Lecture 2 Flashcards
1
Q
Horizontal gene transfer
A
Occurs w/in same generation
2
Q
Vertical gene transfer
A
Happens across generations
3
Q
Gene
A
Sequence of dna
4
Q
Gene = dna = chromosomes
A
5
Q
Bacteria chromosomes (genome) consist of
A
Genes
- non coding dna
6
Q
Structure of DNA
A
Sugar
Base - purine & pyrimidines
Phosphate
7
Q
What make sup a dna backbone
A
Sugar and phosphate
8
Q
Hydrogen bonds
A
Weak bond b/w protons and an electronegative atom
9
Q
Rosalind Franklin, James Watson, and Francis crick discovered what about dna
A
Dimensions of x-ray to figure out base pairings
10
Q
What base pairs match with each other
-Thymine
- Adenine
- Guanine
-Cytosine
A
Adenine - Thymine
➡️ 2 H+ bonds
Cytosine - Guanine
➡️ 3 H+ bonds
11
Q
DNA strands run anti-parallel to one another
TRUE or FALSE
A
True
12
Q
5- end of dna ends with
A
Phosphate
13
Q
3- end of dna ends with
A
Sugar
14
Q
Why is DNA considered semi conservative
A
An old strand is always providing the template sequence for a new strand
- old strand of dna is always paired with a new one.
15
Q
Origin of replication
A
The area in which replication is initiated (starts)
16
Q
Replication bubble
A
Contains 2 replication forks
17
Q
Helicase
A
Unwinds the dna @ replication forks
18
Q
Topoisomerase
A
Releases tension of strain ahead of replication fork
19
Q
Single stranded binding protein (SBP)
A
Stops dna strands from rebinding
20
Q
Primase
A
Synthesizes (creates) RNA primers
21
Q
RNA primer
A
Gives starting point for DNA polymerase to add new nucleotides
22
Q
DNA pol 3
A
➡️ sequences new dna strand by linking nucleotides w/ phosphodiester bonds
23
Q
What direction does dna Pol 3 work from
A
ONLY 5- to 3-
— adding nucleotides to the 3OH end of rna primer
24
Q
What is the difference between DNA and RNA structure?
A
RNA has 2 oh and DNA has 1 oh
25
Leading strand
- continuous in 5- to 3- direction
- only needs one rna primer to start off
26
Lagging strand
- synthesized in small fragments (Okazaki fragments)
- needs multiple rna primers that get replaced with DNA Pol 1 and joined back together with DNA ligase
27
DNA POL 1
Removes rna primers and replaces it with dna on lagging strand (Okazaki fragments)
28
DNA ligase
Joins dna fragments together on lagging strand
29
What are proteins made up of?
Amino acids
30
Why are proteins so important?
They are used for everything!!!
- do many cellular processes
31
Structure of amino acids
- amino group
- carboxyl group
- Side Chain (r group)
32
R group
- side chain
➡️ different in each protein Therfore gives its unique function
33
dehydration
(H2O lost)
Monomer ➡️ polymer
- builds a polymer
34
Hydrolysis
(Adding of H20)
- breaks down polymer
Polymer ➡️ monomer
35
Amino Acids are connected via
Peptide bonds — covalent bonds
36
Transcription
Gene sequence is copied from DNA to molecule called MRNA
37
Promoter (Transcription)
DNA sequence present for each gene that initiates transcription of a specific gene
38
RNA polymerase
Synthesizes messenger RNA during transcription
- binds to promoter unwinding DNA (few nucleotides at a time)
39
RNA polymerase is able to find the promoter by the help of what protein
Sigma factors - help rna polymerase bind to promoter
40
What direction does RNA polymerase make the mRNA travel
5- to 3- direction
41
Terminator sequence
RNA polymerase pops off releasing mRNA strand
42
“Hairpin” structure regarding RNA
Stops transcription by causing rna to close in on itself
43
Template strand
Provides dna sequence
- it is being transcribed
44
RNA transcript
Messenger rna
- follows the coding strand
45
No template strand / coding strand
Is not transcribed
46
Translation
“Switching languages”
- genes sequence is now encoded in mRNA, which directs the production of a protein
47
Difference between dna replication and Transcription/ translation?
