Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

M2M Unit 1 > Learning Objective - hard stuff > Flashcards

Learning Objective - hard stuff Flashcards

1
Q

Peptide bond formation is catalyzed by

A

peptidyl transferase center

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Cells make interferons in response to …

A

viral RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Interferons bind to receptors on neighboring cells to…

A

down regulate their translation, protect them from infection

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

All amino acids are _____ isomers

A

L (CORN clockwise)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Longer side chains have ______ pKas

A

higher

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Essential amino acids (WHR FVT MILK?)

A

tryptophan, histidine, arginine, phenylalanine, valine, threonine, methionine, isoleucine, leucine, lysine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

The main driving force in secondary protein structure is __________ bonds

A

hydrogen

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Alanine and leucine are helix _______

A

formers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Proline and glycine are helix __________

A

breakers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

In parallel beta sheets, neighboring strands go in __________ direction

A

the same

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

In antiparallel beta sheets, neighboring strands go in __________ direction

A

the opposite

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Most peptide bonds are in the _______ conformation

A

trans

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

The two most commonly found amino acids in loops and turns are _______ and ________

A

glycine, proline

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

A molecule that binds is called a _________ and it forms __________ bonds

A

ligand, non-covalent

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

The two types of tertiary structures are ________ and __________

A

globular, fibrous

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Globular proteins (are/are not) water or lipid soluble

A

are

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Fibrous proteins (are/are not) water or lipid soluble

A

are not

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is Kd?

A

[ligand] when 50% of ligand is bound

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What are the two classes of chaperones?

A

chaperonins, HSPs (HSP70)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What does protein prolyl isomerase do?

A

reforms protein from typical trans formation to cis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Small RNAs play an important role in…

A

mRNA silencing and gene expression through a variety of mechanisms

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Longer non-coding RNAs are involved in…

A

regulation, silencing, etc.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Role of miRNAs

A
  • translational repression of mRNAs

- mRNA degradation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Role of siRNAs

A
  • cleave mRNAs
  • transcriptional silencing
  • heterochromatin formation
  • mobile element silencing
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Role of piRNAs

A
  • transcriptional silencing

- mobile element silencing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

A microRNA-induced silencing complex is made up of ________ and __________

A

argonaute, small RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

How are mRNA targets of miRNAs identified in the cell?

A

base-pairing with target mRNA 3’ UTR serves to “guide” effector complexes to particular mRNAs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

dicer

A

cleaves miRNA precursor (pre-miRNA) and double-stranded RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

argonaute

A

binds ssRNA, acts on RNA to do something

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

RISC complex

A

plays a role in how well RNA is cleaved; incorporates siRNA or microRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What is TRC18 and what happens if it is bound?

A

associated with RISC complex; required for miRNA silencing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

drosha

A

RNAse III enzyme that processes newly transcribed miRNA in nucleus; cleavage by drosha determines 5’ and 3’ ends of dicer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Does piRNA involve dicer?

A

No! (Because it’s already single-stranded)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What are RNase H-dependent ASOs?

A

single-stranded, chemically-modified DNA oligonucleotides bind to complementary sequences in target mRNA
-cleaves target RNA and inhibits translation by blocking ribosomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What are exon-skipping ASOs?

A
  • target intron-exon junctions (splice sites)
  • binding to target inhibits splicing, forcing choice of another splice site
  • *MUSCULAR DYSTROPHY
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Anti-miRs and miRNA mimics ________ and ________ the function of endogenous microRNAs

A

antagonize, mimic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

cofactor

A

metal ion required for enzymatic activity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

coenzyme

A

organic ligand that binds to enzyme and allows it to act on substrate (donated a chemical group)

41
Q

To make recombinant DNA, _________ uses ____ to make new bonds

A

DNA ligase, ATP

42
Q

Restriction enzymes only cut ______

A

double stranded DNA

43
Q

Name the three key features of cloning vectors

A
  1. restriction site
  2. origin of replication
  3. selectable marker
44
Q

Resealing DNA strands that were cut with restriction enzymes requires the use of ___ ATP

A

2 (restriction enzymes cut, two ends find each other, seal with ligase - two phosphodiester bonds so two ATP)

45
Q

What happens if elF4E is bound by 4E-BPs?

A

4E-BPs (which have to be dephosphorylated to bind to elF4E) bind to 4E and block its function (rapamycin drug does same thing)

46
Q

elF2-alpha is critical for steps that lead to binding of the __________ to ____________

A

initiator tRNA, ribosome

47
Q

siRNA function relates to

A

defense/immunity

48
Q

piRNA function relates to

A

gametes and control of mobile elements

49
Q

___________ protein is an inhibitor of the cell cycle

A

retinoblastoma (Rb)

50
Q

The _______ family of proteins inhibits all CDKs

A

Cip/Kip

51
Q

The _________ family of proteins specifically inhibits CDK4/6-cyclinD1-3 complexes

A

INK4

52
Q

In the DNA damage checkpoint, _____ and _____ proteins inhibit CDK cyclin complexes

A

p53, Chk2

53
Q

_______ and _______ proteins regulate the ATM/ATR checkpoint pathway for DNA damage

A

BRCA1, BRCA2

54
Q

Homologous recombination occurs during __ and __ phases of the cell cycle

A

S, G2

55
Q

The difference between coenzymes and cofactors is…

A

coenzymes are consumed

cofactors are not consumed

56
Q

T/F: The covalent structures of PrPc and PrPsc (prion proteins) are identical.

