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exam #1 Flashcards

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Biology 101 flashcards
1
Q

genome

A

all DNA/ genes

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2
Q

genes

A

parts of the genome; segments that code for proteins

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3
Q

how many nucleotides in each cell

A

3 billion

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4
Q

how many chromosomes in genome

A

46

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5
Q

how many genes in genome

A

20,000

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6
Q

how much of DNA are genes

A

only 2%

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7
Q

how long can DNA unravel to

A

2 meters

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8
Q

hierarchical structure of DNA

A

-DNA resides in chromosomes
-genes are nucleotides that get expressed in the real world
-nucleotides are multiple segments of DNA base pairs
-DNA is a combo of 4 possible amino acids

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9
Q

structure of a nucleotide

A

-phosphate (PO4): always attached to 5’ C
-deoxyribose sugar (ribose in RNA)
-base (only part that changes): always on 1’C

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10
Q

purines and structure

A

adenine and guanine; 2 rings

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11
Q

pyrimidines and structure

A

cytosine, thymine, and uracil in RNA; single rings

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12
Q

how to tell which is a deoxyribose and ribose

A

deoxy: no hydroxyl group on 2’ C
ribose: hydroxyl group on 2’ C

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13
Q

building a nucleotide process

A

-phosphate on 5’ adds to the 3’ C on the ext nucleotide
-H on 3’ OH group goes to water
-phosphodiester bond is formed between OH and COOH

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14
Q

adenine and thymine bond

A

2 hydrogen bonds

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15
Q

cytosine and guanine bond

A

3 hydrogen bonds; stronger bc need more energy to break

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16
Q

how to tell which is 5’ end and which is 3’ end

A

5’: contains phosphate group
3’: contains hydroxyl group

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17
Q

Avery, MacLeod, and McCarthy discovery of transforming principle

A

adding lethal bacteria to non-lethal bacteria caused mice to die
-cells lysed with RNAse and DNAse

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18
Q

ploidy

A

number of copies of chromosomes in the cell

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19
Q

what cells are haploid and what is this

A

sex cells (egg and sperm); half the number of chrom

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20
Q

diploid

A

double the number of chromosomes

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21
Q

reverse transcriptase

A

turns viral RNA into DNA, incorporates it into cells

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22
Q

retroviruses examples

A

-HIV
-SIV
-HTLV-1
-COVID-19

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23
Q

how can viruses cause cancer

A

activates genes to be expressed at higher rates than normal

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24
Q

linkage of genes

A

-on same chromosome: do not separate from each other in meiosis
-produces only two possible types of gametes
-3:1 ratio in Punnett square

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25
Q

segregation of genes

A

-2 genes on different chromosomes
-creates four possible types of gametes
-makes dihybrid pattern in Punnett
-9:3:3:1 ratio

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26
Q

unlinked genes

A

-2 genes on separate chromosomes or 2 alleles on same chromosome
-can recombine during meiosis

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27
Q

recombination of unlinked genes in meiosis

A

crossing over during meiosis 1, recombination in meiosis 2
-creates lots of variation

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28
Q

genotype

A

internally coded, inheritable info contained by an organism (genome)

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29
Q

phenotype

A

the outward physical manifestation; observable structure, function, or behavior of a living organism

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30
Q

silent mutations

A

changed codon codes for the same amino acid as normal

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31
Q

missense mutations

A

new amino acid created, can create a whole new protein that doesn’t have same function
-usually has largest effect

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32
Q

non-sense mutations

A

early stop codon created

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33
Q

how is protein structure related to function

A

-amino acid sequence dictates protein fold
-protein fold dictates protein function
-different sequences= different fold = different protein

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34
Q

how do mutations effect protein function

A

changes in DNA sequences (primary sequence) changes function

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35
Q

genetic code degeneracy

A

multiple nucleotides can code for the same codon

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36
Q

conservative mutation

A

change in the single amino acid doesn’t change the fold (same polarity)

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37
Q

problem substitution mutations and their effects

A

-functional: changes a critical amino acid, leads to changes in fold and thus change in function
-non-sense: results in stop codon and rest of protein isn’t made

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38
Q

sickle cell

A

substitution causes different amino acid to be made

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39
Q

deletion mutation

A

a single nucleotide or group of nucleotides is skipped
-causes reading frame shift and different protein is formed

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40
Q

insertion mutation

A

addition of unwanted nucleotide
-causes reading frame shift and different protein is formed

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41
Q

RFLP (restriction fragment length polymorphism)

A

-differences in DNA sequences detected bu restriction endonucleases
-RFLP/ band patten specific to clone/enzyme combo
-probe w/ labeled DNA sequence hybridizes fragments of digested DNA and revels unique blotting pattern to a specific genotype at specific locus

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42
Q

how is RFLP applied

A

-genetic testing: detects difference in homologous DNA sequences by looking at fragments made from specific RIs
-genome mapping
-genetic fingerprinting
-disease testing
-paternity testing

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43
Q

DNA sequencing

A

look at frequency of base amounts in DNA
-overlap show different versions of the gene

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44
Q

why do we need 3 nucleotides for a codon?

