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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
Polymerase Gamma
DNA replication in mitochondria | Exonuclease
26
Polymerase Delta
Replication (in lagging strand) DNA repair Exonuclease
27
Polymerase Sigma
Replication (leading strand) DNA repair Exonuclease
28
Polymerase Kappa
DNA repair (bypass polymerase)
29
Polymerase Eta
DNA repair (bypass polymerase)
30
Polymerase Zeta
DNA repair (bypass polymerase)
31
Polymerase Iota
DNA Repair (bypass polymerase)
32
Telomerase
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
Reverse Transcriptase
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
Azidothymidine
Anti-retroviral agent | Used in anticancer chemotherapy
35
Didanosine
Anti-retroviral agent | Used in anticancer chemotherapy
36
Cytarabin
Used in anticancer chemotherapy
37
Vidarabin
Antiviral agent
38
Monocistrionic
Each mRNA encodes for one protein. Eukaryotic cells.
39
Polycistrionic
MRNA encodes for multiple proteins. Prokaryotic DNA
40
CPSF
Transcription termination factor
41
CstF
Transcription termination factor.
42
RNA polymerase I
rRNA
43
RNA polymerase II
mRNA and miRNA
44
RNA polymerase III
tRNA and other small RNAs
45
Prokaryotic RNA polymerase
Holoenzyme with a 4 subunit core and a sigma cap which can detach.
46
Rifampin
Prokaryotic RNA polymerase inhibitor used to treat pulmonary tuberculosis.
47
Actinomycin D
Antibacterial, antitumor medication. Intercalates between the DNA bases, inhibiting initiation and elongation.
48
Alpha-amanitin
Inhibits eukaryotic RNA polymerases (II) Found in Death Cap mushrooms Causes death in 10 days in 10-20% of patients
49
Purpose of 5’ RNA cap
Decreases rate of degradation by nucleases. | Recognition site for binding to the ribosome
50
SnRNAs, Small Nuclear RNA
100-300 nucleotides rich in Uracil For small nuclear ribonucleoprotein particle (snRNPs) designated U1, 2, 4, 5, 6. Remove introns.
51
Codon
Three base pair sequence that codes for a specific amino acid.
52
The genetic code is:
``` Specific Universal Degenerative Continuous Non-overlapping ```
53
TRNA structure
``` Cloverleaf Anticodon loop 3’ acceptor end is site of AA attachment D and TwC loops contain modified bases Variable loop ```
54
Wobble
Nontraditional base-pairing possible between third 3’ position of the codon and the first 5’ position of the anticodon
55
Hypoxanthine (H)
deaminated adenosine
56
RRNA structure and function
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
47S rRNA precursor
Creates 28S, 18S and 5.8S
58
streptomycin
Binds to 30S subunit and distorts its structure, interfering with protein synthesis
59
Tetracyclines
Interact with the 30S subunit, blocking access to the aminoacyl-tRNA to the A site, thereby inhibiting elongation.
60
Peptidyltransferase (ribozyme)
Catalyzes the peptide bond formation, transferring the initiating aa from the p site to the aa at the a site.
61
Puromycin
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
Chloramphenicol
Inhibits prokaryotic peptidyltransferase. High levels may also inhibit mitochondrial protein synthesis.
63
Erythromycin
Binds irreversibly to a site on the 50S subunit and blocks the tunnel by which the peptide leaves the ribosome, inhibiting translocation
64
Spontaneous protein folding
relies on many proteins being available and requires suitable physiological conditions
65
Chaperone-assisted protein folding
Large number of Heat-shock proteins and chaperonins Function as molecular chaperones Require ATP
66
Proteasome
Selectively degrades damaged or short-lived proteins Uses ubiquitin modification to target proteins for degradation Requires ATP
67
Diseases causes by misfolded proteins
Alzheimer’s disease Parkinson disease Transmissible Spongiform Encephalopathies Huntington Disease
68
Amyloids
Insoluble fibrils of misfolded proteins.
69
Post-translational protein modifications
``` 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
I-cell Disease (Mucolipidosis II)
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
Mannose 6C Phosphorylation
Targets protein for the lysosome.

Clinical Foundations (17 decks)

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