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Molecular Genetics > Unit 1 Exam > Flashcards

Unit 1 Exam Flashcards

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1
Q

semiconservative replication

A

each daughter DNA molecule contains 1 strand from parent and 1 newly synthesized strand

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2
Q

DNA structure

A

sugar-phosphate backbone gives DNA molecule overall negative charge
A and G are purines that have 2 rings and C and T are pyrimidines that have 1 ring (most energetically favorable pairings)

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3
Q

DNA bonds

A

phosphodiester bonds: OH group on 3’ carbon forms covalent bond with phosphate group on 5’ carbon below it
hydrogen bonds: A and T (forms 2 H bonds), C and G (forms 3 H bonds), H bonds force sugar-phosphate backbone in anti-parallel directions

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4
Q

nucleosomes

A

DNA wrapped around core of histone proteins- histones have (+) charge and DNA is (-) so this attraction encourages non-specific wrapping, histones form an octamer (2 sets of 4- H2A, H2B, H3, H4)

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5
Q

histone tails

A

1 protein end projecting out from histone, play important role in regulating opening and closing/condensing of chromatin, rich in lysines which give it a (+)

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6
Q

chromatin

A

fibers made up of packed nucleosomes, 30 nm fiber-coiled helix of nucleosomal DNA, requires 5th histone (H1) a linker histone on the edge of nucleosome where DNA exits spool and changes path of DNA promoting a twisting structure

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7
Q

chromosomes

A

organized subunits of genome (1 molecule of DNA), separates genome into manageable units that are organized spatially, 23 pairs in human genome

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8
Q

condensed heterochromatin

A

fits into small spaces and provides protection from damage

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9
Q

decondensed euchromatin

A

“beads on a string”, easier to read and allows access for DNA replication or transcription machinery

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10
Q

HATs and HDACs

A

histone acetyl transferases add acetyl group to histone tails, removing the (+) charge of lysines loosening interaction between histone and DNA, opening chromatin and increasing gene expression
histone deacetylases remove the acetyl group, returning (+) strengthening interaction and “closing” chromatin

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11
Q

chromatin remodeling enzymes

A

HDACs and HATs that modify histone tails to impact chromatin packing, regulating access to DNA

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12
Q

methylation of histone tails

A

“closes” chromatin decreasing gene expression; methyl transferase adds methyl group to histone tails and methylated histone tails bind protein HP1 that oligomerizes bringing nucleosomes together

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13
Q

cytosine methylation

A

cytosines followed by a guanine in the 5’ to 3’ direction receive a methyl group that makes DNA less accessible because it serves as a binding site for other proteins such as HDACs, is heritable (epigenetics)

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14
Q

epigenetics

A

study of heritable changes in gene expression that do not involve changes to underlying DNA sequence (phenotype not genotype change)

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15
Q

active/open chromatin

A

transcription possible, unmethylated cytosines, acetylated histones, unmethylated histone tails

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16
Q

silent/condensed chromatin

A

transcription impeded, methylated cytosines, deacetylated histones, methylated histone tails

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17
Q

inheritance of traits

A

stability of DNA from covalent phosphodiester bonds of phosphate-sugar backbone, protected due to double helix structure with bases H bonded, easily reproducible due to complementary base pairs

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18
Q

evolution of traits

A

DNA sequence is modular (bases can be easily swapped) introducing mutations that provide diversity for evolution to act on

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19
Q

transcription

A

process of making RNA copies of DNA template (gene), 1 DNA molecule used to make many identical RNA copies, in same language of nucleotides

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20
Q

spatial organization of gene expression within cell

A

DNA stored in nucleus but protein synthesis happens in cytoplasm so RNA copies leave nucleus

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21
Q

temporal organization

A

when and how much a gene is being expressed, changes throughout cell’s life and allows cells to specialize

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22
Q

constitutive gene expression

A

always being transcribed at a constant rate, required for normal cell function (housekeeping genes)

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23
Q

conditional gene expression

A

transcribed at different rates depending on conditions (induced or repressed, upregulated or downregulated)

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24
Q

initiation of transcription

A

promoter sequence determines start site (which comes after), TATA box about 25 bp upstream of gene bound by TBP bending DNA and providing landing spot for pre-initation complex to bind promoter region and recruit RNAP opening transcription bubble at start site

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25
Q

pre-initiation complex

A

general transcription factors required for expression of all genes

26
Q

elongation of transcription

A

rNTPs become exposed to noncoding DNA strand and form H bonds with their complementary base pairs, RNAP then catalyzes the phosphodiester bonds forming backbone of mRNA allowing it to leave, DNA strands reform H bonds and exits

27
Q

non-template strand

A

has same sequence as RNA strand, “coding” strand, reverse complement of template strand

28
Q

template strand

A

strand forming H bonds with RNA, strand being read, “non-coding”

29
Q

termination of transcription

A

RNAP reaches terminator sequence (AAUAAA) RNAP falls off and can rebind

30
Q

RNA polymerase

A

includes DNA entry channel, pin that physically separates DNA strands as it enters main cavity forming transcription bubble, rNTP entry channel, RNA exit channel

31
Q

regulation of transcription initiation

A

specific transcription factors

32
Q

specific transcription factors

A

required for expression of specific sets of genes, have to be used with GTFs, often affected by environmental signals, can bind at sites near promoter (proximal) or far away (distal), introns can encode enhancer or silencer regions