A

need to encode for 20 different amino acids, and if we only have 1 or 2 per codon, its not enough combos

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45
Q

why do codons need to be a consistent length

A

don’t know how to adjust the reading frame, and can’t tell where one stops and ends

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46
Q

gel electrophoresis

A

larger= travels slower, stays closer to the top (negative side)

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47
Q

why is DNA attracted to the positive electrode in gel

A

DNA is negatively charged due to its phosphate group, so negative attracts to positive

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48
Q

Southern blot general use and process

A

-after gel: use a DNA probe to detect what fragments contain the gene you are studying
1. DNA digested by RIs, fragments separated by size in gel and then denatured
2. filter/ membrane added to gel to transfer fragments to and fragments are blotted on nitrocellulose paper
3. replica of gel made and is incubated with labeled, complementary radioactive probe
4. probe attaches to the DNA fragments with the complementary sequence (only sticks to where the sequence matches)
5. look at results: any matching fragments shows the presence of that allele (called autoradiography)

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49
Q

similarities and differences between prok and euk

A

prok: oldest, small and simple, no nucleus, no organelles, single celled, circular DNA
euk: larger and more complex, nucleus, organelles, single or multi celled
both: DNA, ribosomes, cytoplasm, plasma membrane, linear DNA

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50
Q

restriction endonucleases

A

-cleave DNA at specific, palindromic sequences, generates single stranded bits of DNA and allows recombinant DNA to form
-fragments made can then be sorted by size in gel
-ex: EcoRI

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51
Q

recombinant DNA

A

-molecular cloning: insert DNA fragment into a DNA molecule (vector)
-can then be grown to amplify the plasmid

52
Q

parts of vectors and functions

A

-origin of replication (ori): tells bacteria to replicate plasmid
-antibiotic resistance gene (Amp^r): allows people to select transformed bacteria by incubation and use its specific antibiotic
-cloning site: 1 or more RI recognition sites; used to insert DNA fragment of interest

53
Q

steps of PCR

A
  1. denaturation
  2. annealing
  3. extension
54
Q

what happens in denaturation of PCR?

A

heat increased, H bonds between strands break

55
Q

what happens in annealing of PCR?

A

-RNA primers added
-forward: binds on left of bottom (antisense strand)
-reverse: binds on right of top (sense strand)
-temperature lowered so that primers can bind to template

56
Q

what happens in extension of PCR?

A

-temp raised a little more
-Taq polymerase uses primers to make complementary strands to each template strand
-moves 5’-3’
-two new DNA molecules form

57
Q

how is DNA packaged

A

-chromosome: at metaphase, has two copies of one chromosome
-uncoils into chromatin

58
Q

structure and functions of parts of euchromatin diagram

A

-nucleosome: contains 4 histones; DNA wraps around
-histone H1: under the nucleosome; clamps it all together
-linker DNA: in between nucleosomes (and nonhistone proteins); nuclease cuts every 200 bp

59
Q

how do DNA polymerases add nuc

A

add to the 3’ hydroxyl group of the growing chain

60
Q

DNA replication: leading strand

A

DNA poly adds; synthesis occurs towards the fork

61
Q

general process of DNA replication

A
  1. helicase unwinds DNA (coupled with ATP)
  2. single stranded binding proteins bind to single stranded DNA and stabilize it
  3. leading (strand with 3’ end unwound): RNA primers added, and DNA polymerase adds nucleotides from the primer towards the replication fork
  4. lagging (strand with 5’ end unwound): RNA primer made by primate and added, extended by DNA polymerase to form an Okazaki fragment; fragments added close to the fork but are attached moving away from fork
62
Q

how are RNA primers removed in prokaryotes

A

DNA polymerase 1: acts as exonuclease and removes RNA from 5’ ends of Okazaki fragments

63
Q

how are RNA primers removed and gaps filled in eukaryotes

A

RNAse H removes primers; gaps filled by DNA polymerase sigma and joined by DNA ligase