A

True (same primary structure)

57
Q

CDK is activated by ______

A

cyclin

58
Q

What does Rad17 do?

A

binds to DNA damage, recruits protein complex ATM/ATR

59
Q

p16 (Ink4) inhibits CDK4,6, preventing passage to _______

A

S phase (R point)

60
Q

The difference between Sanger sequencing and next generation sequencing is…

A

Sanger: millions of copies of one sequence
NextGen: millions of sequences get copied

61
Q

A short read is ________ bases

A

50-250 (illumina)

62
Q

A long read is ______ bases

A

2,500 (pacific biosciences)

63
Q

Nucleotide polymorphisms can be seen on (short/long) reads

A

long

64
Q

For long and short reads, compare…

  • read depth (coverage)
  • error rate
  • contiguity
A

Short: less read depth, lower error rate, can’t link variants
Long: greater read depth, higher error rate, can link variants

65
Q

Exome sequencing sequences the part of the genome that codes for _______

A

proteins

66
Q

Double stranded DNA breaks primarily affect… (3)

A

immune, nervous, and reproductive systems

67
Q

Endogenous causes of double-stranded DNA breaks (3)

A
  • immune system rearrangement
  • ss breaks in DNA replication
  • meiosis
68
Q

Exogenous causes of double-stranded DNA breaks (2)

A
  • radiation

- medical imaging

69
Q

In immune function, DSBs can be formed by ________

A

RAG recombinase

70
Q

Artemis is …

A
  • a nuclease

- an endonuclease and exonuclease used in NHEJ

71
Q

In meiosis, DSBs can be formed by ______

A

Spo11

72
Q

Function of Spo11

A

endonuclease that cleaves DNA (remains attached to it)

73
Q

In HR, using a sister chromatid results in (recombination/no recombination) and using a D-loop results in (recombination, no recombination)

A

no recombination, recombination

74
Q

Using a homologous chromosome instead of a sister chromatid in HR potentially leads to a _________

A

loss of heterozygosity

75
Q

How does wortmannin affect DSB repair in HR?

A

it inhibits histone modifications that are needed to signal DNA damage

76
Q

For VDJ recombination, only use _______ repair

A

NHEJ

77
Q

For meiosis, only use _______ repair

A

HR

78
Q

When CDK is present, _______ pushes for _____ DNA repair

A

BRCA1, HR

79
Q

When CDK is not present, _______ pushes for _____ DNA repair

A

53BP1, NHEJ

80
Q

____ keeps correct broken ends together as a pair

A

Ku, (Rad51 in HR?)

81
Q

NHEJ step

A
  • Ku recognizes
  • Ku recrutis DNA PKcs
  • nuclease removes damaged DNA
  • polymerase fills gap
  • ligase 4 restores phosphodiester backbone
82
Q

HR

A

-BRCA1 recruits complex that does endonuclease cleavage
-exonuclease degrades 5’ end
-Rad51 filament formation
D-loop formation (to bridge gap caused by break)

83
Q

Keq is a constant that defines the __________

A

equilibrium distribution

84
Q

How can enzymes lower the activation energy? (3)

A
  • binding energy between E and S to form ES complex
  • increase “local concentration” of substrates
  • rearrange covalent bonds
  • allosteric regulation
85
Q

Km = ?

A

[substrate] when you are at 1/2 Vmax

86
Q

kcat = ?

A
  • number of substrate molecules turned into product per enzyme per second under saturated conditions
  • rate-limiting
87
Q

inverse of cat = ?

A

time it takes to process one substrate molecule

88
Q

The ratio kcat/Km describes the ______ of an enzyme

A

efficiency

89
Q

A high kcat/Km indicates ________ efficiency of an enzyme

A

high

90
Q

Competitive inhibition changes the _____ but not the ______

A

Km (increases), kcat (changes slope of line weaver-burke plot)

91
Q

Uncompetitive inhibition changes _______

A

Kcat, Km (increases), and Vmax (lowers)

92
Q

For uncompetitive inhibition, if you increase inhibitor concentration, the line shifts ______ and slope _______

A

up; doesn’t change

93
Q

Lesion bypass error rate is __________ times higher than normal

A

100-100,000 times higher

94
Q

Telomerase is an _____-dependent ____-polymerase

A

RNA-dependent DNA polymerase

95
Q

All excision repair pathways require…

A
  • endonuclease and/or exonuclease
  • DNA polymerase
  • DNA ligase
96
Q

swi/snf are ___-dependent ATPases

A

DNA

97
Q

The error rate of DNA repair is…

A

10^-10

98
Q

In lesion bypass, alternate DNA polymerases lack ______________

A

3’ to 5’ proofreading exonuclease

99
Q

The N-termini of histones are rich in …

A

lysine

M2M Unit 1 (4 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions