Section 2 - Module 6 Flashcards
1
Q
What is the significance of 1952?
A
Year that Alfred Hershey and Martha Chase demonstrated that DNA and not proteins is transmitted on to progeny. DNA as the genetics material in Bacteriophages
2
Q
Frederick Griffin’s work
A
Demonstrated cell can be transformed
3
Q
What is the transforming principle?
A
DNA
4
Q
What is Transformation?
A
acquiring new genetic material from uptake of external source
5
Q
What bacteria did Hersey work with?
A
E/coli and their associated bacteriophage
6
Q
Aaron Levene’s work?
A
Proposed tetranucleotide theory. Stating that DNA is made of repeating units called nucleotides
7
Q
Albrecht Kossel’s work?
A
Determined nucleic acids contain four nitrogenous bases.
8
Q
The four nitrogenous bases in DNA
A
Adenine (A), Cytosine (C), Guanine (G), Thymine (T)
9
Q
The four nitrogenous bases of RNA
A
Adenine (A), Cytosine (C), Guanine (G), Uracil (U)
10
Q
Significance of 1953?
A
Year Franklin and Wilkins devise the secondary structure of DNA. The double helix structure of DNA
11
Q
DNA secondary structure
A
Structure of the set interactions between bases. Such as which parts of the strands are bound to each other and phosphate backbone.
12
Q
Significance of 1948?
A
Year Erwin Chargaff discovered pattern in DNA base pairs. Nucleotide compositions DNA - A=T; G=C.
13
Q
Describe nucleotide structure
A
Phosphate group, base (A, G, G, t), and deoxyribose sugar. Purines attached to pyridines
14
Q
Purines
A
Adenine (A) and Guanine (G). They has an additional ring structure
15
Q
Pyridines
A
Cytosine (C) and Thymine (T). They have an amide functional group
16
Q
Phosphate group is attached to the __ carbon of deoxyribose sugar
A
5’
17
Q
Base is attached to the _ carbon in deoxyribose
A
1’
18
Q
What makes up deoxyribose sugars of DNA?
A
5 carbons with OH at 3’ carbon. Between 4’ and 1’ there is an ether (O).
19
Q
What is different in RNA structure?
A
it is a ribose sugar and has an additional OH on carbon 2’. uses the U base T
20
Q
Nucleoside
A
Sugar + Base (exposed nitrogenous bases)
21
Q
Nucleotide
A
Sugar + Base + Phosphate group
22
Q
Chargaff’s Rule
A
Purine(A+G)/Pyrimidines (T+C) = 1.0 approximately
23
Q
Double stranded DNA
A
(C+T) = (A+G)
24
Q
Rosalind Franklin and Maurice Wilkins
A
x-ray diffraction lead to discovery of DNA being a helix of constant diameter
25
Erwin Chargraff
Base pairing
26
Direction DNA spiraling around helix axis
anti-parallel (opposite directions)
27
Direction of reading DNA
5' to 3'
28
What is perpendicular to the helix axis in DNA?
Base pairs
29
DNA two Grooves
Major and minor grooves allow for proteins to bind to and recognize DNA
30
Another way to refer to denaturing of DNA
Melting
31
What is "Melting"
Separation of two DNA strands, to single stranded DNA (ssDNA)
32
What is reversible posses in separation of DNA
Renaturation
33
Ways to denature or "melt" DNA
Increase temperature, reduce salt concentration, increase pH, solvents
34
Melting Temperature (Tm) of DNA
Defined as the temperature when DNA duplex is separated into single strands
35
What can DNA Tm indicate
duplex (hybridized DNA molecules) stability, higher Tm the more stable the DNA helix
36
How to measure DNA denaturation
absorbance. AS DNA duplex separated, the absorbance increases (hyperchromic shift).
37
What does higher Tm indicate?
More stable DNA helix
38
How does GC content (% G+C), effect melting temperature?
Higher GC content increases stability, therefore increasing melting temperature
39
How does salt concentration effect melting temperature?
Higher salt concentration, higher the melting temperature. Salt causes the phosphate backbone to the tightly packed, and this shield the negative charged of the phosphate backbone. Increases stability.
40
How can GC content in DNA classify organisms?
It is species specific
41
Does mutated of normal DNA have higher melting point?
