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AP Biology > Chp. 16, 17 & 20 : Gene Expression & Regulation > Flashcards

Chp. 16, 17 & 20 : Gene Expression & Regulation Flashcards

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1
Q

When did Fred Griffith conduct his experiment?

A

1920s

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2
Q

What did Fred Griffth study?

A

Pneumococcus bacteria

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3
Q

What is the S- strain of Pneumococcus bacteria?

A

pathogenic due to the presence of polysaccharide capsule

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4
Q

What is the R-strain of Pneumococcus bacteria?

A

nonpathogenic lacks capsule

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5
Q

What was the general protocol/results of Fred Griffith’s experiment?

A

Injected live S bacteria= dead mouse
Injected live R bacteria= live mouse
Heat killed S bacteria= live mouse
Injected heat killed Sbacteria & live R bacteria= dead mouse

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6
Q

What was the conclusions of Fred Griffith’s experiment?

A

If the pathogen is dead then how did the mouse die?
Determined that a transforming principle led to the genetic material from S bacteria to transfer in to the live R bacteria

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7
Q

When did Avery, McCarthy and MacLeod’s experiment occur?

A

1940s

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8
Q

What was the purpose of Avery, McCarthy and MacLeod’s experiment?

A

Was trying to find what the transforming principle was

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9
Q

What was the general protocol for Avery, McCarthy, and MacLeod’s experiment?

A

isolate the effects of components in S bacteria
he used enzymes to block proteins, lipids, carbohydrates, DNA and RNA

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10
Q

What were the findings/ results of Avery, McCarty, and MacLeod’s experiment?

A

Found that when DNA was blocked, transformation of R to S did not occur, however with other macromolecules it did occur
this led to him believing that DNA is the transforming material→ disputed amongst many scientists.

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11
Q

When did the Hershey-Chase experiment occur?

A

1950

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12
Q

What was the purpose of the Hershey-Chase experiment?

A

confirm DNA is genetic material

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13
Q

What are bacterophages>

A

viruses that attack bacteria-
phages cause transformation is bacteria; must be injecting bacteria with genetic material

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14
Q

What was the general protocol of the Hershey-Chase experiment?

A

labeled phage with radioactive isotopes of P32 and S35
P32- DNA
S35- proteins

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15
Q

What were the findings/ conclusions of the Hershey-Chase experiment?

A

radioactivity found in bacteria infected with P32 labeled phage
Only DNA got inside bacteria
DNA is responsible for transformation of bacteria
DNA is genetic macterial
DNA not protein is the genetic material

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16
Q

When did Watson and Crick’s experiment/ discovery occur?

A

1953

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17
Q

When did Meselson and Stahl’s experiment occur?

A

in 1957

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18
Q

What was the purpose of Meselson and Stahl’s experiment?

A

determine the type of replication: dispersive replication, conservative replication, semi-conservative replication

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19
Q

What was the general protocol for Meselson and Stahl’s experiment?

A

used two nonradioactive isotopes of nitrogen and would ananlyze the arrangement of them after replications and hypothesize how each replication would look like with each type of replication

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20
Q

conclusions of Meselson and Stahl’s experiment

A

got a result of G3 that 75% of DNA is 14N14N and 25% of DNA is 15N14N
shows that this is semi-conservative replication

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21
Q

What is the Chargaff rule?

A

Equal percentage of A and T; C and G in a given species

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22
Q

What were the contributions of Rosalind Franklin and Maurice Wilkins?

A

Rosalind Franklin found DNA picture in Wilkins lab

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23
Q

What were the contributions for Watson and Crick?

A

formulate an accurate description of the structure of DNA- double helix

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24
Q

What is DNAs structure?

A

double stranded; contains nitrogenous bases and sugar phosphate backbone
strands run in antiparallel direction
5’🡪 3’ runs antiparallel to 3’🡪5’

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25
Q

What are the 4 nitrogenous bases of DNA?

A

Adenine, Guanine, Cytosine, and Thymine

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26
Q

What is the sugar phosphate backbone held together by?

A

held together by covalent phosphodiester bonds

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27
Q

What type of sugar does DNA have?

A

deoxyribose- one less oxygen than ribose

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28
Q

What are the pyrimidines and its structure?

A

Cytosine, Thymine and Uracil
single ring

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29
Q

What are the purines and the structure of it?

