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Bio > C2: Molecular Biology > Flashcards

C2: Molecular Biology Flashcards

Class 2

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1
Q

what is a point mutation?

A

single base pair substitution

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2
Q

what is a gene rearrangement?
how many types of gene rearrangements are there?

A

add, delete or move nucleotides around
- 5 types

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3
Q

what is a transition mutation?
- what does it effect?
- what kind of mutation is it?

A
  • when you pair one pyrimadine with another pyrimadine (or purine w purine)
  • effect on nucleotide
  • point mutation
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4
Q

what is a transversion mutation?
- what does it effect?
- what kind of mutation is it?

A
  • when you swap one of the pyrimidines for one of the purines (or vice versa)
  • effect on nucleotide
  • point mutation
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5
Q

what is a nonsense mutation?
- what does it effect?
- what kind of mutation is it?
- what happens if this mutation happens early in the protein coding region?

A
  • a codon is changed to a stop codon
  • effect on AA
  • point mutation
  • the protein will be severely shortened
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6
Q

what is a missense mutation?
- what does it effect?
- what kind of mutation is it?

A
  • codon is changed to a diff codon, one AA is switched to another
  • effect on AA
  • point mutation
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7
Q

what is a silent mutation?
- what does it effect?
- what kind of mutation is it?

A
  • codon is changed to a diff codon, no change in AA bc genetic code is degenerate (ex: GGU to GGG, both still code for glycine)
  • effect on AA
  • point mutation
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8
Q

what is a conservative point mutation?

A

a type of missense mutation that leads to little change

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9
Q

what is a conservative point mutation?
- what type of point mutation is it?
- does this change the protein structure/ function?

A
  • AA is changed to a diff but similar AA
  • type of missense mutation
  • no
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10
Q

what is an insertion mutation?
- what type of mutation is this?

A

adds nucleotides, can shift reading frame or will not if there are 3 insertions
- gene rearrangement

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11
Q

what is a deletion mutation?
- what type of mutation is this?

A

deletes nucleotides, can shift reading frame or not if there are 3 deletions
- gene rearrangement

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12
Q

what is an inversion mutation?
- what type of mutation is this?

A

chromosome section is flipped
ex: if the code is FED, it is flipped to DEF
- gene rearrangement

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13
Q

what is an amplification/ duplication mutation?
- what type of mutation is this?

A

chromosome section is duplicated, increases copy #
ex: if gene 1 has 2 copies, after amplification/ duplication it will have 3 copies
- gene rearrangement

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14
Q

what is a translocation mutation?
- what type of mutation is this?

A

chromosome segment is swapped w another (non- homologous) chromosome
- gene rearrangement

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15
Q

in DNA replication, it is a ____ process that requires a ____ and a ____. Polymerization happens in the ____ direction and is read in the _____ direction.

A

semiconservative, template, primer, 5’ to 3’, 3’ to 5’

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16
Q

DNA is held together by a variety of molecular bonds. which of the following types of bonds is NOT found in a molecule of double stranded DNA?
a. covalent
b. hydrogen
c. N- glycoscidic
d. peptide
e. phosphodiester

A

D

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17
Q

what is the function of helicase?

A

unwinds DNA (which causes tension), uses ATP

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18
Q

what is the function of topiomerase?

A

decreases tension

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19
Q

what is the function of ssBP?

A

stabilize ss DNA that was caused by unwinding

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20
Q

what is the function of primase?

A

build RNA primer, it is an RNA polymerase enzyme

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21
Q

what is the function of DNA polymerase?

A

replicates, proofreads, edits DNA, removes primer, actually builds DNA

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22
Q

what is the function of ligase?

A

links fragments of DNA called Okazaki fragments

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23
Q

are okazaki fragments present on the leading or lagging strand of DNA?

A

leading strand

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24
Q

what does prokaryotic replication look like?
- what shape is the bacterial genome?
- what is he chromosome made of?