33
Q

activators and enhancers

A

TFs that bind enhancer regions to upregulate transcription

34
Q

repressors and silencers

A

TFs that bind silencer regions to downregulate transcription

35
Q

mediator

A

protein that forms a physical link between GTF complex, specific TFs and chromatin remodeling proteins
1. assembly of GTFs with RNAP at promoter
2. specific proteins bind to DNA and bending/looping brings them in proximity to RNAP
3. mediator links RNAP, GTFs and STFs
activators grant RNAPII permission to proceed with transcription and leave promoter (triggers TFIIH)

36
Q

“committee” of factors controlling gene expression

A

transcription regulators and chromatin remodeling proteins work together to control gene expression

37
Q

mRNA processing

A

pre-mRNAs have to receive 5’ cap, 3’ poly-A tail and undergo splicing to be exported from nucleus for translation in cytosol, cap binding protein and poly-A binding protein are recruited and interact forcing mRNA into circular shape

38
Q

splicing

A

pre-mRNA contains introns (non coding sequences) and exons (coding sequence) so spliceosome removes introns and joins exons

39
Q

spliceosome

A

multi-unit machines made of proteins and folded RNAs, forms intron into lariat by cutting it off at 5’ end and attaching it to 3’ end, then cut off and discarded, exons joined together and labeled with exon junction complexes

40
Q

alternative splicing

A

sometimes some exons are removed during splicing to create different mature mRNAs from same pre-mRNA sequence, order of exons must be maintained, improved efficiency and diversity

41
Q

nuclear pore complex

A

mediates mRNA export, pores are big enough for mRNA but too small for chromatin, lined with proteins that check mRNAs for EJCs and cap and tail binding proteins- proof of processing

42
Q

RNA

A

RNA has 2 OH groups, is usually single-stranded allowing for intramolecular base pairing- 3D folding

43
Q

3 RNA polymerases

A

RNAPI and RNAPIII used for RNA genes while RNAPII is used for protein-coding genes

44
Q

DABFEH

A

TFs forming pre-initiation complex
TFIID binds to promoter, includes TBP subunit that kinks DNA at 90 degrees
TFIIA stabilizes TFIID and TBP
TFIIB stabilizes TFIIA and TFIID
TFIIF carries RNAPII
TFIIE stabilizes RNAPII
TFIIH phosphorylates RNAPII tail adding (-) forcing RNAPII out of PIC- after transcription tails dephosphorylated so can be recruited to promoter

45
Q

tRNA

A

have 3 base anti-codon one one end that pairs with codon on mRNA, have extensive intramolecular basepairing forming a cloverleaf structure

46
Q

ribosomes

A

huge conglomerations of RNA and proteins that synthesize proteins, large subunit forms peptide bonds between amino acids and small subunit matches mRNA codons to proper tRNA

47
Q

A site

A

amino-acyl-tRNA, for tRNAs carrying single amino acid

48
Q

P site

A

peptidyl-tRNA, for tRNAs carrying chains of amino acids

49
Q

E site

A

exit

50
Q

translation steps

A
  1. ribosome assembles around mRNA 5’ end
  2. tRNA containing correct anti-codon and amino acid enters A site and binds to codon
  3. aa forms peptide bond with aa chain linked to tRNA in P site transferring aa chain to the tRNA in A site
  4. translocation- ribosome shifts forward by 1 codon while tRNAs stay base paired with codons (only 2 tRNAs can be in ribosome at once)
51
Q

chromatin remodeling complexes

A

force unwrapping of nucleosome and move histone to adjacent region using ATP, chromatin needs to be decondensed first

52
Q

histone code

A

different patterns of modifications recruit or activate different enzymes and having inherent meaning like DNA sequence

53
Q

replication fork

A

where 2 halves of parent DNA strands are split and each strand is used as a template for a new strand

54
Q

topoisomerase

A

unwinds double helix of DNA

55
Q

helicase

A

separates DNA strands break hydrogen bonds between bases

56
Q

single stranded binding proteins

A

allows fork to stay open by preventing base pairing

57
Q

primase

A

starts new strand by synthesizing short RNA sequence (primer)

58
Q

DNA polymerase

A

elongates from primer catalyzing covalent bonds of sugar-phosphate backbone

59
Q

lagging strand

A

synthesized away from replication fork in short Okazaki fragments
1. new RNA primer synthesis by primase
2. DNA polymerase starts at primer
3. exonuclease removes RNA primer
4. DNAP fills in gaps left by removal of primers
5. DNA ligase catalyzes covalent bonds of backbone of Okazaki fragments
loops around to match up with direction of leading strand (bc protein complex synthesizes work together)

60
Q

origen of replication

A

encoded in specific sequence of bases, rep forks are made creating rep bubble, in order to replicate entire genome multiple bubbles form and rep stops when bubbles join together- machinery falls off and DNA ligase connects backbone

61
Q

PCR (polymerase chain reaction)

A

amplifies specific sequence of DNA by recreating replication, uses DNA sample, DNA primers (designed for specific portions of DNA), free nucleotides, Taq polymerase and buffer

62
Q

1 PCR cycle

A

denaturation- 95 deg. C hot enough to break H bonds separating strands
annealing- 55 deg C allowing H bonds to form and primers to bind
extension- 72 deg C Taq polymerase adds nucleotides
each rounds doubles amount of DNA sequence

Molecular Genetics (2 decks)

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