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Bio 55 > Microbial Genetics > Flashcards

Microbial Genetics Flashcards

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1
Q

Describe “genetics”

A
  • Study of what genes are
    *How they carry information
    *How information is expressed
    *How genes are replicated
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2
Q

What is a gene?

A

A segment of DNA that encodes functional product.
(Usually a protein)

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3
Q

Something to know***

A

A gene is DNA
DNA Is NOT a gene

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4
Q

What is a genome?

A

All of the genetic material of an organism

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5
Q

What is genomics?

A

Molecular study of genomes

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6
Q

What is genotype ?

A

Genes of an organism

(Think dna, non physical)

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7
Q

What is phenotype?

A

Expression of the genes.

(Physical features due to genes.. ex. Blue eyes)

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8
Q

What are the base pairs for structure in DNA / RNA?

A

In DNA:
Guanine (G) pairs w/ Cytosine (C)
Adenine (A) pairs w/ Thymine (T)

In RNA:
Guanine (G) pairs w/ Cytosine (C)
Adenine (A) pairs w/ URACIL (U)

DNA:
G-C
A-T

RNA:
G-C
A-U

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9
Q

How many H+ bonds in G-C base pair?

A

3

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10
Q

How many H+ bonds in A-T/A-U base pair?

A

1 1/2

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11
Q

Describe the structure of DNA.

A

-Double Helix

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12
Q

What makes up the backbone to DNA ?

A

-Phosphate
-Deoxyribose

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13
Q

Are the strands in DNA parallel ?
Y/N and why or why not?

A

-NO
-They are “anti-parallel”

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14
Q

What are the polymers of nucleotides in DNA?

A

-adenine
-thymine
-cytosine
-guanine

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15
Q

The double helix is associated with ?

A

-proteins

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16
Q

“Backbone” is ?

A

Deoxyribose-phosphate

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17
Q

How are the strands of DNA held together?

A

-By weak Hydrogen bonds between AT & CG

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18
Q

In prokaryotes the genome is in what 2 structures?

A

-chromosomes
-plasmids

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19
Q

What is the shape of prokaryotic chromosomes ?

A

Circular

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20
Q

Where are prokaryotic chromosomes located?

A

-nucleoid

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21
Q

Are prokaryotic chromosomes diploid or haploid?
Explain?

A

-Haploid
-does not have a complementary chromosome
(Duplicates ON ITS OWN)

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22
Q

For eukaryotic chromosomes the genome is in what 2 structures?

A

*Nuclear DNA
*Extranuclear DNA (mitochondria & chloroplast)

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23
Q

Describe the shape of eukaryotic chromosomes

A

Several LINEAR chromosomes

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24
Q

Where are eukaryotic chromosomes located?

A

Membrane bound nucleus

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25
Q

Are eukaryotic chromosomes haploid or diploid?
EXPLAIN…

A

-BOTH
They can reproduce asexually (haploid)
Or can reproduce sexually (diploid)

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26
Q

Describe plasmids.

A

-small, circular molecules of DNA

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27
Q

What kind of replicating do plasmids do ?

A

-Autonomously

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28
Q

Plasmids carry information required for their own ______________.

A

Replication

*Not essential for normal bacterial metabolism, growth, or reproduction.

*can confer survival advantages

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29
Q

Describe the many types of plasmids.

A

-fertility factors, resistance factors, bacteriocin factors

-virulence plasmids, cryptic plasmids

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30
Q

For the bacterial genome how are the chromosomes arranged?

A

In loops

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31
Q

Eukaryotic chromosomal packaging
(Structure)

From the smallest component to the whole structure

A

-nucleosome
-chromatin fiber
-euchromatin & heterochromatin
-highly condensed, duplicated chromosome of dividing nucleus

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32
Q

Nucleotides are added by what type of enzyme?

A

Ligase

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33
Q

When a nucleotide is added to DNA, does it get added to 5’ end or 3’ end?

