Exam 2 Flashcards
1
Q
What is the criteria of genetic material?
A
1) Information
2) Transmission
3) Replication
4) Variation
2
Q
What did the Griffith Experiments demonstrate?
A
Strains of one bacterial type can transmit genetic material to another bacterial type which transforms the recipient (did not know what the genetic material was exactly)
3
Q
What did Avery, McLeod, and McCarty discover?
A
Discovered the genetic material in the Griffith Experiments was DNA. Did so by treating samples with RNA-ase and protease and observing that the traits were still transmitted.
4
Q
What did Hershey and Chase discover?
A
Provided evidence that DNA is the genetic material of T2 phage
5
Q
How did Hershey and Chase conduct their experiment?
A
Used radioisotopes to distinguish between DNA and proteins (Proteins contains SULFUR, DNA contains Phosphorus). Found that after infecting a bacteria, the phosphorus containing material moved inside the cell and sulfur remained outside.
6
Q
What are Nucleotides?
A
repeating structural unit of nucleic acids
7
Q
Nucleotides are linked together to form a strand of….
A
DNA/RNA
8
Q
Two strands of DNA (sometimes RNA) interact to form….
A
Double Helix
9
Q
What are the 3 components of a nucleotide?
A
1) At least one phosphate group
2) A pentose sugar
3) A nitrogenous base
10
Q
What are the two categories of nitrogenous bases?
A
Purines and Pyrimidines
11
Q
What are the purines?
A
Adenine and Guanine
12
Q
What are the pyrimidines?
A
Thymine, Cytosine, and Uracil
13
Q
How many hydrogen bonds can form between G and C?
A
3 (stronger bond than A and T)
14
Q
How many hydrogen bonds can form between A and T
A
2 (easier to dissociate two DNA strands with an area rich in these bases)
15
Q
What is a nucleoside?
A
A base attached to a sugar
16
Q
What turns a nucleoside into a nucleotide?
A
Covalent attachment to one or more phosphates
17
Q
What forms the backbone of DNA?
A
Phosphate and Sugar Molecules
18
Q
What is the directionality of DNA
A
5’ to 3’
19
Q
What are Chargaff’s Rules?
A
the amount of guanine should be equal to cytosine and the amount of adenine should be equal to thymine.
20
Q
What is the orientation of the double helix?
A
Backbone on the outside with the bases facing inward
21
Q
What type of bonds stabilize the double helix?
A
Stabilized by base pairs (hydrogen bonds)
22
Q
What are complementary strands?
A
strands that are antiparallel and have opposing base pairs
23
Q
T/F: RNA is usually much longer than chromosomal DNA
A
FALSE
24
Q
What can especially short sequences of RNA from?
A
Double Helices (that are right handed)
25
What stabilizes the RNA double helix structure?
1) H bonding between base pairs
2) Base Stacking (like stacking plates)
3) H bonding between bases and backbone regions
26
T/F: Prokaryotes may contain multiple copies of their chromosome
TRUE
27
Where is/are bacterial chromosome(s) housed?
The nucleoid
28
T/F: Bacterial chromosome(s) is/are in direct contact with the cytoplasm
TRUE
29
What are micro domains in bacteria?
Loops of DNA (around 10K bp) that emanate from the chromosomal core
30
What is the function of micro domains in bacteria?
Aid in chromosomal compaction
31
What is DNA supercoiling?
Twisting the DNA super tight which aids in compaction
32
What are topoisomers?
DNA conformations differing only in regard to supercoiling
33
What does negative supercoiling do?
Can promote the separation of DNA strands in some small areas (separation relieves tension). This causes these areas to be more accessible to replication and transcription.
34
What does DNA Gyrase do?
Introduces negative supercoils using ATP
35
What does topoisomerase (1) do?
Can relax negative supercoils by introducing a break to relieve tension
36
T/F: During replication, bacterial chromosome has 1 origin of replication
TRUE
37
What is the structure of Eukaryotic chromosomes?
It is Linear and much longer than bacterial chromosomes
38
What caps the ends of eukaryotic chromosomes?
Telomeres
39
T/F: Eukaryotic chromosomes also only have one origin of replication
FALSE; they have multiple
40
Where are chromosomes located in eukaryotes?
In the nucleus (separated from the cytosol)
41
What is a kinetochore?
A group of proteins that link the centromere to the spindle apparatus during mitosis and meiosis.
42
T/F: Eukaryotic genome size is variable among different species
TRUE; larger size doesn't necessarily mean more genes, could be due to repetitive sequences
43
What is sequence complexity?
The number of times a base sequence appears in a genome
44
What are transposable elements?
DNA segments that transpose (move from one area on a chromosome to another) themselves (sometimes referred to as Jumping Genes)
45
What is simple transposition?
