quicksheets biochem Flashcards
(127 cards)
1
Q
L - chiral amino acids
A
all except glycine, which isn’t chiral
2
Q
S - conformation amino acids
A
all except cystein
3
Q
nonpolar, nonaromatic AA
A
gly, leu, ala, met, val, ile, pro
4
Q
positively charged AA
A
arg, lys, his
5
Q
negatively charged AA
A
asp, glu
6
Q
polar AA
A
ser, thr, cys, asn, gln
7
Q
aromatic R groups AA
A
trp, phe, tyr
8
Q
primary structure
A
linear sequence of AA
9
Q
secondary structure
A
alpha helices, beta sheets, stabilized by hydrogen bonding
10
Q
tertiary structure
A
3-d structure stabilized by hydrophobic interactions, acid-base interactions (salt bridges), hydrogen bonding, and disulfide bonds
11
Q
quaternary structure
A
interactions between subunits
12
Q
denaturation
A
caused by heat and solutes
13
Q
enzymes
A
lower activation energy w/o changing free energy (delta G) or enthalpy (delta H); change kinetics
14
Q
ligase
A
joins two large biolecules
15
Q
isomerase
A
interconvert isomers
16
Q
lysase
A
cleaves w/o addition of water or electron transfer
17
Q
hydrolase
A
cleaves w addition of water
18
Q
oxidoreductase
A
catalyze redox rxns involving transfer of electrons
19
Q
transferases
A
move functional group from one molecule to another
20
Q
saturation kinetics
A
as substrate conc. increases, rxn rate also increeases until max rate is reached: v=vmax[S]/(Km+[S])
21
Q
one-half vmax
A
[S]=Km
22
Q
competitive inhibitor
A
binding at active site, increases Km, no change to vmax
23
Q
noncompetitive inhibitor
A
binding at allosteric site, no change to Km, decreases vmax
24
Q
mixed inhibitor
A
binding at allosteric site, can increase or decrease Km, decreases vmax
25
uncompetitive inhibitor
binds at allosteric site, decreases Km, decreases vmax
26
structural proteins
fibrous, including collagen, elastin, keratin, actin and tubulin
27
motor proteins
capable of force generation through conformational change; myosin, kinesin, dynein
28
binding proteins
bind a specific substrate, either to sequester it in the body or hold its concentration at steady state
29
cell adhesion molecules
bind cells to other cells or surfaces; cadherins, integrins selectins
30
antibodies (immunoglobins, Ig)
target specific antigen, which may be a protein on surface of pathogen or a toxin
31
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
32
enzyme-linked receptors
participate in cell signaling through extracellular ligand binding and initiation of second messenger cascades
33
G protein-coupled receptors
have a membrane-bound protein associated with a trimeric G protein; they also initiate second messenger systems
34
triose, tetrose, aldose, ketose
3 carbon sugar, 4 carbon sugar, sugar w aldehyde as most oxidized group, sugar with ketone as most oxidized group
35
D-sugars
-OH on the right
36
L-sugars
-OH on the left
37
diastereomer
differ at at least one, but not all, chiral centers; epimers differ at exactly one; anomer type of epimer
38
cyclization
ring formation of carbohydrates from their straight-chain forms
39
anomeric carbon
new chiral center formed in ring closure; it was the carbon containing the carbonyl in the straight-chain form
40
alpha anomer
have the -OH on the anomeric carbon trans to the free -CH2OH group
41
beta anomer
have the -OH group on the anomeric carbon cis to the free -CH2OH group
42
mutarotation
one anomeric form shifts to another, w the straight-chain form as an intermediate
43
monosaccharides
single carbohydrate units that can undergo oxidation-reduction, esterification, and glycoside formation; fructose, glucose, galactose, mannose
44
disaccharides
sucrose, lactose, maltose
45
cellulose
main structural component of plant cells walls; main source of fiber in human diet
46
starches
amylose and amylopectin; main energy storage for plants
47
glycogen
major energy storage form for animals
48
nucleoside, nucleotide
5 carbon sugar bonded to nitrogenous base; w phosphate group(s) added
49
Chargaff's rule
purines and pyrimidines are equal in number in a DNA molecule; amount A=T, G=C
50
histone proteins
DNA is would around H2A, H2B, H3 and H4, to form nucleosomes, which may be stabilitzed by another histone protein H1
51
heterochromatin
dense, transcriptionally silent DNA
52
euchromatin
less dense, transcriptionally active DNA
53
telomeres
ends of chromosomes, contain high GC coneten to prevent unraveling
54
centromeres
hold sister chromatids together until they are separated during anaphase; high GC content
55
origin of replication
one per chromosome in prokaryotes, multiple per chromosome in eukaryotes
56
unwinding of DNA double helix
helicase
57
stabilization of unwound template strands
single-stranded DNA-binding protein
58
synthesis of RNA primers
primase
59
synthesis of DNA
DNA polymerase III (prokaryotes) or alpha delta or epsilon polymerase (eukaryotes)
60
removal of RNA primers
DNA polymerase I 5-->3 (prokaryotes) or RNase H 5-->3 (eukaryotes)
61
replacement of RNA w DNA
DNA pol I (prokaryotes) or DNA pol delta (eukaryotes)
62
joining of okazaki fragments
DNA ligase
63
removal of supercoils head of replication forks
DNA topoisomerases (DNA gyrase in prokaryotes)
64
synthesis of telomeres
telomerase (eukaryotes)
