quicksheets biochem Flashcards
L - chiral amino acids
all except glycine, which isn’t chiral
S - conformation amino acids
all except cystein
nonpolar, nonaromatic AA
gly, leu, ala, met, val, ile, pro
positively charged AA
arg, lys, his
negatively charged AA
asp, glu
polar AA
ser, thr, cys, asn, gln
aromatic R groups AA
trp, phe, tyr
primary structure
linear sequence of AA
secondary structure
alpha helices, beta sheets, stabilized by hydrogen bonding
tertiary structure
3-d structure stabilized by hydrophobic interactions, acid-base interactions (salt bridges), hydrogen bonding, and disulfide bonds
quaternary structure
interactions between subunits
denaturation
caused by heat and solutes
enzymes
lower activation energy w/o changing free energy (delta G) or enthalpy (delta H); change kinetics
ligase
joins two large biolecules
isomerase
interconvert isomers
lysase
cleaves w/o addition of water or electron transfer
hydrolase
cleaves w addition of water
oxidoreductase
catalyze redox rxns involving transfer of electrons
transferases
move functional group from one molecule to another
saturation kinetics
as substrate conc. increases, rxn rate also increeases until max rate is reached: v=vmax[S]/(Km+[S])
one-half vmax
[S]=Km
competitive inhibitor
binding at active site, increases Km, no change to vmax
noncompetitive inhibitor
binding at allosteric site, no change to Km, decreases vmax
mixed inhibitor
binding at allosteric site, can increase or decrease Km, decreases vmax
uncompetitive inhibitor
binds at allosteric site, decreases Km, decreases vmax
structural proteins
fibrous, including collagen, elastin, keratin, actin and tubulin
motor proteins
capable of force generation through conformational change; myosin, kinesin, dynein
binding proteins
bind a specific substrate, either to sequester it in the body or hold its concentration at steady state
cell adhesion molecules
bind cells to other cells or surfaces; cadherins, integrins selectins
antibodies (immunoglobins, Ig)
target specific antigen, which may be a protein on surface of pathogen or a toxin
ion channels
can be used for regulating ion flow in or out of a cell, including ungated channels, voltage-gated channels, and ligand-gated channels
enzyme-linked receptors
participate in cell signaling through extracellular ligand binding and initiation of second messenger cascades
G protein-coupled receptors
have a membrane-bound protein associated with a trimeric G protein; they also initiate second messenger systems
triose, tetrose, aldose, ketose
3 carbon sugar, 4 carbon sugar, sugar w aldehyde as most oxidized group, sugar with ketone as most oxidized group
D-sugars
-OH on the right
L-sugars
-OH on the left
diastereomer
differ at at least one, but not all, chiral centers; epimers differ at exactly one; anomer type of epimer
cyclization
ring formation of carbohydrates from their straight-chain forms
anomeric carbon
new chiral center formed in ring closure; it was the carbon containing the carbonyl in the straight-chain form
alpha anomer
have the -OH on the anomeric carbon trans to the free -CH2OH group
beta anomer
have the -OH group on the anomeric carbon cis to the free -CH2OH group
mutarotation
one anomeric form shifts to another, w the straight-chain form as an intermediate
monosaccharides
single carbohydrate units that can undergo oxidation-reduction, esterification, and glycoside formation; fructose, glucose, galactose, mannose
disaccharides
sucrose, lactose, maltose
cellulose
main structural component of plant cells walls; main source of fiber in human diet
starches
amylose and amylopectin; main energy storage for plants
glycogen
major energy storage form for animals
nucleoside, nucleotide
5 carbon sugar bonded to nitrogenous base; w phosphate group(s) added
Chargaff’s rule
purines and pyrimidines are equal in number in a DNA molecule; amount A=T, G=C
histone proteins
DNA is would around H2A, H2B, H3 and H4, to form nucleosomes, which may be stabilitzed by another histone protein H1
heterochromatin
dense, transcriptionally silent DNA
euchromatin
less dense, transcriptionally active DNA
telomeres
ends of chromosomes, contain high GC coneten to prevent unraveling
centromeres
hold sister chromatids together until they are separated during anaphase; high GC content
origin of replication
one per chromosome in prokaryotes, multiple per chromosome in eukaryotes
unwinding of DNA double helix
helicase
stabilization of unwound template strands
single-stranded DNA-binding protein
synthesis of RNA primers
primase
synthesis of DNA
DNA polymerase III (prokaryotes) or alpha delta or epsilon polymerase (eukaryotes)
removal of RNA primers
DNA polymerase I 5–>3 (prokaryotes) or RNase H 5–>3 (eukaryotes)
replacement of RNA w DNA
DNA pol I (prokaryotes) or DNA pol delta (eukaryotes)
joining of okazaki fragments
DNA ligase
removal of supercoils head of replication forks
DNA topoisomerases (DNA gyrase in prokaryotes)
synthesis of telomeres
telomerase (eukaryotes)
DNA cloning
introduces a fragment of DNA into vector plasmid
restriction enzyme
cuts plasmid and fragment, leaving them w sticky ends that can bind
genomic libraries
contain large fragments of DNA, both coding and noncoding, cannot be used to make recombinant proteins
cDNA libraries (expression libraries)
contain smaller fragments of DNA, only exons, can be used to make recombinant proteins
PCR
automated process by which millions of copies of DNA sequence can be created from small sample thru hybridization
Southern blotting
detects presence of quantity of DNA strands, electrophoresis sample is transferred to a membrane that can be probed w single-stranded DNA molecules to look for sequence of interest
DNA sequencing (Sanger)
