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unit test #3 Flashcards

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1
Q

limit of DNA replication

A
  • no limit, can be replicated repeatedly therefore allows continuity of life
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2
Q

why does DNA need to replicate

A
  • reproduction: pass genetic material to offspring
  • growth + tissue replacement: all cells need DNA
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3
Q

what is semi-conservative replication, how does it work

A
  • two strand separate
  • each original stand acts as a guide/template for new strand
  • new strand created by adding nucleotides following complementary base pairings
  • results in 2 new strands
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4
Q

definition of replisome

A

assemblage of functional subunits that carry out the multistep process of DNA replication

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5
Q

what does helicase do

A
  • ring shaped protein that unwinds/unzips double strand helix by breaking H bonds b/w CBP
  • one strand b/w ring/one strand outside of ring
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6
Q

what does gyrase do

A
  • relieves tension when unwinding/untwisting
  • snips backbones then rebonds
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7
Q

what are single stranded binding (SSB) proteins

A

anneals to newly exposed template strands to prevent strands from rebonding

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8
Q

what is DNA primase

A
  • lays down RNA primer, used by DNA polymerase III
  • starting point in building new complementary strands
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9
Q

function of DNA

A

to pass info b/w generations

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10
Q

function of RNA

A

code for proteins production

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11
Q

use of DNA in organisms/viruses

A

determines relationships b/w organisms

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12
Q

use of RNA in viruses

A

genetic materials in some viruses

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13
Q

pentose sugar in DNA vs. pentose sugar in RNA

A

deoxyribose vs. ribose

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14
Q

nitrogenous bases in DNA vs RNA

A

AGCT vs. AGCU

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15
Q

of backbones/polymer strands in DNA vs. RNA

A

two vs. one

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16
Q

how backbones are held together in DNA vs RNA

A

hydrogen bonds forming double helix vs. can bind to itself

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17
Q

location of DNA in eukaryotic cells

A

nucleus + small amounts in mitochondria and chloroplast

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18
Q

location of DNA in prokaryotic cells

A

nucleoid + small amounts in plasmids

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19
Q

location of RNA in eukaryotic cells

A

made in nucleus, transported to cytoplasm

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20
Q

location of RNA in prokaryotic cells

A

cytoplasm

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21
Q

definition of purine

A

double ring structure

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22
Q

definition of pyrimidine

A

single ring structure

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23
Q

components of a nucleotide

A
  1. purine or pyrimidine nitrogenous base
    2.negatively charged phosphate group
  2. a five carbon pentose sugar
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24
Q

nitrogenous base A

A

adenine

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25
Q

nitrogenous base T

A

thymine

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26
Q

nitrogenous base C

A

cytosine

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27
Q

nitrogenous base G

A

guanine

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28
Q

nitrogenous base U

A

uracil

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29
Q

what is the structure of genetic code

A

group of 3 nucleic acid bases (codon) that signifies structure of amino acid

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30
Q

what is the structure of a gene

A

specific sequence of nitrogenous bases that codes for creation of protein
- can be hundreds or millions of nucleotides long

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31
Q

characteristics of polymer formed by nucleotide monomers

A
  • condensation rxn
  • phosphodiester bond
  • backbone of phosphate, sugar, phosphate, sugar…
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32
Q

how do nucleotide monomers bond

A
  • 5’ phosphate group on nucleotide forms phosphodiester (covalent) bond with 3’ hydroxyl group on another nucleotide
  • continues to form chain (polymer)
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33
Q

nucleotide structure

A
  • pentose sugar (deoxyribose or ribose)
  • nitrogenous base connects off carbon-1
  • carbon-5 branches off carbon-4 and phosphate group branches off carbon-5
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34
Q

definition of antiparallel

A

2 different strands of DNA double helix that. run in opposite directions

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35
Q

DNA’s capacity to store information has limit/no limit

A

no limit

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36
Q

how is the genetic code universal

A
  • genetic code carried by LUCA
  • has been passed down overtime to all descendants
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37
Q

function of DNA polymerase III

A
  • creates complementary strands from template strands
  • brings nucleotides into position
  • forms H bonds with template strand
  • catalyses covalent phosphodiester bonds b/w sugars and phosphate groups
    -proofreads complementary base pairing
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38
Q

what direction does DNA polymerase bond in

A

always 5’(phosphate) end of free nucleotide to 3’(hydroxyl)

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39
Q

what is the leading strand

A

strand built continuously towards replication fork

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40
Q

what is the lagging strand

A

strand built discontinuously away from replication form using short segments of DNA called Okazaki fragments

