Microbial Genetics Flashcards
1
Q
Describe “genetics”
A
- Study of what genes are
*How they carry information
*How information is expressed
*How genes are replicated
2
Q
What is a gene?
A
A segment of DNA that encodes functional product.
(Usually a protein)
3
Q
Something to know***
A
A gene is DNA
DNA Is NOT a gene
4
Q
What is a genome?
A
All of the genetic material of an organism
5
Q
What is genomics?
A
Molecular study of genomes
6
Q
What is genotype ?
A
Genes of an organism
(Think dna, non physical)
7
Q
What is phenotype?
A
Expression of the genes.
(Physical features due to genes.. ex. Blue eyes)
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
9
Q
How many H+ bonds in G-C base pair?
A
3
10
Q
How many H+ bonds in A-T/A-U base pair?
A
1 1/2
11
Q
Describe the structure of DNA.
A
-Double Helix
12
Q
What makes up the backbone to DNA ?
A
-Phosphate
-Deoxyribose
13
Q
Are the strands in DNA parallel ?
Y/N and why or why not?
A
-NO
-They are “anti-parallel”
14
Q
What are the polymers of nucleotides in DNA?
A
-adenine
-thymine
-cytosine
-guanine
15
Q
The double helix is associated with ?
A
-proteins
16
Q
“Backbone” is ?
A
Deoxyribose-phosphate
17
Q
How are the strands of DNA held together?
A
-By weak Hydrogen bonds between AT & CG
18
Q
In prokaryotes the genome is in what 2 structures?
A
-chromosomes
-plasmids
19
Q
What is the shape of prokaryotic chromosomes ?
A
Circular
20
Q
Where are prokaryotic chromosomes located?
A
-nucleoid
21
Q
Are prokaryotic chromosomes diploid or haploid?
Explain?
A
-Haploid
-does not have a complementary chromosome
(Duplicates ON ITS OWN)
22
Q
For eukaryotic chromosomes the genome is in what 2 structures?
A
*Nuclear DNA
*Extranuclear DNA (mitochondria & chloroplast)
23
Q
Describe the shape of eukaryotic chromosomes
A
Several LINEAR chromosomes
24
Q
Where are eukaryotic chromosomes located?
A
Membrane bound nucleus
25
Are eukaryotic chromosomes haploid or diploid?
EXPLAIN…
-BOTH
They can reproduce asexually (haploid)
Or can reproduce sexually (diploid)
26
Describe plasmids.
-small, circular molecules of DNA
27
What kind of replicating do plasmids do ?
-Autonomously
28
Plasmids carry information required for their own ______________.
Replication
*Not essential for normal bacterial metabolism, growth, or reproduction.
*can confer survival advantages
29
Describe the many types of plasmids.
-fertility factors, resistance factors, bacteriocin factors
-virulence plasmids, cryptic plasmids
30
For the bacterial genome how are the chromosomes arranged?
In loops
31
Eukaryotic chromosomal packaging
(Structure)
From the smallest component to the whole structure
-nucleosome
-chromatin fiber
-euchromatin & heterochromatin
-highly condensed, duplicated chromosome of dividing nucleus
32
Nucleotides are added by what type of enzyme?
Ligase
33
When a nucleotide is added to DNA, does it get added to 5’ end or 3’ end?
3’ end
34
What kind of process is DNA replication ?
What does it require?
-anabolic polymerization process
-requires monomers and energy
—Triphosphate deoxyribonucleiotides serve both functions
35
What is the key to replication of DNA?
-complementary structure of the two strands
36
DNA replication is semiconservative
Explain
-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
37
DNA is copied by what ?
DNA polymerase
38
In what direction is DNA copied ?
In the 5’——->3’ direction
39
What does 5’ and 3’ represent ?
Represents carbon number
40
What initiates DNA replication ?
-RNA primer
41
Leading strand is synthesized
Continuously/discontinously?
Continuously
42
Lagging strand is synthesized
Continuously/discontinuously?
Discontinuously
43
DNA polymerase binds to each strand and adds nucleotides to __________ __________ at which end?
-hydroxyl group
-at 3’ end
44
What direction does DNA replicate?
5’——->3’ ONLY
45
***Because strands are ANTIPARALLEL , new strands synthesized differently
-Leading strand synthesized continuously
-Lagging strand synthesized discontinuously
46
Bacterial DNA is what shape?
Round/circular
47
Bacterial DNA replication begins at the ?
Origin
48
DNA polymerase replicates DNA how?
(Direction )
Only 5’ to 3’
49
What are the enzymes that hold strands open for DNA replication ?
DNA Helicase
Or just HELICASE
50
What is the area where synthesis of DNA replication is split?/ The point at which replication occurs ?
Replication fork
51
What type of fragments do lagging strands have ?