Mutated melting rages are just different than "normal" ranges no specification of higher or lower
42
Molecular Biology Techniques involving DNA melting
polymerase chain reaction (PCR) and southern blotting
43
Equation for Melting Temperature
Tm = 81.5 + 16.6 lg [M] + 0.41(%GC) - 675/L
44
The three proposed models of DNA replication
Conservative, dispersive, and semiconservative replication
45
Correct model of DNA replication
semiconservative
46
What results of 1st round of Meselson experiment?
50% light and 50% heavy so NOT conservative replication
47
What is results of 2ndround of Meselson experiment?
There where some DNA that were 100% intermediate. So NOT intermediate replication
48
Semi-conservative replication
Each daughter cell consists of one parental strand and one newly synthesized strands based off a parental strand.
49
DNA synthesis Requirements
1) ssDNA template
2) all four dNTPs
3) DNA polymerase and other supporting enzymes
4) Free 3'-OH group
50
dNTPS
deoxynucleotide triphosphate, with each using a different DNA base: adenine (dATP), cytosine (dCTP), guanine (dGTP), and thymine (dTTP).
51
Mechanism of DNA Synthesis
Catalysis of phosphodiester bond between dNTPS and bases
52
Direction of DNA chain elongation
5' to 3;
53
Template strand reading direction
3' to 5'
54
Origin of Replication
the specific nucleotide sequence where replication begins
55
Where dies synthesis take place
Within a replication bubble
56
Where are DNA strands synthesized simultaneously
replication fork
57
What is a DNA molecule/region of DNA that replicates from a single origin of replication called?
Replicon
58
Replication is ______
Semicontinuous
59
Leading strand synthesis is _ and the direction of the fork
continuous
60
Lagging strand synthesis is _ and occurs in the opposite direction of the fork
discontinuous
61
Bacteria Genome
Circular
62
Bacteria Replication
Theta replication
63
Virus Genome
Circular
64
Virus Replication
Rolling circle replication
65
Eukaryotes Genome
Linear
66
Eukaryotic replication
Linear replication
67
Theta replication
1) single replicon (entire chromosome)
2) bidirectional replication w two forks within a single bubble
3) semi discontinuous in both replications forks
4) results in two circular DNA molecules
68
Rolling circle
1) no replication bubble
2) uncoupling of the replication of the two DNA molecules
3) replication is continuous
4) results in multiple circular DNA molecules
69
Linear
1) multiple replicons, origins or replication, and replication bubbles
2) bidirectional
3) Semi discontinuous at both replication forks
4) results in two linear DNA molecules
70
Four stages of replication
1) Initiation
2) unwinding
3) elongation
4) termination
71
Initiation
Initiator protein bind to the origin of replication (oriC) and a short section of DNA unwinds and proteins bein the ssDNA. ss-binding-protein keeps DNA separated and Helicases binds to the lagging strand template and breaks hydrogen bonds.
72
What bonds to helicases break
hydrogen bonds
73
Unwinding
Helicases break the hydrogen bonds between DNA strands while DNA gyrase (a topoisomerase) travels ahead of the fork and alleviates supercoiling caused by unwinding
74
What does unwinding cause without DNA gyrase to reverse
supercoiling
75
Chain Elongation
RNA primer (RNA nucleotides stretch) is synthesized by Primase. RNA primer provides a free 3' OH for the DNA polymerases to use. RNA primer is replaced with nucleotides
76
Why do we require an RNA primer?
Because the production of RNA does NOT require a 3' end
77
E. Coli principle replication enzyme
Pol III
77
DNA ligase
seals the nick in the sugar phosphate backbone
77
What DNA polymerase activity fills in the gap of DNA nucleotides (E. Coli)
Pol I
77
Exonucleases
Removes primers starting at the 5' ends. Removes Newley incorporated nucletides that do not match the template strand
77
E. Coli polymerase that removes and replication RNA primers with DNA
pol I
78
How many E. Coli DNA polymerases are there
Five (Pol I to Pol V)
79
Eukaryotic DNA polymerases
Alpha, delta, and epsilon (all 5' to 3' activity) (delta and epsilon do 3' to 3' exonuclease activity)
80
Delta DNA polymerase
Lagging-strand synthesis of nuclear DNA, DNA repair, and translesion DNA synthesis
80
Alpha DNA polymerase
Initiation of nuclear DNA synthesis and DNA repair; has primase activity
80
Epsilon DNA polymerase
Leading-strand synthesis
80
Benefit of more origins in human DNA synthesis?