TE is physically removed from its original site and transferred to a new target site (these are called transposons)
46
What is retrotransposition?
TE moves via an RNA intermediate. This means that the TE is transcribed into RNA and then back into DNA again at the target site. Original TE does not move as it is copied, not physically removed.
47
What type of transposition leads to an increase in the amount of genetic material?
Retrotransposition
48
What are autonomous elements?
TEs that contain all of the information necessary for transposition or retrotransposition to occur. Typically carry a Transposase-Encoding Gene
49
What does transposes do?
Catalyzes the removal of a TE from its original site and its subsequent insertion at another location
50
How does transposasefunction?
1) Transposase monomers bind to the inverted repeat sequences at the ends of a TE
2) Monomers then dimerize, which brings the inverted ends close together
3) DNA is cleaved between the inverted and direct repeats, which excises the TE
4) Transposase carries the TE to a new site, cuts the DNA, inserts the TE, and then ligates it back together.
51
What is a 30-nm fiber?
Conglomeration of nucleosomes (forms a more compact structure)
52
How does the eukaryotic genome compact?
Linear DNA wraps around Histone Proteins which forms Nucleosomes
53
After the 30-nm fiber is formed, how is eukaryotic DNA further compacted?
The 30 nm Fiber is anchored into radial loop domains along the nuclear matrix
54
What are the two parts of the nuclear matrix?
Nuclear Lamina: collection of fibers lining the inner nuclear membrane
Internal Nuclear Matrix: Connected to the nuclear lamina and fills the interior of the nucleus
55
T/F: Eukaryotes have microdomains
FALSE; instead the proteins of the nuclear matrix are involved in compacting DNA into radial loop domains, which are similar to micro domains
56
What is euchromatin (eukaryotes)?
Less compacted regions of chromosomes capable of gene transcription
57
What is heterochromatin?
Compacted regions of chromosomes (via Radial Loop Domains); typically transcriptionally inactive
58
Where is heterochromatin typically found on a chromosome?
Near the centromere and telomeres
59
What does it mean that replication is semiconservative?
The newly made DNA helix contains one parental and one daughter strand
60
What are replication forks?
Site where the parental DNA strands have separated and new daughter strands are being made
61
Describe the movement of the replication forks in a bacterial chromosome
The two replication forks move in opposite directions around the bacterial chromosome until they run into each other.
62
How is replication initiated in bacteria?
Binding of DnaA proteins to sequences within the origin known as DnaA boxes
Other DNA binding proteins then cause the DNA to bend around the complex of DnaA proteins which results in the separation of strands in the AT-Rich region
After separation, DNA helicase is recruited to the AT-Rich region and breaks hydrogen bonds holding upstream strands together
63
In what direction does DNA helicase move?
5' to 3'
64
What does Topoisomerase II do?
alleviates positive supercoiling
65
What do Single Strand Binding proteins do?
Keep parental strands separated once they are separated by DNA helicase
66
What does primase do?
Synthesizes an RNA primer required to start transcription
67
What does Polymerase III do?
synthesizes a daughter strand of DNA. Catalyzes the formation of covalent bonds in adjacent nucleotides (attachment of nucleotides is to the 3' end of the primer, and moves in a 5' to 3' mode of attachment)
68
What does Polymerase I do (bacteria)?
Excises the RNA primer and fills the gap with DNA
69
What does Ligase do?
Covalently links Okazaki fragments.
70
T/F: The lagging strand requires multiple primers
TRUE
71
What is a primosome?
A complex formed by the physical attachment of helicase and Topoisomerase II
72
Describe the initiation process for transcription for eukaryotes
1) Requires the assembly of a pre-replication complex during G Phase of the cell cycle
73
Why is the pre-repliciation complex important?
1) Initiates transcription; it contains a group of proteins called the Origin Recognition Complex
2) This acts as the first initiator of pre-RC assembly
3) This promotes the binding of 6 proteins known as MCM helicase; binding of MCM helicase to the leading strand completes DNA replication licensing
74
In eukaryotes, what does polymerase alpha do?
exclusively associates with the primase to synthesize a short RNA-DNA primer
75
In eukaryotes, what does polymerase epsilon do?
Replaces the primase complex to elongate the LEADING strand
76
In eukaryotes, what does polymerase delta do?
replaces the primase complex to elongate the LAGGING Strand
77
In eukaryotes, what does polymerase gamma do?
Involved in the replication of mitochondrial DNA
78
What is flap endonuclease?
In Eukaryotes, removes the primer applied by primase
79
What polymerase generate small RNA flaps to be later digested by flap endonuclease?
Polymerase delta
80
What is telomerase?
Replicates the telomeres that cap the ends of the chromosome. Uses a short RNA molecule as a template to add repeat sequences onto telomeres.
81
What is homologous recombination?
Process whereby DNA segments that are similar (or identical) break and rejoin to form a new combination
82
When does homologous recombination occur?
