosphate

Chargaff’s rule

purines and pyrimidines are equal in number in DNA molecule. The amount of A = T and the amount of C = G

semiconservative

one old parent strand and one new daughter strand (DNA replication)

recombinant DNA

composed of nucleotides from two different sources

hybridization

joining of complementary base pair sequences

osmotic pressure

applied to pure solvent to prevent osmosis and related to [] of solution

passive transport

does not require ATP b/c molecules moving down [] gradient (higher to lower [])

• simple diffusion, osmosis, facilitated diffusn

simple diffusion

no transporter; small/nonpolar molecules move from high to low []

osmosis

diffusion of water across selectively permeable membrane

facilitated diffusion

use transport proteins to move impermeable solutes across cell membrane

active transport

required en. in form of ATP (primary) or an existing favorable ion gradient (secondary)

• symport or antiport