A

3’ end

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34
Q

What kind of process is DNA replication ?
What does it require?

A

-anabolic polymerization process

-requires monomers and energy
—Triphosphate deoxyribonucleiotides serve both functions

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35
Q

What is the key to replication of DNA?

A

-complementary structure of the two strands

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36
Q

DNA replication is semiconservative
Explain

A

-1 strand is the original (conserved) strand “template” and the other strand is new complementary strand

-new DNA composed of one original and one daughter strand

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37
Q

DNA is copied by what ?

A

DNA polymerase

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38
Q

In what direction is DNA copied ?

A

In the 5’——->3’ direction

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39
Q

What does 5’ and 3’ represent ?

A

Represents carbon number

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40
Q

What initiates DNA replication ?

A

-RNA primer

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41
Q

Leading strand is synthesized
Continuously/discontinously?

A

Continuously

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42
Q

Lagging strand is synthesized
Continuously/discontinuously?

A

Discontinuously

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43
Q

DNA polymerase binds to each strand and adds nucleotides to __________ __________ at which end?

A

-hydroxyl group
-at 3’ end

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44
Q

What direction does DNA replicate?

A

5’——->3’ ONLY

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45
Q

***Because strands are ANTIPARALLEL , new strands synthesized differently

A

-Leading strand synthesized continuously
-Lagging strand synthesized discontinuously

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46
Q

Bacterial DNA is what shape?

A

Round/circular

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47
Q

Bacterial DNA replication begins at the ?

A

Origin

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48
Q

DNA polymerase replicates DNA how?
(Direction )

A

Only 5’ to 3’

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49
Q

What are the enzymes that hold strands open for DNA replication ?

A

DNA Helicase

Or just HELICASE

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50
Q

What is the area where synthesis of DNA replication is split?/ The point at which replication occurs ?

A

Replication fork

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51
Q

What type of fragments do lagging strands have ?

A

Okazaki fragments

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52
Q

In lagging strands**
(Just to know)

A

-RNA primers are removed and Okazaki fragments joined by a DNA polymerase and DNA ligase

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53
Q

DNA is methylated
Describe benefits of this

A

-control of genetic expression
-initiation of DNA replication
-protection against viral infection
-repair of DNA

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54
Q

What does topoisomerases do ?

A

Removes supercoils in DNA molecule

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55
Q

3 other characteristics of bacterial DNA ?

A

-bidirectional (strands are 5’-3’ and complementing strand is 3’-5’)
-topoisomerases (removes supercoils in DNA molecule
-DNA is methylated
—provides different benefits. (More on other flashcard)

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56
Q

In replication of eukaryotic DNA is it similar or different than bacterial replication?

A

Similar

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57
Q

What are some differences between eukaryotic DNA replication and bacterial replication ?

In eukaryotes:

A

-uses 4 DNA polymerases (maybe more in some organisms)
-THOUSANDS of replication origins (many origin points)
-SHORTER Okazaki fragments
-plant and animal cells methylate
ONLY cytosine bases

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58
Q

What are Okazaki fragments ?

A

Short strands of DNA made by copying the lagging strand during DNA synthesis

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59
Q

Okazaki fragments are in both leading and lagging strands ? T/F

A

False, they are only in lagging strands

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60
Q

List what happens during DNA replication (6)

A
  1. Enzymes UNWIND the parental double helix (helicase)
  2. Proteins stabilize the unwound parental DNA
  3. The leading strand is synthesized continuously by
    DNA POLYMERASE.
  4. The lagging strand is synthesized discontinuously. RNA polymerase synthesizes a short RNA primer, which is then extended by DNA polymerase.
  5. DNA polymerase digest RNA primer and replaces it with DNA.
  6. DNA LIGASE joins the discontinuous fragment of the lagging strand.
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61
Q

What is the role of DNA polymerase?

A

-editing function (checking for mistakes)
-MISMATCHING bases are pulled out and replaced
-race between finishing replication and fidelity (done correctly)
-1/1,000,000 bases may be incorrect
-mutation from DNA replication= spontaneous mutations

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62
Q

What is transcription ?