65
DNA cloning
introduces a fragment of DNA into vector plasmid
66
restriction enzyme
cuts plasmid and fragment, leaving them w sticky ends that can bind
67
genomic libraries
contain large fragments of DNA, both coding and noncoding, cannot be used to make recombinant proteins
68
cDNA libraries (expression libraries)
contain smaller fragments of DNA, only exons, can be used to make recombinant proteins
69
PCR
automated process by which millions of copies of DNA sequence can be created from small sample thru hybridization
70
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
71
DNA sequencing (Sanger)
uses dideoxyribonucleotides, which terminate the DNA chain bc they lack a 3' -OH
72
initiation codon
AUG (met)
73
termination
UAA, UGA, UAG
74
redundancy and woblle
allow mutation to occur w/o affecting protein
75
silent mutations
no effect on protein synthesis
76
nonsense mutations (truncation)
premature stop codon
77
missense mutations
codes diff amino acid
78
frameshift mutations
result in nucleotide addition or deletion, changing reading frame of subsequent codons
79
mRNA
carries message from DNA via transcription; nucleus --> cytoplasm
80
tRNA
brings in amino acids, recognizes codon on the mRNA using its anticodon
81
rRNA
makes up most of ribosome, enzymatic
82
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
83
posttranscriptional modifications
7-methylguanylate triphosphate cap added to 5' end; poly-A tail added to 3' end; spliceosome removes introns, ligates exons together
84
alternative splicing
combines diff exons to acquire diff gene products
85
translation steps
initiation, elongation, termination
86
posttranslational modifications
folding by chaperones, formation of quaternary structure, cleavage of proteins of signal sequences, covalent addition of other biomolecules
87
Jacob-Monod model
operons are inducible or repressible clusters of genes transcribed as a single mRNA
88
promoter
transcription factor within 25 bp of transcription start site
89
enhancer
transcription factor more than 25 bp of transcription start site
90
osmotic pressure
a colligative property; the pressure applied to a pure solvent to prevent osmosis, pi=iMRT
91
passive transport
does not require ATP because molecule moves down concentration gradient
92
simple diffusion
does not require transporter; small nonpolar molecules move passively down conc. gradient
93
osmosis
describes diffusion of water across selectively permeable membrane
94
facilitated diffusion
uses transport proteins to move impermeable solutes across membrane
95
primary active transport
requires energy in the form of ATP
96
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
97
pinocytosis, phagocytosis
ingestion of liquid/solids from vesicles formed from cell membrane
98
glycolysis
occurs in cytoplasm of all cells, does not require O, yields 2 ATP per cycle
99
glucokinase
present in pancreatic beta islet cells as part of glucose sensor, responsive to insulin in the liver
100
hexokinase
traps glucose
101
phosphofructokinase-1
rate limiting step
102
PFK-2
produces F2, 6-BP, which activates PFK-1
103
GAPDH
produces NADH
104
3-phosphoglycerate kinase and pyruvate kinase
perform substrate-level phosphorylation
105
lactate dehydrogenase
oxidizes NADH producted in glycolysis anaerobically
106
pyruvate dehydrogenase
converts pyruvate to acetyl-coA; stimulated by insulin and inhibited by acetyl-coA
107
citric acid cycle
takes place in mitochondrial matrix, oxidizes acetyl-coA t CO2, generates high-energy electron carriers (NADH and FADH2) and GTP
108
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
109
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
110
proton-motive force
electrochemical gradient generated by the electron transport chain across the inner mitochondrial matrix
111
proton concentration
intermembrane space >matrix
112
chemiosmotic coupling
formation of ATP using electrochemical gradient
113
ATP synthase
generates ATP from ADP and pi
114
glycolysis energy yield
2 NADH, 2 ATP
115
pyruvate dehydrogenase energy yield
1 NADH (2 NADH per molecule of glucose bc each glucose forms two pyruvates)
116
citric acid cycle energy yield
3 NADH, 1 FADH2, 1 GTP (x2 per molecule of glucose)
117
each NADH energy yield
2.5 ATP, 10 NADH form 25 ATP
118
each FADH2 energy yeld
1.5 ATP, 2 FADH2 for 3 ATP
119
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
120
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
121
gluconeogenesis
occurs in cytoplasm and mitochondria, predominantly in liver; mostly just reverse of glycolysis, using same enzymes
122
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)
123
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
124
postprandial/well-fed (absorptive) state
insulin secretion is high, anabolic metabolism prevails
125
postabsorptive (fasting) state
insulin secretion decreases while glycagon and catecholamine secretion increases
126
prolonged fasting (starvation)
dramatically increases glucagon and catecholamine secretion; most tissues rely on fatty acids
127
liver
maintains blood glucose through glycogenolysis and gluconeogensis, processes lipids, cholesterol, bile, urea, and toxins