DNA replication - unwinds the entire genome
Translation/transcription - works with only one single gene
48
Codon
3 nucleotides that code for a amino acid
49
All mRNA start with a start codon and end with a stop codon
TRUE or FALSE
True
50
Redundant
One amino acid codes for many different codons
51
Ambiguous
Each codon only specifies one amino acid
52
Genetic code is ambiguous or redundant?
Redundant = many codons can code for one amino acid
- this allows room for error (buffer to mutations)
53
Highly conserved sequence
One that has remained relatively unchanged far back up the phylogenetic tree, and hence h far back in geological time
Ex) the pig with glowing nose and feet and the tobacco plant that glows
54
Ribosome parts
Large subunit (50s)
- e site
- p site
- a site
Small subunit (30s)
55
tRNA
Reading codon to code for right amino acid
56
tRNA is found where on a ribosome
P site
57
tRNA structure (what is included)
Amino acid
- anticodon = recognizes codon on mRNA
58
Polyribosomes
Multiple ribosomes that can translate the same mRNA at once
59
Shine dalgarno sequence
Sequences to initiate translation with the use of
polycistronic RNA = codes for several polypeptides
60
What is needed for translation to occur
mRNA
tRNA w/ amino acid
Ribosome
61
Starting amino acid binds to what site on the ribosome
The p site
62
New tRNA binds to which site
A site of ribosome
63
Translocation step of translation
Ribosome moves in 5- to 3- direction
- moving peptide chain to p site from A site
E site releases the tRNA that came from a site
64
When stop codon reached in translation what happens
Release factor binds instead of tRNA
- polypeptide chain is released from tRNA
65
Gene expression in bacteria
Very quick!!!
- no mRNA processing
- no nucleolus therefore no mRNA needed
- mRNA is able to be translated while being transcribed
66
What is more stable dna or rna
DNA
- has double helix that are not exposed allowing them to bond together
67
Gene expression
Transcription and translation of a gene to produce a protein
68
Translocation helps maintain reading frame when shifting to the next
TRUE or FALSE
True
69
Reading frame
mRNA reads in 3 nucleotides at a time (Codon)
70
Genes that are constitutively active means they are always on
True
71
Operon
Functioning unit of dna containing a cluster of genes whose products function in a common community
(Get regulated together)
72
Why would using an operon be useful to a bacterial cell?
It saves time and energy by grouping them together
73
Regulatory gene on dna
Codes for repressor
74
Promoter on dna
Where rna polymerase binds to start transcription
75
Operator site on dna
The on/off switch
76
Repressor
Protein that binds to operator blocking RNA Pol
77
How does the repressor protein change its shape?
- binding of a co-repressor
Binds to repressor ➡️ binds to operator ➡️ stops transcription
78
Binding of operon tryptophan (TRP) to the repressor
Is repressible
79
Repressible
Turns off when tryptophan is present
80
As the amount of tryptophan increases the trp operon will
Decrease in expression
81
If the operator in the trap operon were mutated to a different dna sequence (meaning the trp repressor couldn’t bind anymore) what would happen?
Genes that make tryptophan will always be on
- it is always on until repressor binds to operator
82
Lac operon
Enzymes that break down lactose
83
E. coli prefers what glucose or lactose
Glucose : it is easier to breakdown
84
Inducible operon
Turns on when lactose is present
85
No transcription with lac operon
Lactose not present therefore allolactose not present
86
Transcription with lac operon present
Lactose present therefore allolactose present
87
When allolactose is blinded to repressor can it bind to operator
No- it stops it from binding to operator
88
Negative control of operons
Blocks transcription at certain times using repressor
89
Positive control of operon
Activating transcription at certain times using activators
90
Crp
Volume switch of lac operon transcription
91
When Camp is binded to crp repressor means
It can bind to crp site
92
When Camp is not binded to crp repressor it means
It can not bind to crp site
93
Quorum sensing
Ability of bacteria to communicate and coordinate behavior via signaling molecules
94
Auto inducers
Signaling molecule
95
Bacteria secrete and respond to autoinducers
96
Mutation
Change in nucleotide sequence
97
DNA mutations can cause no change, positive change or a negative change
True or False
True
98
Base substitution (point mutation)
Single base replaced w/ different base in dna
99
What are the 3 types of base substitution mutations
Silent
Missense
Nonsense
100
Silent mutation
Mutation that still codes for same amino acid
- error didn’t cause an issue
101
Missense mutation
Mutation changes codon to code for different amino acid
102
What are the two types of Missense mutation
Conservative & non conservative
103
Conservative Missense mutation
New amino acid is not chemically different
104
Non conservative Missense mutation
New amino acid is chemically different
105
Nonsense mutation
Mutation changes amino acid codon to stop codon
- results in nonfunctional protein
106
Insertions
Inserts more nucleotides
- disrupts the reading frame (frame shift)
107
Deletions
Deletes nucleotid
108
Does deletions disrupt the reading frame?