A

Information in DNA Is copied as RNA nucleotide sequences.

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63
Q

What is translation ?

A

Polypeptides synthesized from RNA nucleotide sequences.

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64
Q

Central dogma of genetics theory?
Who made this theory ?

A

-DNA transcribed to RNA
-RNA translated to form polypeptides

DNA—->RNA—->PROTEIN

-Francis Crick made this theory

65
Q

Is DNA genotype of phenotype?

A

Genotype

66
Q

When does transcription begin?

A

When RNA polymerase binds to the promoter sequence.

67
Q

In what direction does transcription proceed?

A

5’-3’

68
Q

When does transcription stop?

A

When it reaches the TERMINATOR sequence

69
Q

What are 3 major types of RNA?

A

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

70
Q

Steps of transcription (5)

A
  1. RNA polymerase binds to the promoter, and DNA unwinds at the beginning of a gene.
  2. RNA is synthesized by a complementary base pairing of free nucleotides with the nucleotide bases on the template strand of DNA.
  3. The site of synthesis moves along DNA: DNA that has been transcribed rewinds.
  4. Transcription reaches the terminator.
  5. RNA and RNA polymerase are released and the DNA helix forms
71
Q

All types of RNA is transcribed from what?

A

DNA

72
Q

Where does transcription occur in prokaryotes?

A

Nucleoid

73
Q

Where does Transcription occur for eukaryotes?

A

-Nucleus
-mitochondria
-chloroplast

74
Q

What three steps are part of transcription?

A

-initiation (RNA polymerase)
-elongation (nucleotides added)
-termination

75
Q

RNA Polymerase vs. DNA Polymerase

A

-RNA polymerase does not require helicase
-RNA polymerase slower than DNA polymerase (transcription is not as fast)
-URACIL incorporated instead of thymine for RNA
-RNA polymerase lacks proofreading function
(Causes more errors)

76
Q

What is the START condon?

A

AUG

(Think “Are U Gonna START”)

77
Q

What is AUG

A

Methionine (MET)

78
Q

What is Sigma Factor?

A

Assist RNA polymerase to bind to gene promoters

79
Q

What is A Codon?

A

A sequence of three nucleotides in mRNA that specifies the insertion of an amino acid into a polypeptide.

80
Q

What is an anticodon?

A

-The three nucleotides by which a tRNA recognizes an mRNA codon.

-a sequence of three bases that is complementary to a codon. (A different definition)

-on tRNA , complementary bases, to bring correct amino acids (professors definition)

81
Q

Another name for stop codon?

A

Nonsense codon

82
Q

The 3 “nonsense codons”?

A

-UAA
-UAG
-UGA

Also know as “stop codons”

83
Q

Where is the anticodon located?

A

tRNA

84
Q

What is an intron?

A

A region in a eukaryotic gene that does not code for a protein or mRNA

85
Q

What is an exon?

A

-A region of a eukaryotic chromosome that encodes a protein

-coding portion of mRNA (professor’s definition)

86
Q

Prokaryotic mRNA can hold more than 1 gene
T/F?

A

True

87
Q

What are the 4 participants in translation ?

A

-messenger RNA
-transfer RNA
-ribosomes and ribosomal RNA
-Need Amino Acids

88
Q

Do eukaryotes or prokaryotes have larger ribosomes? What are the numbers?

A

Eukaryotes have larger ribosomes 80s
Prokaryotes have smaller ribosomes 70s

89
Q

What are the 3 stages in translation ?

A

-initiation
-elongation
-termination

90
Q

What do all of the 3 stages in translation require?

A

-addition protein factors

91
Q

Of the 3 translation stages, which require energy (GTP)

A

-initiation
-elongation

92
Q

Release factors somehow recognize stop codons and modify the ribosome to activate _____________ which sever the polypeptide from the final tRNA.

