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Clinical Foundations > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

Diploid

A

Two sets of homologous chromosomes

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2
Q

Haploid

A

One set of chromosomes

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3
Q

Karyotype analysis

A

Diagnostic tool to detect chromosomal abnormalities in genetic diseases, tumor staging, and gender identification

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4
Q

Repetitive DNA sequences

A

Found near centromeric and telomeric regions, but can also be dispersed throughout the chromosome

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5
Q

Gene Structure

A

Promoter region — 5’ untranslated region — Start codon — Introns and Exons — Stop codon — 3’ untranslated region — Polyadenylation signal

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6
Q

Single copy genes

A

Protein coding DNA 200,000-250,000 human genes

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7
Q

Satellite DNA

A

Generally not transcribed, highly repetitive clusters. Can be Alpha, Mini, and Micro.

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8
Q

Dispersed Repetitive DNA

A

LINES- Long interspersed elements
SINES- Short interspersed elements
Transposons

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9
Q

Where does DNA replication occur?

A

In the nucleus

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10
Q

When does DNA replication occur?

A

S phase of the cell cycle

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11
Q

Semiconservative replication

A

Model of DNA replication in known cells. Each new double stranded DNA contains one strand from original DNA and one newly synthesized.

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12
Q

DNA polymerase III

A

Elongates a new DNA strand by adding dNTPs to the 3’-end of the growing chain.

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13
Q

Primase

A

Synthesizes the short stretches of RNA (10nt) on the lagging strand.

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14
Q

Topoisomerase I and II (gyrase)

A

Removes supercoils in the helix by transiently cleaving one or both of the DNA strands.

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15
Q

DNA Helicase

A

Unwinds short segments of the parental duplex DNA.

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16
Q

DNA Ligase

A

Catalyzes the sealing of nicks (breaks) remaining in the DNA on the lagging strand.

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17
Q

Single-strand binding proteins

A

Prevent premature annealing of the ssDNA back to dsDNA.

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18
Q

Okazaki fragment

A

Short DNA fragments (~ 150 nt) synthesized on the lagging strand.

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19
Q

Camptothecins

A

Target Topoisomerase I

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20
Q

-etoposide, doxorubicin

A

Targets Topoisomerse II

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21
Q

Nalidixic acid and norfloxacin

A

Antibiotics targeting DNA gyrase

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22
Q

3-5’ Exonuclease

A

Proofreads the DNA strand as it is synthesized.

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23
Q

Polymerase alpha

A

Replication (in complex with primase and aids in starting the primer)
DNA repair

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24
Q

Polymerase Beta

A

DNA repair

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25
Q

Polymerase Gamma

A

DNA replication in mitochondria

Exonuclease

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26
Q

Polymerase Delta

A

Replication (in lagging strand)
DNA repair
Exonuclease

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27
Q

Polymerase Sigma

A

Replication (leading strand)
DNA repair
Exonuclease

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28
Q

Polymerase Kappa

A

DNA repair (bypass polymerase)

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29
Q

Polymerase Eta

A

DNA repair (bypass polymerase)

30
Q

Polymerase Zeta

A

DNA repair (bypass polymerase)

31
Q

Polymerase Iota

A

DNA Repair (bypass polymerase)

32
Q

Telomerase

A

A complex of protein TERT and short piece of RNA template. Acts as reverse transcriptase.
Active in Germ line cells and stem cells.
Reactivated in disease states.

33
Q

Reverse Transcriptase

A

Found in retroviruses. Uses ssDNA to make dsDNA. This dsDNA can then be incorporated into human DNA. The viral DNA can then be transcribed.

34
Q

Azidothymidine

A

Anti-retroviral agent

Used in anticancer chemotherapy

35
Q

Didanosine

A

Anti-retroviral agent

Used in anticancer chemotherapy

36
Q

Cytarabin

A

Used in anticancer chemotherapy

37
Q

Vidarabin

A

Antiviral agent

38
Q

Monocistrionic

A

Each mRNA encodes for one protein. Eukaryotic cells.

39
Q

Polycistrionic

A

MRNA encodes for multiple proteins. Prokaryotic DNA

40
Q

CPSF

A

Transcription termination factor

41
Q

CstF

A

Transcription termination factor.

