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lecture 3 Flashcards

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1
Q

what is the monomer of nucleic acids? what is the monomer made up of?

A

the monomer is a nucleotide/nucleoside, the nucleoside is made up of sugar and a base and you add the number of phosphate to the name, the nucleotide includes the phosphate group but doesn’t specify how many phosphate groups there are

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2
Q

what is the main building block for DNA

A

dNTP or 2’ deoxyribonucleoside triphosphate

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3
Q

when building a nucleic acid, we build on what direction? from what direction? and what kind of bond does it create?

A

we always build a nucleic acid on the free 3’ end, we always synthesize from 5’ to 3’, DNA is antiparallel and complementary. it creates a phosphodiester bond

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4
Q

what are the pyrimidine bases?

A

cytosine, thymine, and uracil for RNA

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5
Q

what are the purine bases?

A

adenine, guanine

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6
Q

what are the base pairings

A

AT and has 2h bonds , GC and has 3h bonds

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7
Q

prokaryotes have what kind of DNA? how do they protect their DNA and what enzymes help them do this?

A

they have singular circular DNA, they do METHYLATION: adds ch3 groups to protect from their own RESTRICTION ENZYMES that chop up unknown DNA and SUPER COILING: twisting of DNA to compress it into smaller spaces done by DNA GYRASE

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8
Q

DNA packaging in eukaryotes

A

sugar phosphate backbone wrapped around HISTONE PROTEINS–>a couple of histones are called NUCLEOSOMES–> a strand of nucleosomes are called CHROMATID–> CHROMATID makes up chromosome that is held within nucleus

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9
Q

what are the the two different types of chromatids?

A

EUCHROMATIN: unwound active with light staining and HETEROCHROMATIN: tightly wound inactive with dark staining

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10
Q

what is the centromere

A

region on the chromosome where sister chromatids are held together and where mitotic spindle fibers attach

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11
Q

what are the short arms and long arms on a chromosome called

A

short arms are P and long arms are Q

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12
Q

what are telomeres

A

the ends of eukaryotic linear chromosomes, have short sequence repeats and it stabilizes the ends of the chromosomes

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13
Q

what is the central dogma of DNA? why do we use RNA?

A

DNA (nucleotides) —transcription—> RNA (nucleotides)—translation—>proteins (amino acids), we use RNA to protect DNA to not work with it directly and damage it

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14
Q

codons code for what? what are the codons we must know?

A

codons have 3 nucleotides and code for 1 amino acid, the START codon is AUG , the three STOP codons are UGA, UAG, UAA

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15
Q

how many chromosomes are there in human genome

A

46

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16
Q

what are the four sources for mutations

A

polymerase errors, endogenous damage, exogenous damage, and transposons

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17
Q

what are the two polymerase errors that can occur

A

point mutation and frameshift mutation

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18
Q

what are the three point mutations that can occur

A

missense, nonsense, and silent mutations

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19
Q

what occurs in a missense mutation and what is its effect on the protein

A

in a missense mutation, a codon for an original amino acid turns into a new codon for a new amino acid EFFECT: changes amino acid

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20
Q

what occurs in a nonsense mutation and what is its effect on the protein

A

in a nonsense mutation, a codon for an amino acid becomes a stop codon EFFECT: shortened protein

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21
Q

what occurs in a silent mutation and what is its effect on the protein

A

in a silent mutation, a codon for an amino acid becomes a new codon for the same amino acid EFFECT: no effect

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22
Q

what occurs in a frameshift mutation and what is its effect on the protein

A

in a frameshift mutation, there are insertions and deletions that change the reading frame ex. AUG CCC GAU UGA turns into AUG ACC CGS UUG A when an A has been inserted. EFFECT: addition of the wrong amino acids to the protein and/or the creation of a codon that stops the protein from growing longer.

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23
Q

what is a endogenous mutation? two examples

A

a mutation that occurs due to a reactive oxygen species or physical damage ex. intrastrand cross link of DNA and interstrand cross link of DNA

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24
Q

what is a intrastrand cross link of DNA

A

an unwanted link within the same strand of DNA making it not complimentary

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25
Q

what is a interstrand cross link of DNA

A

an unwanted link within opposite strands

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26
Q

what is a exogenous mutation? two examples

A

a mutation that occurs due to radiation or chemicals ex. uv radiation and x rays

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27
Q

what occurs to DNA under UV radiation

A

pyrimidines linking together causing a pyrimidine dimer

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28
Q

what occurs to DNA under X rays

A

full breakage of chromosomes

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29
Q

what is a transposon mutation and what enzyme is involved

A

jumping genes or “cut and paste” or DNA sequences that move from one location on the genome to another done by an enzyme called transposase.

