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Biochemistry > Exam 4: Nucleic Acids > Flashcards

Exam 4: Nucleic Acids Flashcards

(50 cards)

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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

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A

each chromosome occupies a distinct territory of nucleus

22
Q

Interchromosomal domains

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A

separate chromosomal territories

23
Q

Nuclear envelope

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A

double-membrane, contiguous with endoplasmic reticulum

contains nuclear pores - only way to enter nucleus

24
Q

Nuclear pore

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A

regulate traffic between nucleus ad cytoplasm

Energy-dependent to transfer proteins into nucleus

25
3 main types of large molecues that must be actively and selectively transported into/out of nucleus
mRNA, proteins, ribosomal subunits
26
Ran
small GTP binding protein that mediates import and export from nucleus
27
Import of protein into nucleus requires
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
Export of protein from nucleus requires
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
DNA polymerases
enzymes that synthesize DNA Alpha, Beta, Delta, Epsilon function in replication and/or repair of nuclear DNA Gamma functions in mitochondrial DNA replication
30
DNA polymerases share these properties
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
Primase
primer to initiate DNA replication, made of RNA | degraded by exonuclease - not in final DNA product
32
origin recognition complex (ORC)
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
DNA helicases
unwind DNA double helix using free energy of ATP hydrolysis | Start at origins of replication
34
Single-stranded binding proteins
bind to exposed single strands of DNA to prevent from re-associating
35
Topoisomerases
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
DNA polymerase alpha
synthesizes short RNA primer - primase activity
37
Sliding clamp accessory proteins
adjacent to primer on DNA - allow enzyme to synthesize more DNA before falling off template
38
DNA polymerase epsilon
synthesizes DNA on leading strand (toward growing replication fork) - synthesized continuously in 5' to 3' direction
39
DNA polymerase delta
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
DNA ligase
joins together Okazaki fragments - requires ATP
41
Telomerase
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
Purine
Adenine and Guanine
43
Pyrimidine
Thymine (Uracil in RNA) and Cytosine
44
Guanine-cytosine forms
3 hydrogen bonds
45
Adenine-thymine forms
2 hydrogen bonds
46
Most protein-DNA interactions take place via
major groove (portions of bases exposed to interact with proteins)
47
DNA helical structure is stabilized by
Hydrogen bonding between bases, hydrophobic and stacking interactions between base pairs, interactions of polyanionic backbone with cations
48
Intercalating agents
molecules that fit exactly on rungs of DNA ladder - distort double-helix structure Acridine dyes, Ethidium bromide, Doxorubicin
49
Supercoiled DNA
adding (positive supercoiling) or subtracting (negative supercoiling) twists to double-helix - puts strain
50
Topoisomerase inhibitors
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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