No- reading frame is not disrupted when in multiple of 3
109
Reading frame
Correct 3 nucleotide grouping of codons in mRNA
110
Spontaneous mutations
Accidental mistakes when dna replicates itself that are not corrected
111
What are 4 causes of dna mutations
- spontaneous mutations
- ultra violet radiation in sunlight
- exposure to Chemical mutagens
-intercalating agents
112
Ultra violet radiation in sunlight causes what in dna mutations
Causes “bulge” in dna
113
Mutagens
Agents that directly or indirectly bring about mutations
114
Exposure to chemical mutagens causes what
Change in structure making base pairs bind to the wrong base pair
115
Intercalating agents
Mutagen that insert itself into dna structure
- can cause insertion/ deletion of dna sequence
116
What type of mutation can result from an insertion/deletion?
Frameshift mutation
117
Mismatch pair regarding dna repair
Specific enzymes remove and replace incorrectly paired nucleotides
118
Nuclease
DNA cutting enzyme
119
Natural mutations can help an organism to adapt to
Their environment
120
DNA repair for mismatch repair
Nuclease cuts out damaged portion of dna and then the dna polymerase repairs it. Ligase then goes in to seal the gaps together
121
Importance of synthetic mutations ( create in lab)
Learn more about cellular processes
122
ComER gene plays important role in biofilm formation and sporulation in
Bacillus subtilis and bacillus cereus
123
When and why would it be beneficial to an organism to increase genetic variation?
When the environment Dosnt change
124
DNA transfer by transformation - horizontal gene transfer
DNA released into environment by dead cells and taken up by recipient cell
125
Fredrick Griffith experiment
Inserted smooth & rough strain of streptococcus pneumoniae into mice
126
Smooth strain of streptococcus pneumoniae in Griffith experiment was _____
Virulent - caused disease
127
Rough strain of streptococcus pneumoniae in Griffith experiment was ______
Nonvirulent - did not cause disease
128
What component made the smooth colony more virulent than the rough?
The capsule
129
Transformasome
Helps the cell take up dna in same competent bacteria
130
Competent
Able to take up dna across their cell wall and membrane via transformation
131
What cell is considered competent the donor or recipient
Recipient cell
132
Transformation
Taking up dna from the environment
133
Homologous recombination
Mechanism to integrate linear dna
- similar dna sequences line up and exchange sequences b/w them
134
linear dna can be _______ or ________
Corporated into genome
Not incorporated- broken down
135
Plasmid dna is ______ in cell
Retained - not incorporated into cell
136
Plasmid dna can replicate on its own w/ its own origin or replication
True or false
True
137
Horizontal gene transfer: conjugation
DNA transferred between 2 prokaryotes via conjunction pilus
138
Steps of conjugation gene transfer
1. Sex pilus forms between f+ and f-
2. Mating bridge forms as f+ pulls f- closer
3. One plasmid strand goes from f+ to f-
4. Plasmids replicate (in both) so now they are both F+
139
F+ means
It is “fertile”
- plasmid contains the f factor
140
F factor in plasmid
Information needed to perform conjunction
141
F plasmids can carry genes for antibiotic resistance and cellular toxins
True or false
True
Resistance factors (R factors) are plasmids w/ medical importance
