Biochemistry Flashcards
1
Q
AA structure includes
A
basic amino group, acidic carbonyl group, R group, H atom
2
Q
L-AA are used to
A
synthesize proteins
3
Q
AA under low pH conditions =
A
protonated
4
Q
AA under high pH conditions
A
deprotonated
5
Q
_ AAs can destabilize or break down alpha helical 2 structures
A
glycine and proline
6
Q
proline does NOT contain an
A
aromatic ring
7
Q
_ AAs are the target of phosphorylation b/c they contain a hydroxyl functional group
A
serine, threonine, and tyrosine
8
Q
_ AAs can form salt bridges
A
basic & acidic
9
Q
_ can be used to break disulfide bonds in a western blot
A
BME
10
Q
peptide bond
A
dehydration reaction in which the amino group of 1 AA acts as a nucleophile and attacks the carboxyl group of another AA, releasing a water molecule
11
Q
amino and carboxyl functional group form a
A
amide group
12
Q
formation of a peptide bond is a _ reaction
A
endergonic (E from ATP)
13
Q
_ bonds stabilize secondary structure
A
H
14
Q
_ structure forms optimal conformation of a protein
A
tertiary
15
Q
what are the different forces stabilizing peptide bonds?
A
H bonds, ionic bonding/salt bridges, D-D interactions, LDF, and disulfide linkages
16
Q
proteins fold into a state that _ the entropy of the system
A
maximizes, but minimizes their own energy
17
Q
causes of protein denaturation
A
temperature, salinity, pH
18
Q
solvation layer
A
water molecules that surround a protein
19
Q
isoelectric focusing
A
each protein migrates until its reaches its pI
20
Q
pH < pI =
A
+ charged
21
Q
pH > pI =
A
- charged
22
Q
native PAGE
A
separates proteins in their native tertiary state based on size and charge
23
Q
SDS PAGE
A
separates proteins only based on their molecular mass NOT charge
24
Q
western blot
A
proteins are visualized on a gel to see if a particular protein is present
25
formation of ES complex _ activation energy
lowers
26
oxidoreductase
transfer of electrons which result in change in oxidation state
27
transferase
transfer of a functional group from 1 molecular to another
28
hydrolase
breakdown of a covalent bond using water
29
lyase
breakdown of a covalent bond without water or electron transfer (oxidation)
30
isomerase
rearrangement of bonds within a molecule
31
ligase
formation of a covalent bond between 2 large molecules
32
enzyme approximation
enzyme catalyzes the reaction by bringing reactants in close proximity
33
covalent catalysis
enzyme catalyzes the reaction by forming a temporary covalent bond with the reactant
34
acid-base catalysis
enzyme catalyzes the reaction by acting as a n acid/base
35
metal ion catalysis
enzyme catalyses the reaction by assisting in electrophilic or nucleophilic interactions/binds to substrate
36
cofactors
inorganic ions (like iron or magnesium) that aids in activity
37
coenzymes
organic helpers and vitamins that aid in activity
38
2 ways to affect enzyme kinetics
increasing substrate concentration, increasing enzyme concentration
39
increasing substrate concentration beyond vmax effect:
none since the enzyme's AS is already saturated
40
competitive inhibition
bind to AS, Km increased Vmax no change
41
non-competitive inhibition
bind to enzyme at allosteric site, no change in Km, decrease in Vmax`
42
mixed inhibition
bind to enzyme or allosteric site, decrease in Vmax, increase/decrease in Km
43
uncompetitive inhibition
bind to ES complex, both Vmax and Km decrease
44
3 components of nucleotides
nitrogenous base, pentose sugar, and phosphate group
45
4 nitrogenous bases
adenine, guanine, cytosine, thymine
46
phosphodiester linkages
formed between the 3' carbon of 1 sugar and the 5' carbon of another
47
nucleoside
pentose sugar attached to a nitrogenous base
48
watson-crick & DNA
DNA is a double helix and strands lie anti-parallel to one another
49
chargaff's rule
total number of purines = total number of pyrimidines
50
G-C have a higher melting point b/c
they have more H bonds
51
hybridization of DNA
ssDNA can bind to another ssDNA of different origin if they have sufficient complementarity or base pairing
52
role of water
capable of H bonding (F, O, N) = elevated BP
53
lipid solubility
low solubility in water, high solubility in nonpolar organic solves (NP & hydrophobic)
54
role of lipids
energy storage, cellular organization and structure, precursor molecule for vitamins and hormones
55
fatty acids
building blocks of complex lipids which have a long C chain and carboxylic acid (most energy stroage)
56
triacylglycerols (triglycerides)
3c backbone (glycerol) and 3 FA chains, store E and provide insulation
57
phospholipids
have phosphate that replaces 1 of the FA, amphiphatic
58
glycolipids
carbohydrate replaces the phosphate in phospholipids, found in myelinated membranes
59
sphingolipids
have amino acid backbone` rather than glycerol found in triglycerides, have phosphate head and FA chain
60
steroids
4-ringed structure which contains cholesterol, important for membrane fluidity and precursor to steroid hormones
61
terpenes
pigments in the body (ex. vitamin A)
62
waxes
formed by ester linkage between alcohol chain and long-chain FA
63
eicosanoids
include prostaglandins, thromoxanes, etc Help to regulate BP, body temp, and muscle contraction
64
what allows lipids to be transported into the blood?