A
  • theta because of one origin of replication per chromosome
  • circular and contains one chromosome
  • dsDNA
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25
Q

what does eukaryotic replication look like?

A

replication bubbles up and down linear chromosomes

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26
Q

in prokaryotes,
what is elongation?
- what direction is it in?
- is DNA polymerase 1 fast or slow in this process?
- what about DNA polymerase 2?

A
  • polymerase activity, elongates and builds DNA
  • 5’ to 3’
  • slow
  • fast
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27
Q

in prokaryotes,
what is proofreading?
- is DNA polymerase present in this process?
- what about DNA polymerase 2?

A
  • 3’ to 5’, exonuclease goes backwards to fix mistakes by cutting out nucleotides
  • yes
  • yes
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28
Q

in prokaryotes,
what is repair and primer removal?
- in what direction does this happpen?
- is DNA polymerase present in this process?
- what about DNA polymerase 2?

A
  • exonuclease removes a mistake on the primer
  • 5’ to 3’
  • yes
  • no
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29
Q

in prokaryotes,
where is DNA polymerase 1 located?
- what about DNA polymerase 2?

A
  • starts at the primer
  • takes over wherever DNA pol 1 leaves off
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30
Q

in prokaryotes,
what happens to mRNA?

A

it is NOT processed

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31
Q

what is the central dogma?
- what happens between each one?
- what happens in the reverse of the first step?

A

DNA > RNA > Protein\
- DNA > RNA: transcription
- RNA > Protein: translation
- RNA > DNA: reverse transcription

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32
Q

what enzyme allows reverse transcription to happen?
- what does it make?
- ____ doesn’t contain any ____ so genes are ____ and easier to work with in the lab

A
  • reverse transcriptase
  • makes complementary DNA (cDNA)
  • cDNA, introns, shorter
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33
Q

what is the first step of DNA transcription?
- where does it start?
- what enzyme helps with this and what does it do?
- what happens after this?
- what is the DNA strand that this occurs on called?

A

initiation
- promoter
- RNA polymerase, binds to template strand on 3’ end
- RNA polymerase starts making RNA at the start site
- template, noncoding strand, antisense strand, transcribed strand

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34
Q

what is the 2nd step of DNA transcription?
- what enzyme is moving along the template strand?
- what direction is it moving?
- what is coming out of this enzyme?
- what does this mean for the coding strand?

A

elongation
- RNA polymerase
- to the right, 3’ to 5’
- RNA transcript that is 5’ to 3’ and contains a nucelotide (ex CAT) which is transcribed to its RNA sequence (ex: GUA)
- it codes for the RNA sequence from the template strand (ex: GTA)

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35
Q

what is the last step of DNA transcription?
- what strand does it happen on?

A

termination
- RNA polymerase stops at the termination signal and dissociates, RNA is released
- coding strand, sense strand

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36
Q

what are the similarities between DNA replication and DNA transcription in regard to:
- requires template?
- driving force?
- building direction?

A
  • yes
  • removal and hydrolysis of pyrophosphate (PPi)
  • 5’ to 3’
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37
Q

what are the differences between DNA replication and DNA transcription in regard to:
- requires primer?
- does polymerase repair?
- starts at?
- stops?

A
  • R: yes, T: no (promoter, not primer)
  • R: yes, T: no
  • R: origin of replication, T: start site
  • R: when fragments overlap and all DNA has been replication, T: termination signal
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38
Q

where does transcription occur in eukaryotes?
- prokaryotes?
- do transcription and translation occur simultaneously?

A
  • nucleus
  • cytoplasm
  • only in prokaryotes
39
Q

both prokaryotes and eukaryotes have ____ DNA

A

double stranded

40
Q

what is mRNA?

A

read by ribosomes, template for making proteins

41
Q

what kind of mRNA is monocistronic? what does this mean?
what kins of mRNA is polycistronic?
what does this mean?

