Learning Objective - hard stuff Flashcards
(99 cards)
1
Q
Peptide bond formation is catalyzed by
A
peptidyl transferase center
2
Q
Cells make interferons in response to …
A
viral RNA
3
Q
Interferons bind to receptors on neighboring cells to…
A
down regulate their translation, protect them from infection
4
Q
All amino acids are _____ isomers
A
L (CORN clockwise)
5
Q
Longer side chains have ______ pKas
A
higher
6
Q
Essential amino acids (WHR FVT MILK?)
A
tryptophan, histidine, arginine, phenylalanine, valine, threonine, methionine, isoleucine, leucine, lysine
7
Q
The main driving force in secondary protein structure is __________ bonds
A
hydrogen
8
Q
Alanine and leucine are helix _______
A
formers
9
Q
Proline and glycine are helix __________
A
breakers
10
Q
In parallel beta sheets, neighboring strands go in __________ direction
A
the same
11
Q
In antiparallel beta sheets, neighboring strands go in __________ direction
A
the opposite
12
Q
Most peptide bonds are in the _______ conformation
A
trans
13
Q
The two most commonly found amino acids in loops and turns are _______ and ________
A
glycine, proline
14
Q
A molecule that binds is called a _________ and it forms __________ bonds
A
ligand, non-covalent
15
Q
The two types of tertiary structures are ________ and __________
A
globular, fibrous
16
Q
Globular proteins (are/are not) water or lipid soluble
A
are
17
Q
Fibrous proteins (are/are not) water or lipid soluble
A
are not
18
Q
What is Kd?
A
[ligand] when 50% of ligand is bound
19
Q
What are the two classes of chaperones?
A
chaperonins, HSPs (HSP70)
20
Q
What does disulfide isomerase do?
A
Incorrect disulfide bond formation between free cysteines causes this enzyme to come in, reduce improper bond and reform it correctly
21
Q
What does protein prolyl isomerase do?
A
reforms protein from typical trans formation to cis
22
Q
Small RNAs play an important role in…
A
mRNA silencing and gene expression through a variety of mechanisms
23
Q
Longer non-coding RNAs are involved in…
A
regulation, silencing, etc.
24
Q
Non-coding regulatory RNAs play roles in …
A
- post-transcriptional repression
- transcriptional repression or activation
- epigenetic modifications
- precursors of small RNAs
- modulate alternative splicing
- regulate structural organization
25
Role of miRNAs
- translational repression of mRNAs
| - mRNA degradation
26
Role of siRNAs
- cleave mRNAs
- transcriptional silencing
- heterochromatin formation
- mobile element silencing
27
Role of piRNAs
- transcriptional silencing
| - mobile element silencing
28
A microRNA-induced silencing complex is made up of ________ and __________
argonaute, small RNA
29
How are mRNA targets of miRNAs identified in the cell?
base-pairing with target mRNA 3' UTR serves to "guide" effector complexes to particular mRNAs
30
dicer
cleaves miRNA precursor (pre-miRNA) and double-stranded RNA
31
argonaute
binds ssRNA, acts on RNA to do something
32
RISC complex
plays a role in how well RNA is cleaved; incorporates siRNA or microRNA
33
What is TRC18 and what happens if it is bound?
associated with RISC complex; required for miRNA silencing
34
drosha
RNAse III enzyme that processes newly transcribed miRNA in nucleus; cleavage by drosha determines 5' and 3' ends of dicer
35
Does piRNA involve dicer?
No! (Because it's already single-stranded)
36
What are RNase H-dependent ASOs?
single-stranded, chemically-modified DNA oligonucleotides bind to complementary sequences in target mRNA
-cleaves target RNA and inhibits translation by blocking ribosomes
37
What are exon-skipping ASOs?
- target intron-exon junctions (splice sites)
- binding to target inhibits splicing, forcing choice of another splice site
* *MUSCULAR DYSTROPHY
38
Anti-miRs and miRNA mimics ________ and ________ the function of endogenous microRNAs
antagonize, mimic
39
cofactor
metal ion required for enzymatic activity
40
coenzyme
organic ligand that binds to enzyme and allows it to act on substrate (donated a chemical group)
41
To make recombinant DNA, _________ uses ____ to make new bonds
DNA ligase, ATP
42
Restriction enzymes only cut ______
double stranded DNA
43
Name the three key features of cloning vectors
1. restriction site
2. origin of replication
3. selectable marker
44
Resealing DNA strands that were cut with restriction enzymes requires the use of ___ ATP
2 (restriction enzymes cut, two ends find each other, seal with ligase - two phosphodiester bonds so two ATP)
45
What happens if elF4E is bound by 4E-BPs?
