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Flashcards in DNA replication Deck (85)
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1
Q

DNA polymerase used in eukaryotes for DNA replication

A

alpha/delta DNA polymerase

2
Q

Characteristics of DNA replication in the leading strand

A

Continuous and toward replication fork

3
Q

Characteristics of DNA replication in the lagging strand

A

Starts from Okasaki fragments and directed away from replication fork

4
Q

Main genes involved in mismatch repair

A

hMLH1 and hMSH2

5
Q

Lynch syndrome confers an increased risk for developing which cancers

A
  • Colon (HNPCC)
  • Endometrial
  • Ovarian
  • Gastric
6
Q

Mismatch repair occurs during which phase of the cell cycle

A

G2

7
Q

Subunits of prokaryotic ribosome

A

30S + 50S = 70S

8
Q

Subunits of eukaryotic ribosome

A

40S + 60S = 80S

9
Q

Antibiotics that bind to the 30S subunits

A

“buy AT 30, CCEL at 50”

  • Aminoglycosides
  • Tetracyclins
10
Q

Specific mechanism of action of aminoglycosides

A

Binding to the 30S subunit and inhibit the formation of the initiation complex / they also cause misreading of mRNA

11
Q

Specific mechanism of action of tetracyclins

A

Binding to the 30S subunit and inhibit tRNA binding to the A-site

12
Q

Antibiotics that bind to the 50S subunits

A

“buy AT 30, CCEL at 50”

  • Cloramphenicol
  • Clindamycin
  • Eryhtromycin (Macrolides)
  • Linezolid
13
Q

Specific mechanism of action of macrolides

A

Binding to the 50S subunit and inhibit translocation of ribosome during elongation phase

*Same as clindamycin

14
Q

Specific mechanism of action of clindamycin

A

Binding to the 50S subunit and inhibit translocation of ribosome during elongation phase

*Same as macrolides

15
Q

Specific mechanism of action of chloramphenicol

A

Inhibits peptidyl transferase in the 50S subunit, leading to inhibition of protein chain elongation

16
Q

Specific mechanism of action of linezolid

A

Binding to the 50S subunit and inhibit the formation of the initiation complex

17
Q

Mode of inheritance of Chédiak-Higashi syndrome

A

Autosomal recessive

18
Q

Defective gene in Chédiak-Higashi syndrome

A

Lysosomal trafficking regulator gene (LYST)

19
Q

Pathogenesis of Chédiak-Higashi syndrome

A

There’s a microtubule polymerization defect leading to impaired function of phagosome-lysosome fusion

20
Q

Signs and symptoms of Chédiak-Higashi syndrome

A
  • Neutropenia
  • Recurrent pyogenic infections (staphylococci and streptococci)
  • Partial albinism
  • Peripheral neuropathy
21
Q

Laboratory findings in Chédiak-Higashi syndrome

A
  • Giant granules in granulocytes and platelets
  • Pancytopenia
  • Mild coagulation defects
22
Q

Functions of cilia

A
  • Mucociliary clearance

* Motility of sperm cells

23
Q

How do mismatch repair enzymes distinguish between old and new strands in prokaryotes

A

Template strand’s cytosine and adenine are methylated during DNA replication

24
Q

What does semi-conservative replication refers to

A

To the use of a template strand for the synthesis of a new strand in a complementary and antiparallel fashion

25
Q

Enzyme that excises RNA primer in eukaryotes

A

RNAse H

26
Q

Signs and symptoms of xeroderma pigmentosum

A
  • Extreme sensitivity to sunlight
  • Skin freckling
  • Skin cancer early in life
  • Ulcerations
27
Q

Laboratory diagnosis of xeroderma pigmentosum

A

Measuring excision endonuclease levels in serum white blood cells

28
Q

Treatment of xeroderma pigmentosum

A

Avoid UV light exposure

29
Q

Compounds that can cause base deamination

A

Nitrates

*Found in meat preservatives (hot dogs!)