A
  • eukaryotic
  • there are as many different mRNAs as there are proteins
  • prokaryotic
  • codes for more than one polypeptide
42
Q

what is a 5’ cap?

A

a tag on the mRNA of eukaryotes that is stuck on the 5’ end of the mRNA and is essential for translation and preventing digestion of the mRNA by exonucleases

43
Q

what is a 3’ poly A tail?

A

a tag on the mRNA of eukaryotes that is stuck on the 3’ end of the mRNA and prevents digestion of the mRNA by exonucleases

44
Q

what is rRNA?

A

major component of ribosome

45
Q

what is tRNA?
- where does it bind the AA?
- what enzymes do this?
- how is it decided which AA will be brought into the mRNA

A

binds AA’s and brings them to the ribosome
- 3’ end
- aminoacyl tRNA synthetases, they pair an AA w a tRNA
- by the 3 base pair anticodon that is complementary to the mRNA codon (IF CONFUSED SEE SLIDE * Translation Machinery: tRNA *)

46
Q

what is tRNA loading/ amino acid activation?

A

when an AA is attached to its tRNA molecule

47
Q

what is siRNA?
- what falls under this category?

A

small interfering RNA
- mRNA, tRNA, rRNA

48
Q

what is hnRNA?
- where can this type of RNA be found?

A

heterogeneous nucelar RNA, precursor to mRNA
- only in the nucleus

49
Q

what is the small ribosomal subunit in prokaryotes?
- eukaryotes?

A
  • 30s
  • 40s
50
Q

what is the large ribosomal subunit in prokaryotes?
- eukaryotes?

A
  • 50s
  • 60s
51
Q

what is the total ribosomal in prokaryotes?
- eukaryotes?

A
  • 70s
  • 80s
52
Q

are eukaryotic and prokaryotic translation different? if so, how?

A

mostly same steps BUT prokaryotic translation happens on 70S ribsosome, eukaryotic on 80S

53
Q

what is the first step in RNA translation called?
- what is the first step?
- what is the name of the site in which this happens on the mRNA?
- where does assembly happen?
- what goes into this site?

A

initiation
- assemble ribosome
- APE (but it is assembled backwards on the mRNA) and stands for:
A: aminoacyl
P: peptide
E: exit
- P site
- tRNA- Met goes into the P site

54
Q

during RNA translation, what are the sites that methionine can occupy on the ribosome?

A

A or P site

55
Q

what is the second step in RNA translation called?
- what is the first step?
- second step?
- third step?
- this process ____

A

elongation
- tRNA AA#2 goes into the A site
- peptide bond is formed between the Met and AA#2
- ribosome shifts 3 nucleotides AKA 1 codon
- repeats

56
Q

what is the third step in RNA translation called?
- how is the mRNA read?
- what direction is the peptide chain made?
- how does this process end?
- what are the 3 stop codons?

A

termination
- 5’ to 3’
- N terminus to C terminus
- ribosome dissociates and peptide is released
- UGA, UAG, UAA
(u go away, u are gone, u are away)

57
Q

what is a nuceloside made up of?

A

a 5C sugar and an aromatic base

58
Q

what does truncated mean?

A

smaller/ shortened

59
Q

in eukaryotes, 1 molecule of ____ makes ___ ATP.

A

glucose; 30

60
Q

how many hydrogen bonds does C-G contain?
A-T?

A

3; 2

61
Q

is there proofreading in both DNA replication and transcription?

A

no, only in DNA replication

62
Q

what does hemizygous mean?
- it is often used to describe ____ genes in ____
- ____have ____ chromosomes and are NOT ____

A

a diploid individual who has only one member of a chromosome pair rather than the usual 2
- X linked; males
- females; 2 X, hemizygous

63
Q

what are homologous chromosome pairs?

A

contain the same genes in the same order but may have different alleles of the same genes

64
Q

in the human karyotype, chromosomes are in order from ____ to ____
- the last chromosome pair is the ____ chromosome, ____ or ____
- ____ chromosome is similar in size to chromosome ____ (____), and the X chromosome is 3 times ____ and similar in size to chromosome ____.