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41
Q

function of DNA polymerase I

A

removes DNA primers and replaces with DNA nucleotides

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42
Q

function of DNA ligase

A

joins gaps b/w okazaki fragments by making phosphodiester bonds

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43
Q

what proof reads as DNA is replicated

A

DNA polymerase I and III

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44
Q

what does PCR stand for

A

polymerase chain reaction

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45
Q

what does PCR do

A
  • copies segment of DNA to amplify it
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46
Q

what does PCR need

A

thermal cycler, primers, free DNA nucleotides, taq DNA polymerase

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47
Q

steps of PCR

A
  1. denaturation at 95C, DNA is heated to separate into two strands –> all H bonds broken
  2. annealing at 45C, small DNA primers attach to opposite ends of target sequence –> DNA cooled
  3. elongation at 72C, heat-tolerant taq DNA polymerase copies strands
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48
Q

why dont the DNA strands attach back to each other during annealing process of PCR

A
  • put into a solution that has been flooded with primers so 2 strands will attach to primer before they can attach to each other
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49
Q

steps of gel electrophoresis

A
  1. DNA samples amplified w PCR
  2. restriction endonuclease cut DNA at specific base sequences
  3. fluorescent marker binds to DNA fragments
  4. samples added to gel electrophoresis chamber where electric current is passed through
  5. DNA is dyed to be more visible
  6. banding pattern shows up that can be analyzed and compared
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50
Q

how does gel electrophoresis work

A
  • samples put into gel of 3-4mm thickness w rectangular holes (wells)
  • placed into shallow tank of electrodes and electrolyte solution is poured over
  • DNA separated by size (large = moves less, smaller = moves more)
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51
Q

how is PCR and gel electrophoresis used in testing of COVID 19

A
  1. acquire DNA sample from nose/throat
  2. use reverse transcriptase to convert viral RNA to DNA
  3. use PCR to amplify specific viral sequence that are markers of COVID
  4. fluorescent markers attach to target DNA, if threshold is met, positive test reuslt
52
Q

advantages PCR and gel electrophoresis in testing of COVID 19

A
  • very sensitive = small sample can be amplified
  • very specific, primers detect certain strains
53
Q

disadvantages PCR and gel electrophoresis in testing of COVID 19

A
  • expensive material/equipment
  • results take time
54
Q

what part of DNA is used to analyze DNA in paternity testing/forensic analysis

A
  • 13 short tandem repeats (STRs) (2-7 bases repeated each)
  • varies b/w individuals
55
Q

steps to DNA profiling

A
  1. obtain DNA sample
  2. copy selected tandem repeats via PCR
  3. separate DNA fragments in gel electrophoresis based on length/weight/size
  4. analyze bonding pattern for match
56
Q

somatic (body) cella have even/odd # of chromosomes. why?

A

even, allows for easier splitting

57
Q

somatic cells are haploids/diploids

A

diploids (have 2 copies of each chromosome)

58
Q

gametes (sex cells) are haploids/diploids

A

haploids (have 1 copy of each chromosome)

59
Q

how are zygotes formed

A

when gametes fuze in fertilization to create a diploid

60
Q

what happens when chromosomes are fused in a species?

A

chromosome #s aren’t that important, only that all members of species have same #

61
Q

what is a karyogram

A

image of an individual’s chromosomes

62
Q

what is a karyotype

A

characteristic types of chromosome in species

63
Q

how can chromosomes be identified

A
  • stain (distinct bonding pattern)
  • arrange by size
  • position of centromere
64
Q

alleles definition

A

one of two or more versions of DNA sequence (a single base or a segment of bases) at a given genomic location.

65
Q

single nucleotides polymorphism (SNP) meaning

A
  • position in gene where one base is altered
  • can lead to new allele
  • each person has 4000-5000, makes us unique
66
Q

what does genome size represent

A

number of base pairs
- huge range among species
- large ones can have a lot of non-functional DNA

67
Q

what are transposons

A

“junk DNA,” DNA with no known function but make of 50% of human genomes

68
Q

variation of base sequence in same species

A
  • 2 populations of same species can have differences that accumulate overtime if separated to adapt to environment
  • changes infrequent in vital genes
69
Q

why should we know genome size

A
  • to inform genome evolution research
  • estimate cost/difficulty of genome sequencing
70
Q

how is genome size measured

A

C-value: nuclear DNA content of haploid cell
mass: picograms (1pg = 10^-12g)
# base pairs: (1Mbp = 10^6 base pairs)