64
Q

euchromatin

A

decondensed, transcriptionally active chromatin
-uncoiled

65
Q

heterochromatin

A

condensed, transcriptionally inactive chromatin
-more coiled

66
Q

phases of the cell cycle

A

G1: cell growth
S: DNA replication
G2: prep for mitosis
M: mitosis/ cell division
G0

67
Q

where in the cell cycle do you find euchromatin and heterochromatin

A

euchromatin: interphase
heterochromatin: mitosis

68
Q

primase and difference in euk

A

makes RNA primer complementary to lagging strand
-in complex with polymerase alpha in eukaryotes

69
Q

DNA ligase

A

creates phosphodiester bonds between short fragments of nucleotides

70
Q

DNA polymerase 1 in prokaryotes

A

removes RNA primers and replaces it with DNA

71
Q

lagging strand process

A

primase synthesizes RNA primer and attaches to the complementary sequence, DNA polymerase extends it and creates Okazaki fragment, DNA poly sigma removes RNA primers and ligase fills the gaps
-process continues in general direction towards the replication fork

72
Q

DNA polymerase 3 in prok and euk

A

-prok: major replication polymerase; synthesizes off of primers to make leading strand continuously and lagging strand Okazaki fragments
-euk: proofreading

73
Q

topoisomerase

A

cuts DNA strands ahead of the replication fork and allows the DNA to rotate freely and unwind, and then rejoins it (in euk)
-prevents twists and kinks

74
Q

sliding clamp proteins

A

load polymerase onto DNA at the primer-template junction; maintains stable association of enzyme DNA polymerase with template DNA so that synthesis proceeds for long distances

75
Q

replisome

A

the whole replication complex

76
Q

errors of DNA replication through DNA poly 3 vs base selection/ H bonding of base pairs

A

DNA poly 3 much more error prone

77
Q

proofreading activity of DNA poly 3

A

-detects if nucleotides will be matches or not (5’-3’)
-edits 3’-5’ (exonuclease): when incorrect nucleotide is attached and elongation is blocked, its removed by DNA poly via hydrolysis and moved to its exonuclease domain from the polymerase domain, and then new nucleotide that’s a correct match can come in

78
Q

3 levels of insuring accuracy of DNA replication

A

-polymerase selectivity
-proofreading
-mismatch repair

79
Q

origin of replication in euk and prok

A

-prok: a DNA element, a specific sequence of nucleotides that are identified (recognized by protein complex) as the site to start replication
-euk: multiple ori’s

80
Q

ORC

A

origin recognition complex

81
Q

ORC in yeast

A

-ori: ARs = ACS consensus sequence + elements B1-3
-ORC binds to ACS and B1, and then recruits helices and other proteins to start replication

82
Q

reverse transcriptase

A

takes RNA and makes DNA

83
Q

telomerase

A

a reverse transcriptase; allows ends of chromosomes to replicate

84
Q

telomerase process

A

-binds to 3’ end of telomere sequence along with RNA template
-catalyzes the addition of bases and restores the telomere length (transcribes off the RNA)
-DNA polymerase extends and seals the DNA strands

85
Q

where was Taq polymerase originally found

A

hot springs; stable at very high temperatures

86
Q

deamination damage and type of repair used

A

amino group is let off of a nucleotide that is supposed to be added, and a different nucleotide is formed and added instead
-ex: cytosine -> uracil
-base-excision repair

87
Q

base-excision repair

A

-used for deamination
-DNA glycosylase cuts out the mismatch and DNA poly adds correct one, then ligase joins them together

88
Q

UV light DNA damage and type of repair used (and caveat)

A

-adjacent thymines on the same strand create cyclobutane ring, creating thymine dimers (can be other pyrimidines but thymine is most common)
-photoreactivation
-not present in humans, only in prok and some euk

89
Q

reaction with carcinogen DNA damage and type of repair used

A

-base reacts, addition of bulky group
-nucleotide excision repair

90
Q

photoreactivation

A

enzyme (photolyase) activated by light and cleaves thymine dimer to make 2 thymines

91
Q

nucleotide excision repair

A

damage seen by RAD (protein complex), DNA unwound by helicase and cut by nuclease, gap filled with DNA polymerase, sealed with ligase

92
Q

repair random damage of DNA (mismatch)

A

(in euk): 1. MutS and MutL bind to the mismatch
2. direct excision of the mismatch
3. replication continues

93
Q

repair of double stranded breaks

A

-homologous recombination: detected by protein complex, resection by nuclease/ helicase, D-loop formation and strand invasion, strand extension by DNA polymerase

94
Q

BRCA and DSB repair

A

involved in detection of DSB, and can cause cancer if mutated and break is not detected/ fixed

95
Q

how can polymerases tell which strand is template vs which is copy

A

template strand is methylated

96
Q

what are the non-coding regions and what are their purposes?