A

1 (largest); 22 (smallest)
- sex; XX; XY
- Y; 19; small
- larger; 7

65
Q

x chromosome inactivation and ____ are mediated by ____

A

genetic imprinting; epigenetics

66
Q

true or false:
genomic components include genes that code for proteins and genes that do not code for proteins

A

true

67
Q

true or false:
genomic components include large regions with no known function

A

true

68
Q

true or false:
genomic components include repeating sequences

A

true

69
Q

what is an epigenetic modification?

A

modifications to DNA that regulate whether genes are turned off or on

70
Q

what are the 3 types of epigenetic control?

A
  1. DNA methylation
  2. histone modification via acetylation
  3. RNA interference
71
Q
  • what is DNA methylation?
  • can prokaryotes or eukaryotes do this?
  • what does it do?
  • histone acetylation?
  • can prokaryotes or eukaryotes do this?
A
  • covalently modifies DNA by adding a methyl group
  • both
    turns gene expression off
  • turns gene expression on
  • only eukaryotes, prokaryotes supercoil their genome
72
Q

transcriptionally active parts of the genome have ____ levels of DNA methylation and ____ levels of histone acetylation. what about inactive parts of the genome?

A
  • low; high
  • opposite, high and low
73
Q

can a single gene only be regulated by a single type of epigenetic modification or various?

A

various

74
Q

what is methylation?

A

an epigenetic modification that silences genes

75
Q

to silence gene expression, ____ can be bound by interfering ____ and targeted for ____.

A

mRNA; RNA; degradation

76
Q

histone acetyltransferases upregulate ____

A

gene expression

77
Q

the lac operon is ____ since the enzymes it codes for are part of the ____

A

inducible; lactose catabolism

78
Q

gene expression is influenced by how DNA is ____
- it can do this in 2 ways which are…

A
  • packaged in chromosomes
    1. euchromatin: loosely packaged
      1. heterochromatin: densely packaged
79
Q

the way that DNA is packaged is controlled by ____

A

methylation

80
Q

X chromosome inactivation is an example of ____

A

methylation

81
Q

methylation can lead to deamination which leaves behind a ____, methylated cytosines are therefore prone to ____

A

thymine base; mutations

82
Q

what does a permease protein do?
- what gene codes for it?

A
  • transports lactose into the cell
  • Y genes
83
Q

what genes code for the lac operon?

A

A, Y and Z genes

84
Q

what does a CAP protein do?
- what codes for it?

A
  • helps turn the lac operon on when lactose is present
  • CPR gene
85
Q

what gene(s) code for histone acetylation?

A

I

86
Q

bacteria methylate ____ nucleotides via the enzyme ____

A

adenine; DNA adenine methylase

87
Q

eukaryotes methylate ____ nucleotides in ____ by a family of DNA ____ enzymes

A

cytosine; CpG motifs; methyltransferase

88
Q

both prokaryotes and eukaryotes methylate ____ nucleotides

A

thymine

89
Q

the trp operon codes for…

A

mediate tryptophan biosynthesis or anabolism, it is anabolic

90
Q

the lac operon is ____

A

catabolic

91
Q

post translational modifications of a protein can involve 3 things…

A
  1. covalent linkage of phosphate or carbohydrate groups
  2. cleavage of zymogens to turn inactive proteins into active proteins
  3. ensuring the protein is folded correctly (this is mediated by a chaperone)
92
Q

out of the following options, which would cause a downstream response within a pathway and why?
- double stranded RNA
- single stranded DNA
- single stranded RNA

A
  • yes bc its degraded by RNA interference and is not considered normal
  • yes bc ssDNA is very unfavorable
  • no bc most RNA molecules are single stranded
93
Q

the lac operon promoter has a binding site for…

A

CAP-cAMP and RNA polymerase

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