71
Q

importance of c-value in comparing genome size

A

better at deducing size of genome than chromosome number

72
Q

what is the purpose of gene sequencing

A
  • investigating evolutionary origin
  • comparing genomes b/w species
  • tracing ancestry
  • control/prevent infection disease
  • conserve+protect biodiversity
73
Q

what is the purpose of human genome sequencing

A
  • understanding human origin+migration
  • data of genetic disease and genes that affect human health
  • 71M individuals have had genome sequenced
74
Q

what is one gene equivalent to

A

one polypeptide

75
Q

what are the steps involved in protein synthesis

A

transcription, translation

76
Q

definition of transcription

A

synthesis of RNA using DNA as template (RNA is sequenced)

77
Q

definition of translation

A

translating mRNA sequence to build corresponding chain of amino acids

78
Q

where does transcription occur in eukaryotic and prokaryotic cells

A

euk: nucleus
pro: cytoplasm

79
Q

where does translation occur in eukaryotic and prokaryotic cells

A

euk: cytoplasm
pro: cytoplasm
(where ribosomes are located)

80
Q

what is the initiation of transcription

A

RNA polymerase binds to promoter region site on DNA
- unwinds DNA double helix into template (antisense) strand and coding (sense strand)

81
Q

antisense vs sense strand

A

antisense: strand of DNA that acts as the template for RNA
sense: strand of DNA that matches the sequence of RNA

82
Q

what occurs in elongation process of transcription

A
  • RNA polymerase synthesizes(forms) a complementary RNA copy from antisense DNA strand
  • builds in 5’ to 3’ direction
  • moves along and positions RNA nucleotides according to complementary base pairing
  • links RNA nucleotides with covalent phosphodiester bonds on sugar-phosphate backbone using energy from cleavage to join together
  • thymine turns into uracil
  • creates mRNA
83
Q

mRNA is single/double stranded

A

single

84
Q

what occurs in termination process of transcription

A
  • RNA polymerase comes across termination sequence and will detach from DNA
  • double helix reforms
85
Q

transcriptome definition

A

full range of RNA types made in a cell
- unique to each cell type and can change as cell activity changes

86
Q

importance of stability of DNA templates in protein synthesis

A
  • DNA should remain unchanged in proces
  • mutations are uncommon or else proteins will have increasing errors to point of no function
87
Q

what occurs during post-transcriptional modifications in eukaryotic cells

A
  • RNA transcript has alternating introns and exons after transcription
  • introns: do not code for protein
  • exons: code for protein
  • introns are removed and exons spliced together to form mRNA
  • mRNA let into cytoplasm/ribosome
88
Q

what does mRNA stand for? what does it do?

A

messenger RNA –> holds info in form of genetic code

89
Q

what are the 3 main types of RNA synthesized

A

messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA)

90
Q

functions/purpose/characteristics of a messenger RNA during translation

A
  • a transfer copy of a gene used to encode a polypeptide
  • contains site where ribosomes can bind
  • sequence of codons specify AAs
  • stop and start codons direct ribosomes
  • one mRNA can be translated many time + destroyed if damaged or no longer needed
91
Q

functions/purpose/characteristics of a transfer RNA

A
  • clover leaf shaped sequence that carries AA to ribosome
  • one end has anticodon of 3 bases
  • other end has attachment point for AA corresponding to anticodon
  • specific enzyme recognizes distinct shape to attach to correct AA
92
Q

functions/purpose/characteristics of a ribosomal RNA

A
  • primary component of ribosomes
  • composed of large+small subunit
  • small: has binding site for mRNA
  • large: has binding sites for tRNAs+catalyzes peptide bonds b/w AAs
93
Q

genetic code definition

A

set of rules by which info encoded in mRNA sequences is converted into proteins

94
Q

codon definition

A

triplet of bases

95
Q

how is AA sequence determined

A

by order of codons

96
Q

what is a degenerate genetic code

A

when different codons can translate for same AA

97
Q

what does the wobble hypothesis explain

A

explanation for ability of one AA to be encoded from multiple codons

98
Q

what occurs during initiation of translation

A
  1. an mRNA binds to small sub unit of ribosome
  2. activating enzyme with active site that fits tRNA binds to mRNA and attaches corresponding AA
99
Q

what occurs during elongation of growing a peptide chain

A
  • tRNA, AA and anticodon complementary to first codon of mRNA binds to P (peptidyl) site on large subunit of ribosome
  • second tRNA, AA, and anticodon complementary to second codon binds to A (amino acyl) site
  • peptide bond is created b/w AAs forming dipeptide
  • second tRNA is holding growing peptide chain
  • ribosome moves along mRNA 1 codon at time in 5’ to 3’ direction
  • tRNA in P –> E (exit) site to leave
  • tRNA in A –> P site, forming peptide bond w/ next AA
100
Q

what occurs during termination of growing a peptide chain

A
  • elongation repeats until STOP codon reached
  • polypeptide can now fold and produce functional protein
101
Q

gene mutation definition

A

random change in base sequence of DNA

102
Q

what is the gene mutation substitution

A

1 base is replaced by different base

103
Q

what is gene mutation insertion

A

an extra base is added

104
Q

what is gene mutation deletion

A

a base is removed

105
Q

what are the consequences of substitution mutations

A
  • mostly neutral or deleterious (bad)
  • likely no impact to non-coding DNA
  • coding DNA can have same sense/silent, nonsense, or missense mutation
106
Q

what does SNP stand for? what effects does it have?

