Week 1 - Biochemistry Flashcards
1
Q
two purines
A
adenine and guanine
2
Q
three pyrimidines
A
thymine, cytosine and uracil
3
Q
U replaces what?
A
T
4
Q
5’ end has what?
A
phosphate group
5
Q
3’ end has what
A
hydroxyl group
6
Q
name 3 levels of packing in DNA in order
A
nucleosomes, loops of fibers (beads on a string), and 30 nm fibers
7
Q
how do prokaryotes pack their dna?
A
negative supercoiling and HU proteins
8
Q
how many oriC in prokaryotes?
A
one
9
Q
how many origins of replication in eukarytoes?
A
many many many
10
Q
2 sequences of the OriC
A
3x 13-mer sequence and 4x 9-nucleotide sequence
11
Q
importance of 13 mer tandem sequences?
A
AT rich so will break easily
12
Q
DnaA binds to what?
A
9-nucleotide region
13
Q
what happens after DnaA binds?
A
13 mer sequence opens
14
Q
what delivers DnaB?
A
DnaC - helicase inhibitor
15
Q
what is DnaB?
A
helicase
16
Q
what does helicase do?
A
wraps around both strands of DNA to unwind DNA in both directions away from the OriC
17
Q
what is DnaA
A
initiatior protein
18
Q
what is DnaB
A
helicase
19
Q
what are the importance of single stranded binding proteins?
A
they hold everything open (ssbp)
20
Q
main enzyme of DNA replication?
A
DNA pol III
21
Q
direction of DNA pol III
A
5’-3’, lays down leading and lagging strands
22
Q
what is released after complementary nucleotide is seale
A
pyrophosphate
23
Q
what special thing can DNA pol III do?
A
3’-5’ exonuclease activity
24
Q
what is DNA primase?
A
lays down RNA template so that DNA pol III can begin
25
what is DNA pol I?
removes and replaced RNA primer
26
what is DNA ligase?
ligates okazaki fragments together
27
describe leading and lagging strand
DNA pol III will lay down both, 2 separate going in both directions, leading continuous, lagging has to lay down short bits known as Okazaki fragments
28
what is the central dogma of biology?
DNA --> RNA --> protein
29
direction of RNA pol?
5'-3'
30
template strand?
read by RNA pol to generate mRNA
31
another name for template strand?
antisense strand
32
another name for the non-template strand?
sense strand
33
non-template strand?
not read by RNA pol to generate mRNA but is the sense strand, meaning the mRNA generated is an exact copy except for the U instead of T
34
is a primer needed for RNA pol?
no
35
name the 4 types of RNA
mRNA, tRNA, rRNA, and snRNA
36
how many RNA pol in bacteria?
one
37
how many RNA in euk?
3
38
RNA pol I?
makes rRNA
39
RNA pol II?
mRNA and some snRNA
40
RNA pol III?
tRNA and some snRNA
41
3 regions of prokaryote gene?
promotor, RNA coding sequence, and terminator
42
the holoenzyme form of prok RNA pol has what?
sigma factor
43
when does sigma factor fall off?
after 8-9 nucleotides in
44
pribnow box?
prokaryote promotor region -10, there is also some at -35
45
in euk what is the major sequence in the promotor?
tata box
46
what is TFIID?
distorts DNA helix, has TATA box binding protein
47
what is TFIIB?
part of RNA pol interaction
48
what is TFIIH?
DNA helicase, activates RNA polymerase through phosphorylation
49
what is TFIIE?
positions RNA polymerase
50
what increases levels of transcription in euk?
activators and adaptor molecules
51
what does transcription do to the coils ahead and behind?
positive supercoils in front, and negative supercoils behind
52
what does the cell do during transcription to solve supercoiling
gyrase in front, topoisomerase in back
53
two types of transcription termination?
intrinsic-palindromic region forms hairpin, G-C rich region followed by Us
extrensic-rho factor
54
during post transcriptional processing what happens?
introns spliced out, 5' cap added which is methylated, poly A tail added
55
describe the general structure of an amino acid
central carbon bonded to hydrogen, R group, amino group, and carboxyl group
56
2 amino acids are bound together by a?
peptide bond
57
name the 4 types of amino acids?
acidic, basic, neutral/nonpolar, neutral polar
58
who deciphered the genetic code?
Nirenburg
59
what are the characteristics of the genetic code?
triplet, comma free, nonoverlapping, almost universal, degenerate (more than one codon occurs for each amino acid), start and stop
60
describe base-pairing wobble
if cells do not carry tRNAs for all codons the 5' end of tRNA can wobble as it attaches to the 3' end of mRNA
61
deletion?
causes frameshift mutation
62
addition?
reversion of deletion mutation
63
amino acid attached to what end of tRNA?
3'
64
describe charging of tRNA?
tRNA synthetase (one for each amino acid), adds amino acid onto ATP, AMP left, then add that new structure to 3' end of tRNA
65
prok ribosome structure?
30s. 50s, 70s
66
euk ribosome structure?