Okazaki fragments
52
In lagging strands****
(Just to know)
-RNA primers are removed and Okazaki fragments joined by a DNA polymerase and DNA ligase
53
DNA is methylated
Describe benefits of this
-control of genetic expression
-initiation of DNA replication
-protection against viral infection
-repair of DNA
54
What does topoisomerases do ?
Removes supercoils in DNA molecule
55
3 other characteristics of bacterial DNA ?
-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)
56
In replication of eukaryotic DNA is it similar or different than bacterial replication?
Similar
57
What are some differences between eukaryotic DNA replication and bacterial replication ?
In eukaryotes:
-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
58
What are Okazaki fragments ?
Short strands of DNA made by copying the lagging strand during DNA synthesis
59
Okazaki fragments are in both leading and lagging strands ? T/F
False, they are only in lagging strands
60
List what happens during DNA replication (6)
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.
61
What is the role of DNA polymerase?
-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
62
What is transcription ?
Information in DNA Is copied as RNA nucleotide sequences.
63
What is translation ?
Polypeptides synthesized from RNA nucleotide sequences.
64
Central dogma of genetics theory?
Who made this theory ?
-DNA transcribed to RNA
-RNA translated to form polypeptides
DNA—->RNA—->PROTEIN
-Francis Crick made this theory
65
Is DNA genotype of phenotype?
Genotype
66
When does transcription begin?
When RNA polymerase binds to the promoter sequence.
67
In what direction does transcription proceed?
5’-3’
68
When does transcription stop?
When it reaches the TERMINATOR sequence
69
What are 3 major types of RNA?
-messenger RNA (mRNA)
-ribosomal RNA (rRNA)
-transfer RNA (tRNA)
70
Steps of transcription (5)
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
All types of RNA is transcribed from what?
DNA
72
Where does transcription occur in prokaryotes?
Nucleoid
73
Where does Transcription occur for eukaryotes?
-Nucleus
-mitochondria
-chloroplast
74
What three steps are part of transcription?
-initiation (RNA polymerase)
-elongation (nucleotides added)
-termination
75
RNA Polymerase vs. DNA Polymerase
-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
What is the START condon?
AUG
(Think “Are U Gonna START”)
77
What is AUG
Methionine (MET)
78
What is Sigma Factor?
Assist RNA polymerase to bind to gene promoters
79
What is A Codon?
A sequence of three nucleotides in mRNA that specifies the insertion of an amino acid into a polypeptide.
80
What is an anticodon?
-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
Another name for stop codon?
Nonsense codon
82
The 3 “nonsense codons”?
-UAA
-UAG
-UGA
Also know as “stop codons”
83
Where is the anticodon located?
tRNA
84
What is an intron?
A region in a eukaryotic gene that does not code for a protein or mRNA
85
What is an exon?
-A region of a eukaryotic chromosome that encodes a protein
-coding portion of mRNA (professor’s definition)
86
Prokaryotic mRNA can hold more than 1 gene
T/F?
True
87
What are the 4 participants in translation ?
-messenger RNA
-transfer RNA
-ribosomes and ribosomal RNA
-Need Amino Acids
88
Do eukaryotes or prokaryotes have larger ribosomes? What are the numbers?
Eukaryotes have larger ribosomes 80s
Prokaryotes have smaller ribosomes 70s
89
What are the 3 stages in translation ?
-initiation
-elongation
-termination
90
What do all of the 3 stages in translation require?
-addition protein factors
91
Of the 3 translation stages, which require energy (GTP)
-initiation
-elongation
92
Release factors somehow recognize stop codons and modify the ribosome to activate _____________ which sever the polypeptide from the final tRNA.
Ribozymes
93
What happens to the ribosome in termination ?
Dissociates into subunits
94
Are transcription and translation simultaneously ?
Pretty much yes,
Translation happens slightly after transcription but not by much , indication its pretty much simultaneously
95
Are genes expressed all the time?
Only some are expressed all the time
96
Other genes are regulated so they are only transcribed and translated __________ _________.
When needed
97
Regulation of protein synthesis
characteristics ?
-typically halt transcription
-can stop translation directly
-protein not made until its needed
-no transcription then no translation
98
Operant control a metabolic pathway where?
At transcription
99
Can cells control gene expression ?
Yes
100
Where can cell control gene expression ?
-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
In bacteria are constitutive enzymes always expressed or only as needed?
Always expressed.
102
What types of enzymes are expressed only as needed
-repressible enzymes (on all the time but something represses them )
-inducible enzyme (operant)
103
What is the Operon ?
A genetic operational unit that controls a metabolic pathway by controlling transcription of mRNA
-contains all genes necessary for pathways
-Regulates genes
104
What makes up the operon ?