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30
Q

what are inverted repeats and why are they important for a particular mutation

A

IR is when two exact or approximate copies of a particular DNA sequence are present in reverse complement orientation. they are important for transposons are they set in between these two sequences

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31
Q

what are the three types of transposons

A

IS element, complex transposons, composite transposons

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32
Q

what is an IS (inverted sequence) element

A

DNA has an transposase enzyme and inverted repeats

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33
Q

what is a complex transposon

A

DNA with transposase enzyme, inverted repeats, AND gene insertions

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34
Q

what is a composite transposon

A

DNA with 2 transposase and inverted repeats BUT with central region in between (DNA in between)

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35
Q

how do transposons contribute to genomic variation?

A
  1. they code for the cut and paste enzyme transposase 2. transposase cuts transposon out 3. transposase pastes transposon somewhere else
36
Q

what are the two effects of transposons (list two examples with definitions)

A

if transposon is inserted in the intergenic region: theres no effect. if transposon is inserted in the coding region: there could be a disrupted gene/mutagenic which means the gene can no longer be expressed and its nonfunctional

37
Q

what is the intergenic region in DNA

A

region in between genes and noncoding region

38
Q

what are the two methods of repairing bad bases

A
  1. mismatch repair pathway and 2. the base/nucleotide excision repair
39
Q

what occurs in the mismatch repair pathway and what mutation triggers this rxn

A

this OCCURS during or shortly after replication and this is DONE BY methylating the parent strand but not the daughter strand this way you can identify the daughter and the parent strand. BAD BASES trigger this

40
Q

what occurs in base/nucleotide excision repair and what mutation triggers this rxn

A

this OCCURS at any time in the cell cycle (ideally before replication) and this is DONE BY removing the bad base and replacing it with a good base. BAD BASES trigger this

41
Q

what are the two methods of repairing broken chromosomes (physical damage)

A

homology directed repair and non homologous end jointing

42
Q

what occurs in homology directed repair and what triggers it

A

this OCCURS and MUST happen after replication(when sister chromatid is present) and this is DONE BY using the identical sister chromatid as a template to fix the broken chromosome. this is triggered by a BROKEN CHROMOSOME

43
Q

what occurs in non homologous end jointing and what triggers it

A

this OCCURS at any time in the cell cycle and this is DONE BY a ligate that binds the end together but this is mutagenic bc it loses some bases during this and and also result in translocation. this is triggered by a BROKEN CHROMOSOME

44
Q

DNA rearrangement (transposons) cause what mutation repair

A

generally dont lead to repair mechanisms

45
Q

what are the four rules for DNA replication

A
  1. it must be semiconservative (half old DNA and half new DNA) 2. 5’ to 3’ (always add to free 3’ OH group) 3. requires a primer (always requires an RNA primer) 4. requires a template (parent strand)
46
Q

what is a helicase enzyme? topoisomerase?

A

helicase unwinds DNA, topoisomerase cuts DNA and relaxes supercoilng

47
Q

what is a primase enzyme? DNA polymerase? Ligase?

A

primase synthesizes the RNA primer, DNA polymerase replicates DNA, proofreads, and removes primer. ligase links okazaki fragments together

48
Q

what are okazaki fragments

A

the short lengths of DNA that are produced by the discontinuous replication of the lagging strand.

49
Q

what is prokaryotic DNA replication called? how many DNA polymerases do they have? how many origins do they have? which ones should we focus on?

A

its called theta replication, it has ONE origin, and they use five DNA polymerases. we should focus on the DNA polymerases 3 and 1

50
Q

DNA polymerase 3***

A

very fast processivity, fast 5’ to 3’ polymerase and 3’ to 5’ exonuclease (proofreading), the main replicating enzyme and no known function in DNA repair

51
Q

DNA polymerase 1***

A

very slow processivity, slow polymerase and exonuclease, has 5’ to 3’ exonuclease to remove primer and involved in DNA excision repair

52
Q

DNA polymerase 2

A

does 5’ to 3’ and 3’ to 5’ proof reading and polymerase, helps with DNA repair and back up for DNA poly 3

53
Q

DNA polymerase 4 and 5

A

error prone 5’ to 3’ polymerase activity. helps with DNA repair

54
Q

in eukaryotic replication what occurs

A

we have many origins, several replication bubbles, and several DNA polymerases, as well as complex multisubunit enzymes

55
Q

when telomeres shorten, what is this mostly associated with?