A

Adenine and Guanine; double ring

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30
Q

How many hydrogen bonds are between A-T

A

double hydrogen bonds

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31
Q

How many hydrogen bonds are there between G-C?

A

Triple Hydrogen Bonds

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32
Q

What is the 5” end?

A

where phosphate is attached to carbon 5

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33
Q

What is the 3” end?

A

where carboxyl group is attached to carbon 3

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34
Q

Where does DNA replication occur in eukaryotes?

A

in the nucleus

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35
Q

Define replication fork

A

the strands get separated as helicase moves down the fork grows bigger

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36
Q

Define DNA helicase

A

breaks hydrogen bonds between nitrogenous bases

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37
Q

Define single stranded binding protein

A

prevents the two strands that are separated from joining again

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38
Q

Define DNA polymerase

A

bonds new nucleotides with A, T, C and G

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39
Q

Define Topoisomerase

A

prevents super coiling of a DNA molecule; releases Tension

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40
Q

Define RNA primer

A

short stretch of nucleic acid complementary to the template- necessary for DNA polymerase to work

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41
Q

Define DNA Primase

A

creates RNA primer

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42
Q

Define DNA Ligase

A

binds Okazaki fragments tighter

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43
Q

Define leading strand

A

strand of DNA that is continuously synthesized

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44
Q

Define the lagging strand

A

synthesize strand in Okazaki fragments

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45
Q

Define Okazaki Fragments

A

fragments of synthesized DNA on lagging strand

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46
Q

In what direction are nucleotides added?

A

3’ end of existing strands (both leading and lagging), but the new forming strands elongate in a 5’—> 3’ direction

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47
Q

what is the central dogma of biology?

A

DNA🡪mRNA🡪 Protein

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48
Q

What is the exception to the central dogma of biology and define it?

A

Retroviruses: these are RNA viruses that convert RNA->DNA

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49
Q

Describe the sequence of integration of retroviral DNA into host cell and expression of viral proteins

A

Retroviral RNA🡪 DNA🡪 DNA replication🡪 DNA integration into host chromosome
use host cell machinery to transcribe and translate Retroviral DNA to
express retroviral genes and synthesize retroviral proteins

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50
Q

Where does transcription occur?

A

in the nucleus

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51
Q

What are the 3 steps of Transcription?

A

Initiation
Elongation
Termination

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52
Q

What occurs during initiation in transcription?

A

the template strand is used to code for the new strand; transcribed for DNA

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53
Q

What is the promoter region?

A

where RNA polymerase begins transcription & template strand is determined

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54
Q

What allows the promoter sequence to be recognized?

A

TATA box sequence

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55
Q

What is the enzyme that synthesizes mRNA?

A

RNA polymerase

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56
Q

In prokaryotes where does the RNA polymerase stop?

A

At the terminator sequence

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57
Q

What occurs during Elongation in Transcription>

A

nucleotides are added to 3’ end of growing RNA molecule; RNA polymerase elongates 5’———3’ and the DNA template strand is read 3’———5’

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58
Q

What occurs during termination during transcription?

A

stop signal; Terminator region

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59
Q

Where does translation take place in eukaryotes?

A

in the cytoplasm

60
Q

What are 3 steps of translation?

A

initiation
elongation
termination

61
Q

What occurs during initiation during translation?

A

rRNA interacts with mRNA at first codon

62
Q

What occurs during Elongation in translation?

A

tRNA brings new amino acids and rRNA adds them

63
Q

What occurs during termination during translation?

A

stops when STOP codon is reached

64
Q

Where does mRNA processing occur in eukaryotes?

A

in the nucleus for eukayotes

65
Q

What is the difference between replication in eukaryotes and prokaryotes?

A

eukaryotes have multiple origins of replication while prokaryotes have 1

66
Q

What DNA is strand is used to code for the new strand?

A

the template strand

67
Q

What are some other names for the template strand?

A

antisense, noncoding, and minus strand

68
Q

What are some names for the no template strand?

A

sense, coding, plus strand

69
Q

What are the steps for a Pre-mRNA to become a mature RNA?

A

Occurs after transcription
- Will go through eukaryotic mRNA processing
- RNA splicing

70
Q

What occurs during the eukaryotic mRNA processing?