40s, 60s, 80s
67
describe initiation of prok transcription
30s + initiation factors + GTP bind to fMet initiator tRNA, all that ish binds to shin-delgrano sequence, 50s comes along to form 70s, GTP hydrolyzed as initiation factors pop off
68
describe initiation of euk transcription
40s binds to methylated 5' cap then migrates to first AUG
69
how are appropriate tRNA brought to A site?
elongation factors and GTP
70
role of peptidyl transferase
forms peptide bond between P site and A site leaving elongated chain on A site
71
what is a polysome?
a number of ribosomes each translating the same mRNA sequentially
72
how is translation terminated?
releasing factors associated with UAG, UAA, and UGA, euk have 1 releasing factor, prok 3 releasing factors
73
what does an oxidoreductase do?
oxidation-reduction
74
what does a transferase do?
transfer of C N and P
75
what does a hydrolase do?
adds water
76
what does a lyase do?
cleaves carbon sulfer or nitrogen bond
77
what does an isomerase do?
rearranges
78
what does a ligase do
formation of bonds coupled to ATP hydrolasis
79
what does a kinase do?
adds an phosphate to something
80
what does a phosphatase do?
cuts a phosphate off something
81
what is a cofactor?
inorganic component
82
what is a coenzyme?
non-protein component like a vitamin
83
what is a holoenzyme?
enzyme plus cofactor
84
apoenzyme
enzyme without cofactor
85
porsthetic group
a coenzyme that is tightly (usually covalently) attached
86
what is proteolytic cleavage?
zymogen to active form through truncation
87
what is covalent modification?
increase or decrease activity through phosphorylation
88
what is sequestration?
enzyme=inactive polymers
89
what is allosteric regulation?
other site regulation; homotropic positive and heterotropic negative
90
what is induction?
upregulation through gene expression
91
what is repression?
downregulation through gene expression
92
what are isozymes?
catalyze the same reaction but are different molecular sizes
93
shape of curve with allosteric enzymes?
sigmoid
94
shape of curve with Michaelis-Menten kinetics
hyperbolic
95
Describe michaelis-menten kinetics
km=concentration of substrate at 1/2Vmax, high concentration velocity zero order meaning high velocity and not dependant on concentration, low concentration velocity first order meaning proportional to substrate concentration
96
what is reversible inhibition?
weak, non-covalent bonds readily dissociate, enzyme inactive when inhibitor is present
97
what is irreversible inhibition?
covalent bonds, or strong non-covalent
98
examples of reversible inhibition
competitive inhibitors which resemble sustrate, non-competitive inhibitors that bind other site, uncompetative - binds to other site but only during ES complex
99
examples of irreversible inhibition
permanently inactive enzymes, heavy metals and such
100
what does a competitive inhibitor do to the graph?
vmax same, km increased
101
what does a non-competitive inhibitor do to the graph?
vmax decreased, km same
102
what does a uncompetitive inhibitor do to the graph?
vmax decreased, km decreased
103
how many amino acids?
20
104
how many organization levels of proteins?
4: primary, secondary, tertiary, and quaternary
105
key to primary structure
sequence of amino acids, peptide bond which is very strong
106
characteristics of the peptide bond
doesn't rotate, trans configuration, uncharged but polar so can experience hydrogen bonding, rigid and planar
107
how is a peptide bond formed
condensation reaction
108
how to determine protein composition
acid hydrolysis, chromatography, quantitative with ninhydrin (spectrophotometry)
109
how to sequence a protein
Edman's reagent breaks off piece by piece
110
key to secondary structure
hydrogen bonding
111
3 structures of secondary structure
alpha helices, beta sheets and random chain
112
what disrupts alpha helices
proline and glycine, high number of charged aas, or aas with bulky R groups
113
characteristics of parallel beta sheets
up and down, same direction
114
characteristics of anti parallel beta sheets
up and down, opposite directions
115
characteristics of the beta bend
proline, glycine, charged, hydrogen bonding
116
what is three demensional structure
3D structure of the protein
117
characteristics of globular proteins
spherical, good water solubility, dynamic metabolic function
118
quarternary structure
two or more subunits
119
what stabilizes tertiary structure?
hydrogen bonds, disulfide bonds between Cysteines, hydrophobic interactions, ionic and polar interactions
120
what helps protein folding?
chaperones
121
what can denature a protein?
heat, organic solvents, mechanical shearing, heavy metals, detergents, chaotropic agents; may be reversible or irreversible, loss of biologic activity
122
name a protein that can renature
ribonuclease
123
what stabilizes Quaternary structure?
hydrogen bonds, hydrophobic interactions, electrostatic interactions
124
features of catabolism
degradation, convergence, oxidation
125
products of catabolism
ATP, FADH2, NADH, NADPH
126
features of anabolism
synthesis, reduction, divergence, uses ATP
127
products of anabolism
NAD+, FAD, ADP, NADP+
128
stages of catabolism
I - hydrolysis of complex molecules, II - conversion to acetyl CoA, III - oxidation of acetyl CoA
129
what does regulation depend on?
intercellular signals, and intracellular signals
130
types of intercellular signals
synaptic (nerves), endocrine (hormones), direct (gap junctions)
131
4 types of signal transduction
steroid, gated ion, receptor enzyme (or catylitic receptor), G-protein coupled receptor
132
example of steroid receptor
goes inside the cell for upregulation or downregulation of genes
133
example of gated ion receptor
receptor linked to ligand, voltage-gated ion; ex nicotinic ACh
134
example of receptor or catalytic receoptor
insulin and tyrosine kinase
135
example of G-protein coupled receptor
produce second messenger (beta andrenergic receptor), cAMP, IP3, DAG, Calcium
136
describe complete process of adynelate cyclase system
1) Epinephrine or Norepinephrine binding
2) GDP replaced by GTP on Gs
3) Gs (alpha subunit) moves to adenylyl cyclase and activates it
4) adenylyl cyclase catalyzes formation of cAMP from ATP
5) protein kinase A activated by cAMP
6) protein kinase A phosphorylates other proteins
7) cAMP is degraded by cyclic nucleotide phosphodiesterase
137
describe complete process of phosphoinositide system
1) ligand binds
2) GDP replaced by GTP on Gq
3) Gq (alpha subunit) moves to phospholipase C and activates it
4) phopholipase C cleaves PIP2 to IP3 and DAG
5) IP3 causes calcium to be released from the ER lumen
6) protein kinase C activated by DAG in cell membrane and calcium released from ER lumen
7) protein kinase C then phosphorylates proteins