During Meiosis (chromosomes cross over)
83
What are the two types of homologous recombination?
Sister Chromatid Exchange and Homologous Chromosome Crossover
84
What is sister chromatid exchange?
crossing over takes place between sister chromatids. Does NOT produce new allele combination
85
What is homologous chromosome crossover?
Crossover between homologous chromosomes to produce new genetic combination. This occurs during Meiosis 1.
86
Homologous Recombination can lead to gene expression through:
1) DNA mismatch repair
| 2) DNA gap repair synthesis
87
Where does transcription being?
At a promoter REGION (NOT Codon)
88
Where does transcription end?
At a termination SEQUENCE (not codon)
89
In prokaryotic transcription, what does the sigma subunit of RNA polymerase do?
Recognizes different promoter sequences; provides specificity to the initiation of transcription
90
T/F: In prokaryotes, promoters have consensus sequences at -35 and -10 sites
TRUE
91
What type of transcription requires mRNA processing?
Eukaryotic
92
In eukaryotes, what are the three types of Promoters?
1) Regulatory Elements
2) TATA Box
3) Transcription Start Site
93
What is alternative splicing?
Intron splicing also sometimes removes exons. This makes it so one gene can code for multiple proteins.
94
What are cis acting elements?
DNA sequences that exert effects over a particular gene (particularly, the DNA sequences and the gene they effect are on the same chromosome)
95
What are trans acting factors?
Regulatory proteins that bind to CIS ACTING ELEMENTS
96
What is translation?
Biological polymerization of amino acids into polypeptide chains
97
What does degeneracy refer to?
The fact that many amino acids are specified by more than one codon
98
What codon signals TRANSLATIONAL start?
AUG, which also codes for Methionine
99
What are anti codons?
Base sequence in tRNAs that base pairs with the codon in mRNA
100
Describe translational initiation
Ribosome binds to the mRNA 5' UTR (upstream of the start codon) and begins searching for a start codon
The 1st tRNA (carrying Methionine in Eukaryotes and Formylmethionine in prokaryotes) is added when the ribosome finds start codon
101
How do transcription factors work?
Recognize base sequences in the DNA and control rate of transcription.
Some bind directly to the promotor to facilitate transcription, others recognize regulatory sequences.
102
What are regulatory sequences?
Short stretches of DNA involved in the regulation of transcription.
103
What is the transcriptional start site?
It is the first base used as a template for RNA transcription, generally just downstream of the promoter
104
What is the significance of the consensus sequence?
There is a strong correlation between maximal rate of RNA transcription and the degree to which the -35 and -10 sequences agree with the consensus sequence (prokaryotes)
105
Where is the -10 sequence located?
10 bp upstream from the initiation site (same logic holds true for -35 sequence)
106
When is bacterial transcription initiated?
When RNA polymerase holoenzyme binds at a promoter
107
What 5 subunits make up the core enzyme?
2 alpha, 1 Beta, 1 Beta Prime, and 1 Omega
108
What is the significance of the sigma factor?
Associates with the core enzyme to create the RNA polymerase holoenzyme
109
What do the 2 alpha subunits of the core enzyme do?
Important for holoenzyme assembly and binding to DNA
110
What are the Beta and Beta Prime subunits used for (of the core enzyme)?
Needed for DNA binding and also carry out catalytic synthesis of RNA.
111
What is the omega subunit of the core enzyme responsible for?
Proper core enzyme assembly
112
T/F: The holoenzyme is required to initiate transcription
TRUE
113
What is the closed complex?
Forms when the sigma factor binds to the promoter
114
How is the open complex formed (bacteria)?
Unwinding of the TATAAT sequence at the -10 site
115
What marks the start of transcriptional elongation (bacteria)?
A short strand of RNA is made in the open complex and the sigma factor is RELEASED
116
What is the significance of the coding strand in transcription?
Has the same sequence as the RNA transcript being synthesized except the T in DAN is replaced with U in the RNA transcript
117
In what direction is the coding strand presented in?
In the 5' to 3' direction
118
In bacteria, how is transcription terminated?
Either by an RNA binding protein or an intrinsic terminator
119
In bacteria, what are the two mechanism for transcriptional termination?
1) P-dependent
| 2) P-independent
120
What is p-dependent termination?
Termination requires two sequences:
1) rut site: upstream from the terminator
2) termination site
121
In p-dependent termination, what is the rut site?
Upstream from the terminator, it serves as a recognition site for the binding of rho protein. This functions as a helicase.
122
In p-dependent termination, how does the termination site function?
1) DNA encodes for an RNA sequence containing GC base pairs
2) Forms stem loop which binds to RNA Polymerase
3) Binding causes a conformational change, which poses RNA synthesis
4) Pause allows rho (p) protein to pass through stem loop which breaks the H-Bonds with the DNA and RAN within the open complex
5) RNA strand is now separated from the DNA, and RNA polymerase is kicked off
123
What is p-independent termination?