A

involves the addition of poly-A tail to 3’ end, and a guanine cap is added to 5’ end;

71
Q

What occurs during RNA splicing?

A

introns removed; exons remain; role of spliceosomes

72
Q

What are ribozymes?

A

RNA molecules that act as enzymes and splice their own introns (self- splicing

73
Q

What did the discovery of ribozymes lead to?

A

a conclusion that not all enzymes are proteins

74
Q

Define alternative splicing

A

produces a variety of mRNA transcripts, leading to a variety of polypeptide chains

75
Q

What are SnRNPs?

A

splice out introns; recognize splice sequences to cut

76
Q

What are SnRNPS made of?

A

small nuclear RNA, protein

77
Q

What is a sliceosome?

A

a group of SnRNP

78
Q

what are transcription factors?

A

bind to promoter and enhances affinitiy to start transcription occurs during initiation

79
Q

What is a UTR?

A

untranslated region with the exons, but does translate to amino acids, poly-A tail after

80
Q

what does AUG codon code for?

A

start sequence

81
Q

what is the purpose of the modified guanine added as a 5’ cap?

A

has phosphate that help protect the beginning of mRNA & help attach to ribosome

82
Q

What is teh purpose of the poly-A tail?

A

extends life of mRNA–> enzymes cuts off DNA in cytoplasm

83
Q

Define origin of replication

A

the area in the gene where the DNA replication starts

84
Q

Prokaryotes cell traits

A

circular chromosomes
smaller
has plasmids in cytosol

85
Q

Eukaryotes cell traits

A

multiple linear chromosomes
bigger
contains plasmids in nucleus

86
Q

define plasmids

A

small, extra-chromosomes, double stranded, circular DNA molecule

87
Q

Define replication bubble

A

where the two strands of DNA open up

88
Q

Describe the steps of DNA replication

A
  1. Helicase separates the DNA, so the DNA opens up into two
    2.RNA primer is placed which is made by DNA primase
    3.One strand (runs from 5’ to 3’) is continuously synthesized through DNA polymerase. The other strand runs from 3’ to 5’ and it is not continuously synthesized because it runs in a different direction. It is synthesized by DNA polymerase in Okazaki fragments.
    4.DNA Ligase connects the Okazaki fragments
89
Q

what does upstream of the DNA mean?

A

above the promoter sequence

90
Q

What can happen to amino acid chain after translation?

A

Binding of 2 or more polypeptide chains
Cleave the chain

91
Q

Name some post translation additions

A

Glycosylation, Phosphorylation, Ubiquitylation, Methylation and Acetylation

92
Q

Define glycosylation

A

adding sugar resides to proteins→ glycoproteins; cell surface receptors

93
Q

Define phosphorylation

A

activating proteins in signal transduction pathways

94
Q

Define ubiquitylation

A

death tag- protein should be degraded- sent to proteasome- proteins get broken down

95
Q

define methylation

A

shut down gene expression- silences the gene

96
Q

Define Acetylation

A

enhances gene expression

97
Q

Why is a codon made up of 3 bases?

A

smallest unit of uniform length that can code for all amino acids–> there can be 64 possible code forms

98
Q

define mRNA codon

A

three nucleotides that instructs what amino acid to get

99
Q

define tRNA anticodon

A

complementary base nucleotides to mRNA codon; attached to mRNA codon

100
Q

How is there redundancy in genetic code?

A

an amino acid can be coded for by more than one codon

101
Q

How do you read a codon chart>

A

Remember to look at codons (not anticodons) when determining the sequence of amino acids

102
Q

How many codons are there and amino acids?

A

64 codons (including 1 start= Methionine; 3 stop=no amino acids) but only 20 amino acids).

103
Q

What are ribosomes made out of?

A

small subunits made of rRNA and proteins

104
Q

How do ribosomes interact with mRNA?

A

mRNA is between the large unit and small unit

105
Q

What are EPA sites?

A

three sites for tRNA binding, designated the P (peptidyl), A (aminoacyl), and E (exit) sites.

106
Q

Difference between prokaryotic ribosome subunits and eukaryotes?

A

smaller than eukaryotes

107
Q

How do bases bond in tRNA?

A

hydrogen bonds

108
Q

How do tRNA and amino acids bond?