multiple origins ensure efficient genome replication in limited time
80
Eukaryotic DNA is packaged into ____
Chromatin
80
Telomeres
1) are the end of linear chromosomes
2) made up of G-rich short repeated sequences
3) stabilize chromosomes
specialized reverse transcriptase
4) extends the end of the parental DNA by RNA-templated DNA synthesis
5) responsible for the replication of the chromosomes ends
6) extends the DNA, filling int he gap due to the removal of the RNA primer
81
Transcription + translation =
gene expression
82
DNA replication
information transferred from one DNA molecule to another
83
Transcription
Information transferred from DNA to an RNA molecule
84
Translation
Information is transferred from RNA to a protein through a code that specify the amino acid sequence
85
Prokaryotes gene expression
transcription and translation both occur in the cytoplasm
86
Eukaryotic gene expression
Transcription in nuclear then pre-mRNA is processed to mRNA and leaves into the cytoplasm for translation
87
Protein coding RNA
mRNA
88
RNA unique to prokaryotes
CRISPR RNA (crRNA)
89
Folded complex of RNA called _
Hairpin-loops and stem-loops
90
Synthesis in respect to DNA template strand
complementary and antiparallel
91
Transcription
1) initiation does not require a primer
2) ribonucleotides are added to the 3'OH group of the growing RNA chain
3) DNA unwinds at the front of the transcription bubble
4)rewinds
92
Three requirements of transcription
1) DNA template
2) RNA nucleotides (rNTP's)
3) RNA polymerase and other proteins
93
RNA transcription
Template is read in 3' to 5' direction, while RNA is synthesized in the 5' to 3' direction
ONLY the RNA coding region is transcribed
94
Promoter
upstream of the start site, adjacent to gene. Indicates the direction of transcription. Orients the enzyme towards the start site
95
RNA coding region
downstream of start site
96
Termination site
downstream of start site
97
Initiation (prokaryotic)
assembly of transcription apparatus on the promoter and begins synthesis of RNA
98
Elongation (prokaryotic)
DNA is threaded through RNA polymerase, unwinds the DNA, ass new nucleotides to the 3' end of the growing RNA strand.
99
Termination (prokaryotic)
the recognition of the end of transcription
100
What do bacteria use to recognize promoters?
Sigma factors
101
what would happen without sigma?
core enzyme would initiate transcription randomly
102
Holoenzyme
in prokaryotes it is the complete enzyme complex composed of the core RNA polymerase and the sigma factor
103
Consensus sequences
short stretch of DNA that is conserved among promoters of different genes (prokaryotic thing)
104
Common sequences (or elements)
-10 (pribnow box) and -35 nucleotides which are upstream of the start site (+1). They are NOT identical in all promoters
105
Promoter sequences strength =
frequency of trasnciription
106
Strong promoter
recA
107
Down mutations
base substitutions that make the sequence less similar to the consensus sequences reduce the rate of transcription
108
up mutation
sequence become more similar to the consensus sequences
109
RNA transcription in prokaryotes
is initiated when core RNA polymerase binds to the promoter with the help of sigma
110
Terminators in bacteria
Rho-dependent (requires Rho protein) and Rho-independent (also called intrinsic terminator)
111
Rho-dependent termination
1) rho bind to RNA upstream of terminator
2) RNA polymerase pauses when it reaches terminator and Rho catches up
3) Rho unwinds DNA-RNA hybrid using helicase activity
112
Rho-independent termination
1) inverted repeats
2) polymerase pauses at Us
3) hairpin formation destabilize DNA-RNA hybrid
4) RNA transcript dissociated from RNA polymerase, DNA reanneals
113
Consensus sequences in order for eukaryotic transciption
TFIIB (-35), TATA(-25), initiator(+1), and DCE (+30)
114
Core promoter
extend upstream/downstream of transcription start site. Minimal sequence required for accurate transcription initiation. Includes a number of consensus sequences
115
Regulatory Promoter
located upstream of the core promoter, exact location can be variable. Transcriptional activator proteins binds to consensus sequences and affect the rate of transcription.
116
Order of Basal transcription apparatus assembly
TATA binding protein, general transcription factors, basal transcription apparatus
117
What is required for termination
cleavage of the mRNA at a specific site
118
What degrades the remaining mRNA terminating transcription?
5' to 3' exonuclease