-regulator
-promoter
-operator
-repressor
105
What does the regulator do in operon ?
The one that codes for repressor protein/molecule
-produces repressor
106
What does the promoter do in the operon?
-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
What is the operator in the operator?
-the region of DNA adjacent to structural genes that controls their transcription
Where if hindered will not go past. Transcribing structural genes
108
What is the repressor in the operon?
-Bond to operator if transcription is not necessary
-stop transcription
109
inducible operons , how are they activated?
Must be activated by inducers
110
Example of inducible operons
Lactose operon
111
Repressible operons are transcribed continuously until deactivated by what?
Repressors
112
Example of repressible operons
Tryptophan operon
113
What is happening to a repressor when and inducible operon is running ?
Repressor is inactive
114
What is a mutation ?
Any permanent change in the DNA (genetic material)
115
How can mutation be passed down?
Can be passed down from parent to progeny
116
What are the effects of mutation?
Effects can be:
Neutral- (change in amino acid)
Beneficial - (very rare)
Harmful -(worst mutation can be harmful)
117
What is a mutagen?
An agent that causes mutation
118
What is spontaneous mutations?
Occur in the absence of a mutagen
(Mistake that was not caught)
119
Change in the nucleotide base sequence of a genome is : common or rare
Rare
120
Mutations are almost always ______________.
Deleterious (harmful)
121
Once in a while mutations can lead to a protein with novel properties (very rare), what can this do ?
Improves ability of organism and its descendent to survive and reproduce
122
Types of mutations ?
*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
Most common mutation that gets passed polymerase?
Point mutation
124
Missense mutation ?
On of the nucleotide base is changed
AUU turns into AAU
125
Nonsense mutation ?
The mutation causes the nucleotide to produce a stop codon
Ex.
AUG…AAU… STOP CODON
126
Frameshift insertion ?
Adds and extra nucleotide base, therefore shifting the rest of the sequence
AUG…AAU…AGA…
AUG…AA(G)…UAG…A
127
Frameshift deletion ?
One of the nucleotide base is not added therefore shifting the sequence back one.
Ex.
AUG…AAU…AGA…
AUG…AA A…GAG…
128
Types of mutagens?
-radiation
-chemical mutagens
129
What are examples of radiation mutagens?
*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
Examples of chemical mutagens?
*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
What type of chemical mutagen is used to treat viruses? Why?
-Nucleotide analogs
-because this disrupts DNA and RNA replication and cause point mutations
132
What is the frequency in mutation ?
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
What are mutagenic agents?
Cause mutations in DNA
134
Types of mutagenic agents ?
UV light- wide range of frequencies (thymines, dyers)
Chemicals (ethidium, bromide, some dyes, base analogs)
135
Does dna have repair mechanisms if there is a mutation found ? Y/N
Yes
136
What is the easiest mutation to repair?
UV light mutation/ thymine dimer
137
What are mutants?
Descendants of cell that does not successfully repair a mutation
138
What are “ wild types”?
Cells normally found in nature
139
Methods to recognize mutants?
-positive selection
-negative(indirect) selection- look for holes in growth
-ames test
140
How does positive(direct) selection work?
Detects mutant cells because they grow or appear different
141
How does negative (indirect) selection work?
Detects mutant cells because they do not grow
142
Is replica plating negative or positive selection ?
Negative
143
What is the Ames test used for?
It is a test for all chemicals for ability to cause mutations to bacteria
144
Three types of genetic recombination methods?
(Horizontal transfer of genetic information)
-Transformation
-transduction
-bacterial conjugation
145
How to remember transformation
-“naked DNA”
Cells with no DNA (naked) take up other cells WITH DNA
146
How to remember transduction?
Requires bacteria virus (phage)
Virus infects host cell and replicates
147
How to remember bacterial conjugation ?
Conjugation pilus
Donor cell attaches to recipient cell via pilus,
Replicates and transfers its strand
148
Jumping genes?
Segments of DNA that move form one location to another in the same or different molecule.
149
What is the result of jumping genes?
Results in a kind of frameshift insertion
150
What is a transposon?
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
Simplest transposons?
Are insertion sequences which have no more than two inverted repeats and gene for transposase
152
Complex transposons?
Contain one or more genes not connected with transposition (e.g. antibiotic resistance)
153
Transposase?
Insertion sequence for cutting and resealing DNA
154
Complex transposons carry other _______?
Genes
155
If gene flow is controlled at transcription, the action is happening on which of the following:
-DNA
-mRNA
-ribosome
-RNA polymerase
-DNA
156
In bacteria, transcription and translation can occur simultaneously ?
T/F
True
157
In an inducible operon, the repressor molecule is bound to the ____________?
Operator
158
DNA replication occurs from which carbon toward which carbon ?
5’—-3’