lipoprotein!
65
carbohydrates
have C-H bonds and alcohol chains, less E storage than lipids. join together via dehydration reactions
66
topoisomerase
works at the region ahead o the replication fork to prevent supercoiling by introducing breaks in the DNA and then resealing them
67
DNApol3
extends the primers, adds nucleotides in the 5' to 3' direction
68
DNApol1
replaces the primers with new DNA
69
DNApolII
has DNA proofreading ability and serves a repair fucntion
70
telomerase
not usually active in somatic cells, but is active in germ cells
71
mismatch repair
correct small insertions and deletions as well as correcting errors that occur right after replication is completed
72
glycosylases
detects and removes a specific kind of damaged base
73
2 pathways involved in double-stranded break repair
1. Non-homologous end joining: two broken ends of the chromosomes are glued back together
Introduces a small mutation
2. Homologous recombination: information from the homologous chromosomes that matches the damaged one is used to repair the break
74
amber codon
mutation occurs and causes an early stop codon in an mRNA sequence
75
degenerate genetic code means
many AA are encoded by a few different codons
76
missense codons
encode an incorrect AA
77
nonsense coons
encode a premature stop codon
78
Aminoacyl tRNA synthetases:
enzymes that load individual amino acids onto the tRNA
79
eukaryotic transcription occurs in the
nucleus
80
prokaryotic. transcription occurs in the
cytoplasm
81
eukaryotes require _ to first bind to the promoter region
transcription facotrs
82
RNA pol1
synthesizes rRNA
83
RNApol2
located in the nucleus and syntehsizes all protein coding nucleuar premRNAs
84
RNApol3
in nucleus, transcribes a variety of structural RNAs
85
prokaryotes have 2 types of termination signals
Rho-dependent termination (protein dependent) and Rho-independent termination which is controlled by specific DNA sequences)
86
small ribosome subunit
binding of the mRNA template
87
large ribosome subunit
binds tRNAs (have A, P, and E sites)
88
most post-translational mods happen in the
ER and Golgi
| -ex: glycosylation, lipidation, ubiquitination, phosphorylation
89
only AA that can undergo phosphorylation are
serine, tyrosine, and threonine
90
euchromatic
part of coding regions
91
heterochromatic
highly condensed, no coding, have regions that are silenced or suppressed by DNA mehtylation
92
monocistrionic expression
a single DNA promoter directs the synthesis of an mRNA containing 1 gene (seen in eukaryotic mRNA)
93
repressible operons
as long as the product of the pathway continues to be required by the cell, a repressible operon will continue to be expressed
94
inducible operons
expression of this (lac) is typically induced only in the presence of the substrate
95
lac operon
subject to activation in the absence of glucose, lactose must be present
96
CAP
protein that binds to the promoters of operons that control in the processing of alternative sugars
97
corepressor
protein that decreases gene expression by binding to a transcription factor that contains a DNA-binding domain
-Needs to recruit histone deacetylase which catalyzes the removal of acetal groups from lysine residues which makes the DNA less accessible to transcription
98
oncogenes
cause cancer
99
tumor suppressor genes
active in normal cells to prevent uncontrolled cell growth
| Ex: p53: functions as a tsg and transcription factor
100
proto-oncogenes
positive cell-cycle regulators, when mutated can become oncogenes and cause cancer
101
acetylation
increases gene epxression
102
Cpg islands
stretches of DNA with a high frequency of C and G pairs found in the promoter regions of genes, can be methylated
103
what are the non-coding RNA
mi-RNA, snRNA, rRNA, tRNA
104
mi-RNA
involved in post-transcriptional regulation of gene expression and silencing of RNA, suppress translation