A

Ribozymes

93
Q

What happens to the ribosome in termination ?

A

Dissociates into subunits

94
Q

Are transcription and translation simultaneously ?

A

Pretty much yes,
Translation happens slightly after transcription but not by much , indication its pretty much simultaneously

95
Q

Are genes expressed all the time?

A

Only some are expressed all the time

96
Q

Other genes are regulated so they are only transcribed and translated __________ _________.

A

When needed

97
Q

Regulation of protein synthesis
characteristics ?

A

-typically halt transcription
-can stop translation directly
-protein not made until its needed
-no transcription then no translation

98
Q

Operant control a metabolic pathway where?

A

At transcription

99
Q

Can cells control gene expression ?

A

Yes

100
Q

Where can cell control gene expression ?

A

-transcription level of control of DNA =no mRNA
-translation level of control of mRNA = block ribosomes
-post transitional level of protein= protein is inactive until it is needed

101
Q

In bacteria are constitutive enzymes always expressed or only as needed?

A

Always expressed.

102
Q

What types of enzymes are expressed only as needed

A

-repressible enzymes (on all the time but something represses them )
-inducible enzyme (operant)

103
Q

What is the Operon ?

A

A genetic operational unit that controls a metabolic pathway by controlling transcription of mRNA

-contains all genes necessary for pathways

-Regulates genes

104
Q

What makes up the operon ?

A

-regulator
-promoter
-operator
-repressor

105
Q

What does the regulator do in operon ?

A

The one that codes for repressor protein/molecule

-produces repressor

106
Q

What does the promoter do in the operon?

A

-the starting site on a DNA strand for transcription of RNA by RNA polymerase.

What is going to be transcribed starts here/ RNA polymerase will bind here

107
Q

What is the operator in the operator?

A

-the region of DNA adjacent to structural genes that controls their transcription

Where if hindered will not go past. Transcribing structural genes

108
Q

What is the repressor in the operon?

A

-Bond to operator if transcription is not necessary

-stop transcription

109
Q

inducible operons , how are they activated?

A

Must be activated by inducers

110
Q

Example of inducible operons

A

Lactose operon

111
Q

Repressible operons are transcribed continuously until deactivated by what?

A

Repressors

112
Q

Example of repressible operons

A

Tryptophan operon

113
Q

What is happening to a repressor when and inducible operon is running ?

A

Repressor is inactive

114
Q

What is a mutation ?

A

Any permanent change in the DNA (genetic material)

115
Q

How can mutation be passed down?

A

Can be passed down from parent to progeny

116
Q

What are the effects of mutation?

A

Effects can be:
Neutral- (change in amino acid)
Beneficial - (very rare)
Harmful -(worst mutation can be harmful)

117
Q

What is a mutagen?

A

An agent that causes mutation

118
Q

What is spontaneous mutations?

A

Occur in the absence of a mutagen

(Mistake that was not caught)

119
Q

Change in the nucleotide base sequence of a genome is : common or rare

A

Rare

120
Q

Mutations are almost always ______________.

A

Deleterious (harmful)

121
Q

Once in a while mutations can lead to a protein with novel properties (very rare), what can this do ?

A

Improves ability of organism and its descendent to survive and reproduce

122
Q

Types of mutations ?

A

*point mutation [one or a few base pairs affected]
—substitutions
—insertions
—deletions
*frameshift mutations [nucleotide triplets after the mutation displaced]
—insertions
—deletions

(Anything before insertions is the same)

123
Q

Most common mutation that gets passed polymerase?

A

Point mutation

124
Q

Missense mutation ?

A

On of the nucleotide base is changed

AUU turns into AAU

125
Q

Nonsense mutation ?

A

The mutation causes the nucleotide to produce a stop codon

Ex.

AUG…AAU… STOP CODON

126
Q

Frameshift insertion ?

A

Adds and extra nucleotide base, therefore shifting the rest of the sequence

AUG…AAU…AGA…
AUG…AA(G)…UAG…A

127
Q

Frameshift deletion ?