Termination that doesn't involve the rho protein; instead uses a uracil rich sequence in its place.
124
In p-independent termination, what two things make up the terminator?
1) Uracil rich sequence at 3' end
2) sequence promoting stem loop
(adjacent and within the RNA)
125
How does p-independent termination work?
Production of a stem loops results in a pause while the uracil rich sequence in RNA transcript is bound to the DNA template strand (which is a weak bond)
The weak bond causes a dissociation of the RNA strand from the DNA (intrinsic termination)
126
What is intrinsic termination?
Physical removal of RNA transcript without p-protein
127
T/F: Eukaryotes have multiple RNA polymerases while prokaryotes only have one type
TRUE
128
What is RNA Polymerase 1 responsible for?
transcribes all of the genes for ribosomal RNAs (except 5S rRNA)
129
What is RNA Polymerase II responsible for?
Transcribes all protein encoding genes (synthesizes all mRNAs)
130
What is RNA polymerase III responsible for?
Transcribes all genes for tRNAs (and the gene for 5S rRNA
131
In eukaryotes, what does the core promotor consist of?
1) TATAAA sequence (TATA Box)
| 2) Transcriptional Start Site
132
Why is the TATA box important?
Roughly 25 bp upstream from the start site, it determines the PRECISE transcriptional start point
133
In Eukaryotes, when does initiation of transcription occur?
When RNA Polymerase II and general transcription factors bind to a promoter sequence (RNA polymerase also requires 5 different proteins called GTFs in order to start)
134
What is a mediator used for?
Mediates interactions between RNA polymerase II and regulatory transcription factors in eukaryotic transcription
135
What is colinearity?
1:1 correspondence between the sequence of codons in the DNA-coding strand and the amino acid sequence of the polypeptide
136
Where does splicing of pre-mRNA occur?
In the nucleus
137
What are snRNPs?
Small nuclear riboproteins; make up the splicosome
138
In splicing, what is a repressor?
Inhibits the splicosome from recognizing a splice sire by binding to a 3' splice site which hides it. This causes the splicosome to skip the masked site and splice another site, which may cut out an exon (exon skipping)
139
Why is capping important?
1) Ensures proper mRNA exit from the nucleus
2) Cap structure is recognized by initiation factors needed during translation
3) Cap structure may be important for efficient intron splicing
140
What is RNA editing?
Modification of nucleotide sequence of RNA after the RNA is already made
141
What are the three types of RNA editing?
1) Additions
2) Deletions
3) Conversions
142
In what species was RNA editing first discovered?
Trypanosomes
143
How does conversion RNA editing work?
A base in RNA is deaminated (NH3+ is removed). Turns:
1) Cytosine into Uracil
2) Adenine into Hypoxanthine (recognized as guanine during translation)
144
An example of conversion RNA editing in mammals is in....
mRNA encoding for apoliprotein B
145
What is the primary role of DNA?
Store the information needed for the synthesis of all proteins?
146
What are structural genes?
Another word for protein encoding genes - genes that encode for an amino acid sequence
147
What is the central dogma?
States that the flow of information is from DNA to RNA (mRNA) to Protein
148
What are sense codons?
Sequence of 3 bases that species a particular amino acid
149
Which terminal on a polypeptide corresponds to the 5' end of mRNA?
The N-terminus
150
What is the N-Terminus?
The first amino acid of a polypeptide; an amino is found at this site.
151
What is the C-Terminus?
The last amino acid in a completed polypeptide; contains a carboxyl group (COO-)
152
What gives each amino acid its unique characteristics?
Their side chains (R group)
153
T/F: Codon to Anti-Codon binding is antiparallel
TRUE
Example:
If the anticodon is 3'-AAG-5'
the the codon is 5'-UUC-3'
154
In what loop is the anti codon located in a tRNA?
The second loop
155
What do aminoacyl-tRNA synthetases do?
Charge tRNAs by attaching the appropriate amino acid to the 3' end (acceptor stem)
156
The _____ is the site of translation
Ribosome
157
Describe the structure of ribosomes
Composed of a small and a large subunit; each subunit is formed from ribosomal RNA and proteins.
158
T/F: In bacteria, ribosomal proteins and rRNA are synthesized in the cytoplasm, and the ribosomal subunits are also assembled there
TRUE
159
Where is the synthesis of Eukaryotic rRNA?
Within the nucleus
160
Where does assembly of the ribosomal subunits occur in eukaryotes ?
In the nucleolus
161
Where are ribosomal proteins made in eukaryotes?
In the cytoplasm
162
What is an initiator tRNA?
tRNA that recognizes the start codon in mRNA