A

through covalent bonds

109
Q

What is a wobble codon

A

allows the anticodon of a single form of tRNA to pair with more than one triplet of the codon, 3rd nucleotide in the codon making it looser

110
Q

Define point mutation

A

1 2, or 3 base affected

111
Q

What are the two results of a point mutation?

A

substitution and frame shift mutations

112
Q

define substitution & what can it lead to

A

substitute a base
missense, nonsense, and silent mutations

113
Q

Missense mutations

A

substitution changes amino acids

114
Q

define nonsense mutations

A

substitution leads to STOP codon

115
Q

define silent mutation

A

substituting base doesn’t do anything

116
Q

define frame shift mutations

A

changes everything downstream, making more problematic - addition or deletion of a base pair which can result in missense or nonsense mutations
-more likely to cause problems in resulting protein than base substitutions

117
Q

define multiple base pair mutations

A

substitution, insertion, or deletion of more than one base pair.

118
Q

What are the 4 types of chromosome mutations?

A

translocations, duplication, inversions and deletions

119
Q

define translocations

A

: breaking off a piece and adding to non-homologous

120
Q

define duplication

A

copies of specific DNA segments are made on the chromosome

121
Q

define inversions

A

order of genes are inverted

122
Q

define deletions

A

removal of 1 or more bases from the chromsome

123
Q

what is the mutation is base excision repair?

A

fixes mutations with chemical changes resulting in messed up bases
Deamination: removal of nitrogen atoms
Methylation
Alkylation

124
Q

Define glycosylase

A

makes a snip between sugar- base excision repair

125
Q

Define endonucleases

A

makes a snip in the phosphate backbone

126
Q

define DNA polymerase role in base exicion repair

A

acts as an endonuclease

127
Q

What are the mutation in nucleotide excision repair

A

Thymine Dimers- UV damage
Bulky Lesions- affects shape

128
Q

What are the are the cutting enzymes in nucleotide excision repair

A

UVr repair enzymes

129
Q

what is the mutation in mismatch repair

A

Wrong letter was inserted

130
Q

what are the cutting enzymes in mismatch repair

A

exonucleases

131
Q

What is the nucleotide insertion enzyme for all repair mechanisms

A

DNA polymerase

132
Q

What is the DNA sealing enzyme for all repair mechanisms>

A

DNA ligase

133
Q

Define transformation

A

uptake of naked DNA- DNA not protected by proteins or other molecules, comes from external sources

134
Q

define transduction

A

transmission of foreign DNA into a cell when a viral genome integrates with a host genome

135
Q

Define conjugation

A

cell to cell transfer fo DNA
allows small segments of DNA to move from one cell to another
connects cells and allows transfer

136
Q

define transposition

A

movement of DNA segments within and between DNA molecules

137
Q

lytic cycle

A
  1. bacteriophage injects its DNA into the bacteria
  2. bacteria- host DNA falls apart by the viral DNA
  3. Viral proteins produce more viruses which breaks open the bacterial cell
138
Q

lysogenic cycle

A
  1. virus injects DNA into bacteria cell
    2, viral DNA integrates itself into the host DNA
  2. Cell will start to divide and will have the small piece of viral DNA
  3. phage induction: puce of viral DNA pops out and will have to do the lytic cycle
139
Q

define generalized transduction

A

a segment of DNA is transferred b/w bacterial cells by a bacteriophage

140
Q

generalized transduction steps

A
  1. phage injects DNA. phage enzyme breaks down the host DNA into smaller fragments
  2. phage DNA is replicated and proteins are produced
  3. phage heads may surround bacterial DNA instead of phage DNA
    when the DNA is integrated- integrated into host cells’ DNA, transferring genes now multiplies and carries new genetic material
141
Q

define homologous recombination

A

A+ and A-
occurs during transduction

142
Q

define specialized transduction

A

transfer of specific genes between bacterial cells through a phage

143
Q

specialized transduction steps

A
  1. injects phage DNA & integrates onto a specific site of the host chromosome
  2. sometimes bacterial DNA is attached to phage and phage DNA is left behind - can still affect other cells
144
Q

define transposons

A

moving sections fo DNA that can move within and between genomes

145
Q

define conjugation pilus

A

binds other bacteria

146
Q

define competer

A

bacteria able to bind to large amounts of DNA- increased cell wall and cell permeability

AP Biology (38 decks)

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