A

One of the nucleotide base is not added therefore shifting the sequence back one.

Ex.
AUG…AAU…AGA…
AUG…AA A…GAG…

128
Q

Types of mutagens?

A

-radiation
-chemical mutagens

129
Q

What are examples of radiation mutagens?

A

*ionizing radiation-induces breaks in chromosomes; organism cannot reproduce.

X-rays, gamma rays can cause ionizing radiation

*nonionizing radiation-induces thymine dimers; cause DNA to not replicate

130
Q

Examples of chemical mutagens?

A

*nucleotide analogs-disrupt DNA and RNA replication and cause point mutations

*nucleotide-altering chemicals- result in base-pair substitution mutations and missense mutations

*frameshift mutations- result in nonsense mutations

131
Q

What type of chemical mutagen is used to treat viruses? Why?

A

-Nucleotide analogs
-because this disrupts DNA and RNA replication and cause point mutations

132
Q

What is the frequency in mutation ?

A

Spontaneous mutation rate= 1 in 10^9 base pairs or 1 in 10^6 replicated genes

Mutagens increase to 1 i n10^5 or 1 i 10^3 per replicated gene

133
Q

What are mutagenic agents?

A

Cause mutations in DNA

134
Q

Types of mutagenic agents ?

A

UV light- wide range of frequencies (thymines, dyers)

Chemicals (ethidium, bromide, some dyes, base analogs)

135
Q

Does dna have repair mechanisms if there is a mutation found ? Y/N

A

Yes

136
Q

What is the easiest mutation to repair?

A

UV light mutation/ thymine dimer

137
Q

What are mutants?

A

Descendants of cell that does not successfully repair a mutation

138
Q

What are “ wild types”?

A

Cells normally found in nature

139
Q

Methods to recognize mutants?

A

-positive selection
-negative(indirect) selection- look for holes in growth
-ames test

140
Q

How does positive(direct) selection work?

A

Detects mutant cells because they grow or appear different

141
Q

How does negative (indirect) selection work?

A

Detects mutant cells because they do not grow

142
Q

Is replica plating negative or positive selection ?

A

Negative

143
Q

What is the Ames test used for?

A

It is a test for all chemicals for ability to cause mutations to bacteria

144
Q

Three types of genetic recombination methods?
(Horizontal transfer of genetic information)

A

-Transformation
-transduction
-bacterial conjugation

145
Q

How to remember transformation

A

-“naked DNA”

Cells with no DNA (naked) take up other cells WITH DNA

146
Q

How to remember transduction?

A

Requires bacteria virus (phage)

Virus infects host cell and replicates

147
Q

How to remember bacterial conjugation ?

A

Conjugation pilus

Donor cell attaches to recipient cell via pilus,
Replicates and transfers its strand

148
Q

Jumping genes?

A

Segments of DNA that move form one location to another in the same or different molecule.

149
Q

What is the result of jumping genes?

A

Results in a kind of frameshift insertion

150
Q

What is a transposon?

A

A small piece of DNA that can move from one DNA molecule to another

-segments of DNA that can move from one DNA to another (professor definition)

151
Q

Simplest transposons?

A

Are insertion sequences which have no more than two inverted repeats and gene for transposase

152
Q

Complex transposons?

A

Contain one or more genes not connected with transposition (e.g. antibiotic resistance)

153
Q

Transposase?

A

Insertion sequence for cutting and resealing DNA

154
Q

Complex transposons carry other _______?

A

Genes

155
Q

If gene flow is controlled at transcription, the action is happening on which of the following:

-DNA
-mRNA
-ribosome
-RNA polymerase

A

-DNA

156
Q

In bacteria, transcription and translation can occur simultaneously ?

T/F

A

True

157
Q

In an inducible operon, the repressor molecule is bound to the ____________?

A

Operator

158
Q

DNA replication occurs from which carbon toward which carbon ?

A

5’—-3’

Bio 55 (19 decks)

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