Biochemistry Two Final

nucleotide

pentose, nucleic base, phosphate group

nucleoside

pentose, nucleis base

nucleic acid

chain of nucleotides

purines

adenine, guanine

pyrimidines

cytosine, uracil, thymine

adenine

guanine

cytosine

uracil

thymine

functional group at 3’ end of nucleic acid

OH group

functional group at 5’ end of nucleic acid

phosphate group

cause of DNA/RNA negative charge

-1 charge on phosphate group

features of Watson and Crick double helix

double helix, bases on interior of helix, phosphodiester backbone, antiparallel strands

stabilizing interactions of DNA helix

H bonds between complementary base pairs, base stacking interactions

base stacking interactions

noncovalent forces between DNA bases within the same stand- include H bonds and pi stacking

DNA vs. RNA comparison

No OH group at 3’ position in DNA, no uracil base in DNA, RNA typically single stranded

denature DNA

break noncovalent interactions

anneal DNA

reform noncovalent interactions

DNA length impact on T_M

increased length increases melting temperature

GC content impact on T_M

increased GC bps, increased Tm

salt concentration impact on Tm

increased salt concentration, increased melting temp

melting point of DNA using melting curve

melting point is when 50% of DNA is denatured

restriction enzymes

cleave palindromic sites 4-8 bp in length at the phosphodiester backbone

ethidium bromide

used to detect DNA restriction fragments in gels

components needed for PCR reaction mixture

4 dNTPs, template DNA, 2 primer sequences, Mg²⁺, DNA Polymerase I

impact of increased annealing temperature

higher specificity

effect of increased extension time

less specific gene amplification

characteristics of good DNA primer

18-25 nucleotides, 40-60% GC content, no hairpin structure, no primer dimer, high specificity, annealing temperature less than 5 degrees below Tm but between 50-62 degrees, primers within 5 degrees

3 types of membrane lipids

phospholipid, glycolipid, cholesterol

general form of chemical formula of fatty acid

number of carbons in FA:double bonds (delta^{double bond carbon numbers})

impact of double bonds on melting temp

more double bonds, lower melting temp

impact of FA chain length on melting point

increased chain length, increased melting temp

solubility of peripheral proteins

water soluble

solubility of integral proteins

extracted with detergent

delta G in hydropathy plot

energy associated with transferring AA from a hydrophobic to hydrophillic environment

active transport

ATP directly required, moving up concentration gradient

secondary active transport

uses ATP indirectly to move one molecule down its concentration gradient, then use that energy to move another molecule up its concentration gradient

facilitated diffusion/passive transport

allows movement of polar, large molecules down their concentration gradient

example of facilitated diffusion

K⁺ ion channel

selectivity filter

helps filter out ions based on size and interactions with amino acid backbone

hydration free energy

energetic cost of dehydrating and ion and replacing interactions with water with interactions with channel amino acids

N domain function

binds ATP and hydrolyses ATP, transfers P to P domain

P domain

phosphorylated by N domain

A domain

dephosphorylates the P domain and restores the P-type ATPase to its original conformation

effector enzyme (like adenylate cyclase)

modulate reactions in response to cellular signals

agonist

binds and mimics natural ligand

antagonist

blocks activity of receptor

inverse agonist

decreases activity

K_d

binding constant, lower means better binding

AKAP5

binding site for the enzymes, effector molecules, signaling molcules present in epinephrine signaling cascase

turn off B2-adrenergic receptor

self inactivation, reduction in ligand concentration, desensitization of receptor, removal of secondary messenger, dephosphorylation of activated enzymes

high phosphoryl transfer potential

high standard free energy of hydrolysis

reasons why ATP hydrolysis drives reactions forward

orthophosphate released is resonance stabilized, electrostatic repulsion decreases with release of orthophosphate, release of orthophosphate increases entropy, hydration stabilizes the released ADP+Pi

creatine phosphate

molecule wiht higher phosphoryl transfer than ATP, meaning it can regenerate ATP

constitutional isomer

different connectivity

stereoisomer

multiple chiral centers reversed

enantiomer

every chiral center is exactly flipped

epimer

only one chiral center reversed

d-isomer of sugar

OH group on right side

L-isomer of sugar

OH group on left side

2 phases of glycolysis

energy investment and payoff phase

first committed step fo glycolysis

#3- PFK. product has to be part of glycolytic pathway

activators of glycolysis in muscle

F-1,6-P (activates pyruvate kinase), AMP (activates PFK)

inhibitors of glycolysis in muscle

ATP (PFK and pyruvate kinase), G-6-P (hexokinase)

inhibitors of glycolysis in liver

citrate, glucokinase, phosphorylation (pyruvate kinase)

activators of glycolysis in liver

F-2,6-P (PFK)

location of glycolysis

cytoplasm

location of CAC

matrix

location of electron transfer chain

inner nitochondrial membrane

location of oxidative phosphorylation

inner mitochondrial membrane

E1 of PDC

pyruvate dehydrogenase

E2 of PDC

dihydrolipoyl transacetylase

E3 of PDC

dihydrolipoyl dehydrogenase

E1 prosthetic group

TPP

E2 prothetic group

lipoamide swinging arm

E3 prosthetic group

FAD⁺

reaction catalyzed at E1

oxidative decarboxylation of pyruvate

reaction catalyzed at E2

transfer of acetyl group to CoA

reaction catalyzed at E3

regeneration of the oxidized form of the lipoamide

prosthetic group

covalently (or very tightly) attached group to an enzyme

cofactors of PDC

NAD⁺and CoA