42
Q

RNA polymerase I

A

rRNA

43
Q

RNA polymerase II

A

mRNA and miRNA

44
Q

RNA polymerase III

A

tRNA and other small RNAs

45
Q

Prokaryotic RNA polymerase

A

Holoenzyme with a 4 subunit core and a sigma cap which can detach.

46
Q

Rifampin

A

Prokaryotic RNA polymerase inhibitor used to treat pulmonary tuberculosis.

47
Q

Actinomycin D

A

Antibacterial, antitumor medication. Intercalates between the DNA bases, inhibiting initiation and elongation.

48
Q

Alpha-amanitin

A

Inhibits eukaryotic RNA polymerases (II)
Found in Death Cap mushrooms
Causes death in 10 days in 10-20% of patients

49
Q

Purpose of 5’ RNA cap

A

Decreases rate of degradation by nucleases.

Recognition site for binding to the ribosome

50
Q

SnRNAs, Small Nuclear RNA

A

100-300 nucleotides rich in Uracil
For small nuclear ribonucleoprotein particle (snRNPs) designated U1, 2, 4, 5, 6.
Remove introns.

51
Q

Codon

A

Three base pair sequence that codes for a specific amino acid.

52
Q

The genetic code is:

A 
Specific
Universal
Degenerative
Continuous
Non-overlapping
53
Q

TRNA structure

A 
Cloverleaf
Anticodon loop
3’ acceptor end is site of AA attachment
D and TwC loops contain modified bases
Variable loop
54
Q

Wobble

A

Nontraditional base-pairing possible between third 3’ position of the codon and the first 5’ position of the anticodon

55
Q

Hypoxanthine (H)

A

deaminated adenosine

56
Q

RRNA structure and function

A

Make up 80% of all RNA
4 different sizes in eukaryotic cells
Produced from larger precursors
Together with the ribosomal proteins form the small and large subunits to create proteins.

57
Q

47S rRNA precursor

A

Creates 28S, 18S and 5.8S

58
Q

streptomycin

A

Binds to 30S subunit and distorts its structure, interfering with protein synthesis

59
Q

Tetracyclines

A

Interact with the 30S subunit, blocking access to the aminoacyl-tRNA to the A site, thereby inhibiting elongation.

60
Q

Peptidyltransferase (ribozyme)

A

Catalyzes the peptide bond formation, transferring the initiating aa from the p site to the aa at the a site.

61
Q

Puromycin

A

Bears a resemblance to aminoacyl-tRNA and accepts peptide from the P site, causing inhibition of elongation, and premature termination in pro and eukaryotes.

62
Q

Chloramphenicol

A

Inhibits prokaryotic peptidyltransferase. High levels may also inhibit mitochondrial protein synthesis.

63
Q

Erythromycin

A

Binds irreversibly to a site on the 50S subunit and blocks the tunnel by which the peptide leaves the ribosome, inhibiting translocation

64
Q

Spontaneous protein folding

A

relies on many proteins being available and requires suitable physiological conditions

65
Q

Chaperone-assisted protein folding

A

Large number of Heat-shock proteins and chaperonins
Function as molecular chaperones
Require ATP

66
Q

Proteasome

A

Selectively degrades damaged or short-lived proteins
Uses ubiquitin modification to target proteins for degradation
Requires ATP

67
Q

Diseases causes by misfolded proteins

A

Alzheimer’s disease
Parkinson disease
Transmissible Spongiform Encephalopathies
Huntington Disease

68
Q

Amyloids

A

Insoluble fibrils of misfolded proteins.

69
Q

Post-translational protein modifications

A 
Carbohydrate addition:
O-Glycosylation
N-Glycosylation
Lipid Addition:
Palmitoylation
Prenylation
Myristoylation

All can target the protein for a destination in or out of the cell.

70
Q

I-cell Disease (Mucolipidosis II)

A

Very rare autosomal recessive disease caused by a deficiency in the enzyme that phosphorylates mannose at C6.
Skeletal abnormalities, restricted joint movement, coarse facial features, severe psychomotor impairment.
Death occurs in early childhood.

71
Q

Mannose 6C Phosphorylation

A

Targets protein for the lysosome.

Clinical Foundations (17 decks)

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