A
  • single nucleotide polymorphism (point mutations)
  • common in individuals
  • can relate to certain diseases, scientists can make connections
107
Q

what is a same sense/silent mutation

A
  • codon changes but codes for the same AA
  • genetic code is degenerate
108
Q

what is a missense mutation

A
  • codon changes and codes for different AA
  • can have no impact if AA is similar to original
  • severe/lethal when new AA prevents function
  • beneficial when new AA gives beneficial change
109
Q

what is a nonsense mutation

A
  • codon changes and codes for a stop codon
  • can make protein too short = non functional
  • protein usually ends up non-functional, can be lethal or no consequences depending on protein
110
Q

how does sickle cell disease occur

A
  • mutated gene: beta globin polypeptide in hemoglobin
  • inherited through gamete cell
  • single base is mutated in 6th codon of DNA GAG–> GTG (glutamic acid–>valine)
111
Q

consequences of sickle cell disease mutation

A
  • in areas of low O2,2 hemoglobin links tgt in chains to form rigid bundles, distorting RBC shape into sickle
  • new RBCs get stuck in capillaries, less blood flow
  • normal shape again in high O2 conc. (lungs)
  • reduces lifespan of RBC 4 days
  • body cannot replace RBCs fast enough –> anemia
112
Q

sickle cell disease in relation to malaria

A
  • malaria causes RBCs to lyce, but cannot affect sickle cells
  • ppl with sickle cell are immune
  • sickle cell anemia is more common in areas where malaria is common
113
Q

consequences of insertion and deletion mutations

A
  • less likely to be beneficial
  • major: cause polypeptide to be non-functional
  • minor: total loss of function of polypeptide
114
Q

what is an insertion frameshift mutation

A
  • an addition of a base, changing the reading frame and impacts all codons after it
115
Q

what is a deletion frameshift mutation

A
  • a deletion of a base, changing the reading frame and impacts all codons after it
116
Q

what happens when frameshift mutation happens in multiple of 3

A
  • impact varies
  • doesn’t affect reading frame
  • just one extra or missing AA
  • could have a major/minor impact on structure
117
Q

what is the BRCA1 gene, what does it do

A
  • codes for BRCA1 protein in humans
  • tumor suppressor gene –> functions in DNA repair
  • mends double strand breaks + corrects mismatches in base pairing
118
Q

what can a mutation in BRCA1 gene cause

A
  • increased risk of other mutations bcuz less repairing
  • increased risk of breast, ovarian, prostate cancer
  • over 20,000 variants, using sub, ins, del
  • some same-sense while others can increase breast cancer risk in women by 80%
119
Q

what are the causes of gene mutation? when can it occur?

A
  • at any time, chances are low tho
  • increased risk during DNA replication (errors in base-pairing are uncorrected)
  • mutagens: increase mutation frequencies (radiation, carcinogens)
120
Q

randomness in mutation, can you manipulate mutations?

A
  • organism cannot control mutations, cannot change base intentionally (outcome does not influence occurrence)
    -unlikely to be beneficial
121
Q

why do some bases have higher probability of mutating than others?

A
  • some chemical changes occur more easily that other
  • position of base can influence chance of mutation, but mutation can occur anywhere in genome
122
Q

mutations in gamete and somatic cells, which one can be passed down?

A
  • mutations occurring in gamete can be inherited, somatic cannot
123
Q

what are germ-line cells? what are the consequences of mutation?

A
  • they produce gametes
  • mutations can be passed to offspring
  • new allele can be inherited (typically results in genetic disease)
124
Q

how do mutations in somatic cells occur? consequences of mutations in somatic cells

A
  • dies with individual
  • proto oncogenes can change into oncogenes which are cancer causing genes
125
Q

proto oncogenes definition

A

genes that help cells grow/divide and are involved in the cell cycle

126
Q

how is mutation a source of genetic variation

A
  • increases # of alleles in population
  • increases genetic diversity + required for natural selection
127
Q

what is the bond between complementary base pairing

A

hydrogen bond

sl biology (4 decks)

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