30
Q

Consequence of a mutation in hMLH1 and hMSH2

A

Microsatellite instability

31
Q

What are microsatellites

A

Repeating sequences of noncoding DNA

32
Q

RNA processing modification that occurs co-transcriptionally (while mRNA is being transcribed)

A

Capping of the 5’ end (addition of 7-methylguanosine cap)

33
Q

RNA processing modifications that occur post-transcriptionally (after mRNA has being transcribed)

A
  • Polyadenylation of 3’ end (around 200 A’s)

* Splicing out of introns

34
Q

Function of tRNA

A

Carries activated aminoacid for translation

35
Q

Enzyme that catalyzes aminoacid activation

A

Aminoacyl-tRNA synthetase

36
Q

Where does translation occur

A

Cytoplasm

37
Q

Where in mRNA does the 40S subunit (eukaryotes) bind to in the initiation phase of protein synthesis

A

It binds to the 5’ cap structure

38
Q

Where in mRNA does the 30S subunit (prokaryotes) bind to in the initiation phase of protein synthesis

A

Shine-Delgarno sequence

39
Q

Ribosomal site where tRNA initially binds

A

Peptidyl site (P site)

40
Q

Ribosomal site where the incoming tRNAs bind

A

Aminoacyl site (A site)

41
Q

Mechanism by which shiga toxin inhibits protein synthesis

A

Cleaves an aminoacid from the 28S RNA of the 60S subunit of the ribosome

*Inhibits binding of tRNA to the A site

42
Q

Enzyme that catalyzes the formation of the peptide bond inside the ribosome in protein synthesis

A

Peptidyl transferase

43
Q

Part of the elongation phase of protein synthesis in which eEF-2 is required

A

Translocation of the growing peptide from the A site to the P site

44
Q

Mechanism by which Pseudomonas and diphteria toxin inhibit protein synthesis

A

ADP-ribosylation of eEF-2

45
Q

Cellular organelle affected in X-linked adrenoleukodystrophy

A

Peroxisomes

46
Q

Trinucleotide repeat expansions are generated during which phase of the cell cycle

A

S phase

47
Q

Types of mutation that a tumor suppressor gene needs to undergo to contribute to cancer

A

Deletions or los-of-function mutations

48
Q

CDK2NA mutations can be found in what pathology

A

Melanoma

49
Q

Protein products of CDK2NA gene

A

2 tumor suppressor genes:

  • p16 protein is an inhibitor of cyclin D-Cdk4/6 complexes, causing the cell to stop at G1
  • p14 protein inhibits MDM2, which normally targets p53 for degradation
50
Q

Laboratory technique used in paternity testing to analyze repeated units of 2 to 6 base pairs

A

PCR to amplify the microsatellite repeats

*Microsatellite testing detects genetic differences between individuals

51
Q

Laboratory technique that uses PCR to detect mutations occuring at sites where restriction enzymes cut

A

Restriction fragment length polymorphisms (RFLP)

52
Q

What is the difference between 10 nm and 30 nm chromatin

A

The prescence of H1

53
Q

Molecule needed by the prokaryotic RNA polymerase to start transcription

A

Protein factor sigma

54
Q

Molecule needed by the prokaryotic RNA polymerase to end trasncription

A

Protein factor rho

55
Q

Process inhibited by actinomycin D

A

Transcription, by inhibitng RNA polymerase in both eukaryotes and prokaryotes

56
Q

Lecture direction of RNA polymerase

A

3’ to 5’ (reads the template strand)

57
Q

Direction of synthesis of RNA polymerase

A

5’ to 3’

*The mRNA sequence will be identical to the DNA of the coding strand (uracil instead of thymine)

58
Q

What is the primary level of protein structure

A

The sequence of aminoacids

59
Q

What is the secondary level of protein structure

A

The folding of the aminoacid chain into energetically stable structures (alpha helix and beta sheets)