uses dideoxyribonucleotides, which terminate the DNA chain bc they lack a 3’ -OH
initiation codon
AUG (met)
termination
UAA, UGA, UAG
redundancy and woblle
allow mutation to occur w/o affecting protein
silent mutations
no effect on protein synthesis
nonsense mutations (truncation)
premature stop codon
missense mutations
codes diff amino acid
frameshift mutations
result in nucleotide addition or deletion, changing reading frame of subsequent codons
mRNA
carries message from DNA via transcription; nucleus –> cytoplasm
tRNA
brings in amino acids, recognizes codon on the mRNA using its anticodon
rRNA
makes up most of ribosome, enzymatic
steps of transcription
helicase and topoisomerase unwind DNA; RNA pol II binds to TATA box within promoter region of gene (25 bp upstream from first transcribed base); hnRNA synthesized from DNA template (antisense) strand
posttranscriptional modifications
7-methylguanylate triphosphate cap added to 5’ end; poly-A tail added to 3’ end; spliceosome removes introns, ligates exons together
alternative splicing
combines diff exons to acquire diff gene products
translation steps
initiation, elongation, termination
posttranslational modifications
folding by chaperones, formation of quaternary structure, cleavage of proteins of signal sequences, covalent addition of other biomolecules
Jacob-Monod model
operons are inducible or repressible clusters of genes transcribed as a single mRNA
promoter
transcription factor within 25 bp of transcription start site
enhancer
transcription factor more than 25 bp of transcription start site
osmotic pressure
a colligative property; the pressure applied to a pure solvent to prevent osmosis, pi=iMRT
passive transport
does not require ATP because molecule moves down concentration gradient
simple diffusion
does not require transporter; small nonpolar molecules move passively down conc. gradient
osmosis
describes diffusion of water across selectively permeable membrane
facilitated diffusion
uses transport proteins to move impermeable solutes across membrane
primary active transport
requires energy in the form of ATP
secondary active transport
transporter protein couples the movement of an ion down its electrochemical gradient with the movement of a molecule against its conc. gradient
pinocytosis, phagocytosis
ingestion of liquid/solids from vesicles formed from cell membrane
glycolysis
occurs in cytoplasm of all cells, does not require O, yields 2 ATP per cycle
glucokinase
present in pancreatic beta islet cells as part of glucose sensor, responsive to insulin in the liver
hexokinase
traps glucose
phosphofructokinase-1
rate limiting step
PFK-2
produces F2, 6-BP, which activates PFK-1
GAPDH
produces NADH
3-phosphoglycerate kinase and pyruvate kinase
perform substrate-level phosphorylation
lactate dehydrogenase
oxidizes NADH producted in glycolysis anaerobically
pyruvate dehydrogenase
converts pyruvate to acetyl-coA; stimulated by insulin and inhibited by acetyl-coA
citric acid cycle
takes place in mitochondrial matrix, oxidizes acetyl-coA t CO2, generates high-energy electron carriers (NADH and FADH2) and GTP
electron transport chain
takes place on matrix-facing surface of inner mitochondrial membrane, NADH donates electrons to chain, which are passed thru complexes, reduction potentials increase down the chain until electrons end up on oxygen which has the highest reduction potential
glycerol 3-phosphate shuttle, malate-aspartate shuttle
how NADH transfers its electrons to energy carriers in the mitochondrial matrix, since it cannot cross the inner mitochondrial membrane
proton-motive force
electrochemical gradient generated by the electron transport chain across the inner mitochondrial matrix
proton concentration
intermembrane space >matrix
chemiosmotic coupling
formation of ATP using electrochemical gradient
ATP synthase
generates ATP from ADP and pi
glycolysis energy yield
2 NADH, 2 ATP
pyruvate dehydrogenase energy yield
1 NADH (2 NADH per molecule of glucose bc each glucose forms two pyruvates)
citric acid cycle energy yield
3 NADH, 1 FADH2, 1 GTP (x2 per molecule of glucose)
each NADH energy yield
2.5 ATP, 10 NADH form 25 ATP
each FADH2 energy yeld
1.5 ATP, 2 FADH2 for 3 ATP
glycogenesis
building of glycogen, using glycogen synthase which creates alpha 1,4 links between glucose molecules and is activated by insuline; and branching enzume, which moves a block of oligoglucose from one chain and connects it as a branch using an alpha 1,6 glycosidic link
glycogenolysis
breakdown of glycogen using two main enzymes, glycogen phosphorylase (breaks alpha 1,4 glycosidic links, activated by glucagon in liver and epinephrine and AMP in muscle); and debranching enzyme
gluconeogenesis
occurs in cytoplasm and mitochondria, predominantly in liver; mostly just reverse of glycolysis, using same enzymes
3 irreversible steps of glycolysis and the enzymes that bypass them
pyruvate kinase (bypassed by pyruvate carbozylase and PEP carbozykinase); PFK-1 (bypassed by fructose-1,6-biphosphate); hexokinase/glucokinase (bypassed by glucose-6-phosphatase)
pentose phosphate pathway
occurs in cytoplasm of most cells, generates NADPH and sugars for biosynthesis, rate-limiting enzyme is glucose-6-phosphate dehydrogenase which is activated by NADP+ and insulin and inhibited by NADPH
postprandial/well-fed (absorptive) state
insulin secretion is high, anabolic metabolism prevails
postabsorptive (fasting) state
insulin secretion decreases while glycagon and catecholamine secretion increases
prolonged fasting (starvation)
dramatically increases glucagon and catecholamine secretion; most tissues rely on fatty acids
liver
maintains blood glucose through glycogenolysis and gluconeogensis, processes lipids, cholesterol, bile, urea, and toxins