A

-telomeres: protects ends of DNA
-promoter: tells enzymes for DNA transcription where to start
-regulators: tells RNA transcriptase to enhance (make lots of copies) certain parts

97
Q

differences between RNA and DNA

A

-RNA: single stranded, less stable, uracil, has second OH group on 2’ C and one on 3’ C
-DNA: double stranded, more stable, thymine, only one OH group on 3’ C

98
Q

what would happen if telomeres were too short

A

ends of DNA wouldn’t be protected and over time the DNA is eaten away

99
Q

what would happen if telomeres were too long

A

telomere sequences are repetitive, so the longer the telomeres remain, the more chances for mutations and thus cancer

100
Q

how to tell where the forward and reverse primers are

A

forward: same sequence as the beginning of the sense (5’ on left) strand
reverse: same sequence as the end of the antisense (5’ on right) strand

101
Q

what happens in first cycle of PCR

A

forward and reverse primers bind to their template strands and transcribe all the way to the end of the DNA, left with two strands that end at same place but one is slightly shorter

102
Q

what happens in second cycle of PCR

A

forward and reverse primers bind to templates and the new strands made in first cycle, primers bound to original make two strands with one shorter than the other, and primers bound to the new strands make 2 strands of same length (shortened, only contains the parts that were within the primer region)

103
Q

what do you need to have lots of in order to run many cycles of PCR

A

free nucleotides and forward/ reverse primers

104
Q

how many copies of DNA are made per PCR cycle

A

1: 2 copies
2: 4 copies
3: 8 copies
4: 16 copies

105
Q

what gave us fundamental knowledge about mutation, genetic linkage, and the relationships between genes and chromosomes?

A

Drosophila

106
Q

bonds linking polysaccharides

A

glycosidic

107
Q

what type of cell are animal and most higher plant cells

A

diploid

108
Q

RNA functions in cells

A

-catalyst or enzymes
-regulator of gene expression
-carrier of info from the nucleus to the cytoplasm

109
Q

what did Meselson and Stahl’s experiment do and show

A

-grew cells with different nitrogen isotopes, transferred DNA from one isotope to other and made new DNA, the DNA was made of a mix of the light and heavy isotopes
-showed that replication is semiconservative

110
Q

type of bonds between nucleotides

A

phosphodiester

111
Q

when do sugars cyclize

A

if they contain five or more carbons

112
Q

oligosaccharide

A

a few sugars joined together

113
Q

meiosis products

A

formation of eggs and sperm: one member of each chromosome pair is transmitted to each progeny cell

114
Q

complementary sequence to 5’-TCAAGG-3’

A

5’-CCTTGA-3’

115
Q

bonds between complementary base pairs

A

hydrogen

116
Q

in mitosis, where do highly condensed chromosomes, consisting of two sister chromatids, join

A

centromere

117
Q

what is the purpose of PCR

A

amplify specific fragments of DNA in vitro

118
Q

kinetochores

A

sites of spindle fiber attachment to chromosomes

119
Q

DNA in euk cells is wrapped around histones to form ___________

A

nucleosomes

120
Q

telomeres

A

chromosome end structures required for complete replication of linear chromosomes

121
Q

nucleic acid hybridization

A

formation of a double-stranded molecule from the interaction of two complementary sequence single-stranded molecules

122
Q

what is the mechanism that DNA polymerases use to synthesize DNA

A

add dNTPs to a hydroxyl group on the growing polynucleotide chain hydrogen-bonded to a strand of DNA

123
Q

proliferating cell nuclear antigen (PCNA)

A

a sliding clamp protein

124
Q

how far apart are nucleosomes spaced

A

200 bp apart

125
Q

homology directed repair

A

-used to repair double stranded breaks
-greater accuracy compared to non-homologous end joining
-mediated recombination of homologous chromosomes during meiosis

126
Q

difference between a phosphodiester and ester bond

A

phosphodiester: the whole bond between the 5’ and 3’ of two nucleotides
ester: bond between the 3’ C and oxygen of phosphate; also between 5’ C and oxygen of phosphate

127
Q

polymerases that synthesize leading and lagging strands in eukaryotes

A

-leading: DNA polymerase epsilon
-lagging: DNA polymerase sigma

bio 205 (2 decks)

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