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Biochemistry > Exam 4: Nucleic Acids > Flashcards

Exam 4: Nucleic Acids Flashcards

1
Q

Noncoding DNA sequences

A

DNA that does not code for proteins (Spacer sequences, Introns, Genes encoding nonprotein-coding RNAs, Repetitious DNA)

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2
Q

Spacer sequences

A

DNA sequences that separate genes

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3
Q

Introns

A

Noncoding sequences within gene - spliced out of primary RNA and transcribed into mRNA or protein

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4
Q

Repetitious DNA sequences

A 
Satellite DNA (repeats of relatively short sequences, give DNA weight, mostly confined to centromere and telomere), interspersed repeats (dispersed throughout the genome, many copies of transposons and retrotransposons)
half of DNA - noncoding sequences
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5
Q

Exons

A

sequences of DNA translated into protein

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6
Q

Gene families

A

genes that have similar nucleotide sequence and encode similar proteins
come from gene duplication that accumulates mutations over time
can be clustered at one chromosomal locus or dispersed throughout the genome

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7
Q

pseudogene

A

Gene family duplicate that was inactivated by mutation

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8
Q

Chromatin

A

complex of DNA and protein (1/3 DNA, 2/3 protein)
DNA wrapped around histones, then associated to form a fiber, then fiber forms wide loop domains
During condensation for cell division looped domains attach to protein scaffold to form wide fibers

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9
Q

Nucleosomes

A

DNA wrapped around histone proteins
146 bp wrapped around two of each of 4 histones (H2A, H2B, H3, H4)
5th histone (H1) attaches and seals structure

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10
Q

Chromosomes

A

DNA organized into large linear molecules

in division each chromosome consists of two identical DNA strands - chromatids - attached to each other at centromeres

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11
Q

Chromatid

A

identical DNA strands attached to form chromosome during G2 & M phases of cell cycle

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12
Q

Telomeres

A

special sequences at ends of chromatids

DNA forms a loop to protect free end from degradation

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13
Q

Haploid

A

cells containing one copy of each chromosome

In humans only egg and sperm are haploid

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14
Q

Diploid

A

cells containing a maternal and paternal copy of each chromosome - homologous chromosomes

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15
Q

Mitochondrial genome

A

different from nuclear genome
Circular, multiple copies per organelle
not extensively associated with proteins

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16
Q

Nuclear envelope regulates

A

Access of proteins to DNA;

Separation of translation and transcription - allows for post-transcriptional modification of RNA

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17
Q

Heterochromatin

A

intensively stained on electron micrograph - complexed with proteins, highly condensed, and transcriptionally inactive
Located on periphery of nucleus

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18
Q

Euchromatin

A

translucent on electron micrograph - transcriptionally active, decondensed DNA, not associated with as much protein

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19
Q

Nucleolus

A

large, intensely stained area on electron micrograph - internal structure, contains genes encoding ribosomal RNA
Actively transcribed

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20
Q

nuclear matrix

A

protein scaffold that attaches to chromosomes

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21
Q

Chromosomal territory

A

each chromosome occupies a distinct territory of nucleus

22
Q

Interchromosomal domains

A

separate chromosomal territories

23
Q

Nuclear envelope

A

double-membrane, contiguous with endoplasmic reticulum

contains nuclear pores - only way to enter nucleus

24
Q

Nuclear pore

A

regulate traffic between nucleus ad cytoplasm

Energy-dependent to transfer proteins into nucleus

25
Q

3 main types of large molecues that must be actively and selectively transported into/out of nucleus

A

mRNA, proteins, ribosomal subunits

26
Q

Ran

A

small GTP binding protein that mediates import and export from nucleus

27
Q

Import of protein into nucleus requires

A

Protein associated with importin, inside nucleus importin associates with Ran-GTP an releases protein, importin/Ran complex transported out of nucleus, Ran-bound GTP hydrolyzed -release of importin, Ran-GDP reenters nucleus and converted back to Ran-GTP