4E-BPs (which have to be dephosphorylated to bind to elF4E) bind to 4E and block its function (rapamycin drug does same thing)
46
elF2-alpha is critical for steps that lead to binding of the __________ to ____________
initiator tRNA, ribosome
47
siRNA function relates to
defense/immunity
48
piRNA function relates to
gametes and control of mobile elements
49
___________ protein is an inhibitor of the cell cycle
retinoblastoma (Rb)
50
The _______ family of proteins inhibits all CDKs
Cip/Kip
51
The _________ family of proteins specifically inhibits CDK4/6-cyclinD1-3 complexes
INK4
52
In the DNA damage checkpoint, _____ and _____ proteins inhibit CDK cyclin complexes
p53, Chk2
53
_______ and _______ proteins regulate the ATM/ATR checkpoint pathway for DNA damage
BRCA1, BRCA2
54
Homologous recombination occurs during __ and __ phases of the cell cycle
S, G2
55
The difference between coenzymes and cofactors is...
coenzymes are consumed
| cofactors are not consumed
56
T/F: The covalent structures of PrPc and PrPsc (prion proteins) are identical.
True (same primary structure)
57
CDK is activated by ______
cyclin
58
What does Rad17 do?
binds to DNA damage, recruits protein complex ATM/ATR
59
p16 (Ink4) inhibits CDK4,6, preventing passage to _______
S phase (R point)
60
The difference between Sanger sequencing and next generation sequencing is...
Sanger: millions of copies of one sequence
NextGen: millions of sequences get copied
61
A short read is ________ bases
50-250 (illumina)
62
A long read is ______ bases
2,500 (pacific biosciences)
63
Nucleotide polymorphisms can be seen on (short/long) reads
long
64
For long and short reads, compare...
- read depth (coverage)
- error rate
- contiguity
Short: less read depth, lower error rate, can't link variants
Long: greater read depth, higher error rate, can link variants
65
Exome sequencing sequences the part of the genome that codes for _______
proteins
66
Double stranded DNA breaks primarily affect... (3)
immune, nervous, and reproductive systems
67
Endogenous causes of double-stranded DNA breaks (3)
- immune system rearrangement
- ss breaks in DNA replication
- meiosis
68
Exogenous causes of double-stranded DNA breaks (2)
- radiation
| - medical imaging
69
In immune function, DSBs can be formed by ________
RAG recombinase
70
Artemis is ...
- a nuclease
| - an endonuclease and exonuclease used in NHEJ
71
In meiosis, DSBs can be formed by ______
Spo11
72
Function of Spo11
endonuclease that cleaves DNA (remains attached to it)
73
In HR, using a sister chromatid results in (recombination/no recombination) and using a D-loop results in (recombination, no recombination)
no recombination, recombination
74
Using a homologous chromosome instead of a sister chromatid in HR potentially leads to a _________
loss of heterozygosity
75
How does wortmannin affect DSB repair in HR?
it inhibits histone modifications that are needed to signal DNA damage
76
For VDJ recombination, only use _______ repair
NHEJ
77
For meiosis, only use _______ repair
HR
78
When CDK is present, _______ pushes for _____ DNA repair
BRCA1, HR
79
When CDK is not present, _______ pushes for _____ DNA repair
53BP1, NHEJ
80
____ keeps correct broken ends together as a pair
Ku, (Rad51 in HR?)
81
NHEJ step
- Ku recognizes
- Ku recrutis DNA PKcs
- nuclease removes damaged DNA
- polymerase fills gap
- ligase 4 restores phosphodiester backbone
82
HR
-BRCA1 recruits complex that does endonuclease cleavage
-exonuclease degrades 5' end
-Rad51 filament formation
D-loop formation (to bridge gap caused by break)
83
Keq is a constant that defines the __________
equilibrium distribution
84
How can enzymes lower the activation energy? (3)
- binding energy between E and S to form ES complex
- increase "local concentration" of substrates
- rearrange covalent bonds
- allosteric regulation
85
Km = ?
[substrate] when you are at 1/2 Vmax
86
kcat = ?
- number of substrate molecules turned into product per enzyme per second under saturated conditions
- rate-limiting
87
inverse of cat = ?
time it takes to process one substrate molecule
88
The ratio kcat/Km describes the ______ of an enzyme
efficiency
89
A high kcat/Km indicates ________ efficiency of an enzyme
high
90
Competitive inhibition changes the _____ but not the ______
Km (increases), kcat (changes slope of line weaver-burke plot)
91
Uncompetitive inhibition changes _______
Kcat, Km (increases), and Vmax (lowers)
92
For uncompetitive inhibition, if you increase inhibitor concentration, the line shifts ______ and slope _______
up; doesn't change
93
Lesion bypass error rate is __________ times higher than normal
100-100,000 times higher
94
Telomerase is an _____-dependent ____-polymerase
RNA-dependent DNA polymerase
95
All excision repair pathways require...
- endonuclease and/or exonuclease
- DNA polymerase
- DNA ligase
96
swi/snf are ___-dependent ATPases
DNA
97
The error rate of DNA repair is...
10^-10
98
In lesion bypass, alternate DNA polymerases lack ______________
3' to 5' proofreading exonuclease
99
The N-termini of histones are rich in ...
lysine