A

aging

56
Q

telomerase definition and characteristics

A

elongate telomeres on parent strand of DNA. 1. it carries their own RNA template and reverse transcription activity 2. not all cells express this enzyme

57
Q

what are the cells that express telomerase and what are they called

A

theyre called immortal cells and they are spermatogonia, stem cells, and cancer cells, they always be replicating

58
Q

DNA vs RNA

A

DNA: double stranded, thymine, deoxyribose, double helix, and only one type of DNA
RNA: single stranded, uracil, ribose, lots of 3d shapes, several types

59
Q

what are the 5 types of RNA

A

rRNA: ribosomal RNA, mRNA: messenger RNA, tRNA: transfer RNA, hnRNA: heterogenous nuclear RNA (unprocesses mRNA initial transcripts miRNA and SiRNA: microRNA small interfering RNA

60
Q

what are the similarities between replication and transcription

A
  1. they share a start site 2. occur in the 5’ to 3’ direction 3. both use DNA as a template
61
Q

what are the differences between replication and transcription

A
  1. the stop site is different as replication really doesnt stop 2. theres no primer in transcription3. theres no editing in transcription
62
Q

why is it okay for there to be no editing in transcription

A
  1. RNA is transient and doesnt stay long 2. its not passed off to offspring 3. transcriptions are more tolerant to mutations
63
Q

what is a promoter

A

where RNA polymerase binds to the DNA

64
Q

what is a start site

A

where the RNA polymerase starts creating RNA

65
Q

what is a operator

A

its a regulatory region

66
Q

what is the coding strand

A

identical to the RNA

67
Q

what is transcription

A

the primary point of regulation for translation

68
Q

what is a strong promoter vs a weak promoter? can you change this?

A

a strong promoter has a high affinity for RNA polymerase and where alot of RNA is transcribed. a weak promoter has a low affinity for RNA polymerase where less RNA is transcribed. There is no way to change a promoter as its written within the DNA

69
Q

what are DNA binding proteins and define them

A

these proteins are better regulators, theres two repressor which turns off transcription and enhancers that turns on transcription

70
Q

what is a locoperon

A

an enzyme that when it has no substrate, it doesnt allow transcription. when there is a substrate, it starts the process

71
Q

how is transcription done in prokaryotes

A
  1. translation and transcription happens at the SAME TIME at the SAME PLACE. 2. there is no mRNA processing 3. its polycistronic: makes different proteins from a single mRNA 4. theres ONE RNA polymerase
72
Q

how is transcription done in eukaryotes

A
  1. transcription and translation occurs at DIFFERENT TIMES in DIFFERENT PLACES.
  2. there is mRNA processing
  3. its monocistronic: one mRNA one protein
  4. there are 3 RNA polymerases
73
Q

in transcription, what are the three RNA polymerases

A

real men tiptoe 1. RNA polymerase #1 rRNA 2. RNA polymerase #2 mRNA 3. RNA polymerase #3 t RNA

74
Q

what is tRNA and what enzyme is used

A

has a key role in protein synthesis as it stores 2 ATPS and has an AA attachment site and we at least 20 tRNA’s for 20 AA’s. the enzyme is aminoacyl tRNA synthase

75
Q

what is aminoacyl tRNA synthase

A

this enzyme puts the AA onto the tRNA and requires 2 ATP’s to work

76
Q

what is the wobble hypothesis

A
  1. the first 2 codon-anticodon pairs bind normally
  2. the third anticodon is more flexible
  3. an adenine on tRNA can get converted to inosine allowing for more flexibility
77
Q

when does wobble base pairing occur

A

when there is G U or I at the 5 prime end of the anticodon

78
Q

the 5’ anticodon is what RNA? the 3’ codon is what RNA

A

anticodon in transcription is tRNA and codon is mRNA

79
Q

the start AA for translation is what

A

methionine

80
Q

in translation, what is the p site and the a site

A

p site: growing Protein held here, a site: new Amino Acid added here

81
Q

how does the process of translation occur

A

as tRNA begins to translate, as each codon passes, it binds to the tRNA at the A site and as we go on, the AA at the A sitelinks all tRNA that have been used. ex. AA1-AA2-AA3-AA4

82
Q

what occurs during the stop codon at the A site

A

theres no tRNA thats recognized the stop codon and instead it binds to a release factor, this release factorbreaks the bond between final tRNA and final AA

83
Q

what are the energy requirements for translation:
tRNA loading
initiation
A site binding

A

t rna loading: 2 ATP per AA or 100 ATP for 50 AA’s
initiation: 1 ATP or 1 ATP for 50 AA’s
A site binding: 1 ATP per tRNA or 49 ATP

84
Q

what are the energy requirements for translation:
translocation
termenation

A

translocation:1 ATP each time or 49 ATP for 50 AA’s
termination: 1 ATP or 1 ATP for 50 AA’s

85
Q

how to calculate ATP needed for translation

A

of AA times 4

86
Q

what are the three post translation modifications

A

protein folding: guided by chaperons
covalent modification: disulfide bridges, phosphorylation
processing: cleavage to form an active protein guided by zymogens

mcat bio lectures (5 decks)

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