60
Q

What is the tertiary level of protein structure

A

Positioning of secondary structures in relation to each other to generate 3 dimentional shape

61
Q

What is the quaternary level of protein structure

A

The interaction among multiple subunits in proteins

62
Q

Types of proteins translated in the RER

A
  • Secreted proteins
  • Membrane-bound proteins
  • Lysosomal enzymes
63
Q

Types of proteins translated in the cytoplasm (free ribosomes)

A
  • Cytoplasmic proteins

* Mitochondrial proteins

64
Q

Aminoacid sequence that when translated directs the nascent protein to the RER for the rest of its translation

A

Hydrophobic aminoacid sequence (branched-chain aminoacids)

*Ribosome stays attached to the RER

65
Q

Name the 2 domains found in transcription factors

A
  1. DNA binding domains

2. Activation domains

66
Q

Name the 3 types (and examples) of DNA binding domains in transcription factors

A
  • Zinc fingers (eg, steroid hormone receptors)
  • Leucine zippers (eg, cAMP-dependent transcription factors)
  • Hélix-turn-helix (eg, embryonic gene expression transcription factors)
67
Q

Function of the activation domain of transcription factors

A
  • Binding to other transcription factors
  • Interaction with RNA polymerase
  • Recruitment of chromatin modifying proteins
68
Q

Name and describe the types of transcription factors

A
  • General: these are found in most genes within most cells, and are involved in basal transcription of genes
  • Specific: localized to specific cells and tissues, they bind to specific enhancer/silencer regions modulating the formation of the initiation complex
69
Q

Name the response element, function, and protein class of steroid receptors (transcription factors)

A
  • Response element: HRE
  • Function: steroid response
  • Protein class: zinc finger
70
Q

Name the response element, function, and protein class of cAMP response element binding (CREB) proteins (transcription factors)

A
  • Response element: CRE
  • Function: response to cAMP
  • Protein class: leucine zipper
71
Q

Name the response element, function, and protein class of peroxisome proliferator activated receptors (PPARs) (transcription factors)

A
  • Response element: PPREs
  • Function: regulate multiple aspects of lipid metabolism
  • Protein class: zinc fingers
72
Q

Name the response element, function, and protein class of NFkB transcription factor

A
  • Response element: kB elements
  • Function: regulate expression of many genes in immune system
  • Protein class: rel domains
73
Q

Name the response element, function, and protein class of homeodomain proteins (transcription factors)

A
  • Response element: ?
  • Function: regulate gene expression during development
  • Protein class: helix-turn-helix
74
Q

Definition of recombinant DNA

A

Splicing together of a human gene into a bacterial plasmid vector

75
Q

Uses of recombinant DNA

A
  • Provides a means of analyzing and altering genes and proteins
  • Provides reagents for genetic testing
  • Provides a source of specific proteins (eg, insulin)
76
Q

Type of DNA sequence where restriction endonucleases cut

A

Palindrome sequences

*Yielding restriction fragments of chromosomes

77
Q

Source of DNA in genomic libraries

A

Chromosomal DNA

78
Q

Source of DNA in expression (cDNA) libraries

A

mRNA

79
Q

Enzymes used to make genomic libraries

A
  • Restriction endonuclease

* DNA ligase

80
Q

Enzymes used to make expression (cDNA) libraries

A
  • Reverse transcriptase

* DNA ligase

81
Q

Main advantage of genomic libraries

A

When a non-coding sequence of a gene (like promoters or enhancers) needs to be studied

82
Q

Main disadvantage of genomic libraries

A

That the gene of interest may be fragmented by endonuclease treatment

83
Q

Main advantage of expression (cDNA) libraries

A

That the entire reading sequence of a particular gene is obtained intact, and therefore can be used in gene therapy

84
Q

Vectors used in gene therapy to deliver the gene sequence to the somatic cell

A
  • Modified virus

* Liposome

85
Q

Will the gene delivered to the cells be inherited in gene therapy

A

No, because it is in a somatic cell