28
Q

Export of protein from nucleus requires

A

protein to associate with exportin and Ran-GTP, outside nucleus, Ran-GTP is hydrolyzed to Ran-GDP and complex dissociates, Exportin and Ran-GDP transported back into nucleus, and Ran-GDP converted to Ran-GTP

29
Q

DNA polymerases

A

enzymes that synthesize DNA
Alpha, Beta, Delta, Epsilon function in replication and/or repair of nuclear DNA
Gamma functions in mitochondrial DNA replication

30
Q

DNA polymerases share these properties

A

enzymes template-directed
primer required (can’t initiate DNA synthesis)
synthesize DNA only in the 5’ to 3’ direction
dATP, dGTP, dCTP, and dTTP are nucleotide donors for DNA synthesis

31
Q

Primase

A

primer to initiate DNA replication, made of RNA

degraded by exonuclease - not in final DNA product

32
Q

origin recognition complex (ORC)

A

binding proteins that mark origins of replication
during S phase, activation of proteins associated with ORC allows initiation of replication - then inactivated, replication can’t be re-initiated

33
Q

DNA helicases

A

unwind DNA double helix using free energy of ATP hydrolysis

Start at origins of replication

34
Q

Single-stranded binding proteins

A

bind to exposed single strands of DNA to prevent from re-associating

35
Q

Topoisomerases

A

relieve supercoiling of adjacent regions of unwound DNA for replication to progress
Nick & re-ligate DNA strands - allow supercoils to unwind
Type I: cut backbone of one strand of DNA & re-ligate
Type II: manipulate two double helices at same time

36
Q

DNA polymerase alpha

A

synthesizes short RNA primer - primase activity

37
Q

Sliding clamp accessory proteins

A

adjacent to primer on DNA - allow enzyme to synthesize more DNA before falling off template

38
Q

DNA polymerase epsilon

A

synthesizes DNA on leading strand (toward growing replication fork) - synthesized continuously in 5’ to 3’ direction

39
Q

DNA polymerase delta

A

synthesizes DNA on lagging strand (away from replication fork) - synthesized discontinuously in 3’ to 5’ direction (even though actual synthesis still occurs in 5’ to 3’ directions, just smaller fragments - Okazaki fragment)
Fills in gaps after RNA primers removed

40
Q

DNA ligase

A

joins together Okazaki fragments - requires ATP

41
Q

Telomerase

A

contains an RNA molecule that is complementary to repeat sequence of telomere - acts as a template (TTAGGG) for extension of 3’ end of DNA so ends of chromosomes don’t get shortened

42
Q

Purine

A

Adenine and Guanine

43
Q

Pyrimidine

A

Thymine (Uracil in RNA) and Cytosine

44
Q

Guanine-cytosine forms

A

3 hydrogen bonds

45
Q

Adenine-thymine forms

A

2 hydrogen bonds

46
Q

Most protein-DNA interactions take place via

A

major groove (portions of bases exposed to interact with proteins)

47
Q

DNA helical structure is stabilized by

A

Hydrogen bonding between bases, hydrophobic and stacking interactions between base pairs, interactions of polyanionic backbone with cations

48
Q

Intercalating agents

A

molecules that fit exactly on rungs of DNA ladder - distort double-helix structure
Acridine dyes, Ethidium bromide, Doxorubicin

49
Q

Supercoiled DNA

A

adding (positive supercoiling) or subtracting (negative supercoiling) twists to double-helix - puts strain

50
Q

Topoisomerase inhibitors

A

inhibits ligase activity of type II topoisomerases - accumulation of DNA double strand breaks, causes cell death
Doxorubicin acts on human topoisomerase II - anticancer agent
Nalidixic acid and ciprofloxacin act on bacterial topoisomerase II - antibiotics

Biochemistry (15 decks)

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