Exam 3 Flashcards
1
Q
Closing and opening the vestibule in voltage gated mechanisms are by what
A
Voltage sensors
2
Q
What are three common ions in chemically gated channels
A
Na
K
Ca
3
Q
Nicotinic if AcChRs are _________ and binds two ACh molecules which opens the channel. All 5 subunits contribute to forming the ion channel
A
Pentamers
4
Q
What are the three states of channels
A
Resting (closed)
Open
Desensitized (closed)
5
Q
What are the 4 important second messengers
A
Ca
cAMP
DAG
IP3
6
Q
What are the 6 important classes of receptors
A
GCPR
Receptor Tyrosine Kinases
Receptor guanyl kinases
Chemically gated ion Chanel’s
Nuclear steroid hormone receptor
Adhesion receptors
7
Q
How many receptors are in GCPRs
A
Several hundred
8
Q
What are GCPRs used for
A
Mediate signaling by photons, odorants, tastants, hormones, NTs, inflammatory
9
Q
What receptor responds to the “stress hormone” epinephrine, and initiates the “flight or fight” response
A
Beta-adrenergic receptor
10
Q
What does Gs do
A
Beta-adrenergic R
Stimulate Adenylate
11
Q
What does Gi/o do
A
a2-adrenergic R
Inhibit adenylate cyclase
12
Q
What does Gq/11 do
A
some muscarinic ach Rs
a1-adrenergic R muscle contraction
Increase IP3 and intracellular calcium
13
Q
What does G12/13 do
A
Angiotensin II, serotonin, thrombin
Activates RhoGEF -> Rhokinase
14
Q
PLC generates ____ and _____ from PIP2
A
IP3 and DAG
15
Q
What kind of receptor is insulin
A
Tyrosine Kinase Receptor
16
Q
What is the name of the GTP-binding protein that is activated by the insulin receptor
A
IRS-1
17
Q
What are the three members of families of kinases
A
MEK
Raf-1
ERK
18
Q
What are nucleic acids made out of
A
sugar
phosphate
base
19
Q
What bond link sugars together
A
Phosphodiester bonds
20
Q
What makes DNA more stable than RNA
A
DNA has an H on the 2’ instead of an OH like RNA
21
Q
Nucleic acids are always written and read in what direction
A
5’ to 3’
22
Q
What is on the 5’ end of a nucleic acid and what is on the 3’ end
A
5’ : Phosphate
3’ : Hydroxyl
23
Q
How many rings do purines have and which bases are present
A
2 rings
A and G
24
Q
How many rings do pyrimidines have and which bases are present
A
1 rings
T, U, and C
25
What is the difference between a nucleotide and a nucleoside
nucleotide: phosphate
nucleoside: no phosphate
26
Watson and Crick model of DNA structure
Double helix
Stands run in opposite directions
Phosphates point outwards and bases point inward
Have major and minor grooves
~10 bases per turn
27
What is chargaff rule
Amount of A = amount of T
Amount of C = amount of G
28
What stabilizes a helix
Hydrogen bonds
Base Stacking
Hydrophobic Interactions
29
Why does DNA have major and minor grooves
N-glycosidic bonds between the bases and sugar do not point into exactly opposite diections
30
A-form: handedness, shape, groove, occurrence
handedness: Right-handed
shape: Broad
minor: Deep but narrow
major: Shallow and broad
occurrence: Double-stranded RNA, some DNA-RNA hybrids
31
B-form: handedness, shape, groove, occurrence
handedness: right-handed
shape: intermediate
major: deep and wide
minor: deep and narrow
occurrence: very common
32
Z-form: handedness, shape, groove, occurrence
handedness: left-handed
shape: narrowest
major: flat
minor: deep and narrow
occurrence: rare
33
Physical characteristics of DNA
Melting: separates strands by using heat
Anneal: cooling allows strands to come back together
Absorbance at 260nm if single strand is higher than A260 of double strand
34
If there is sequences similarity between two samples duplexes between DNA1 and DNA2 will form also called ________
Hybrids
35
Hybridization increases with _____________ similarity between DNA1 and DNA2
sequence
36
Palindromic sequences form __________ when single stranded and cruciforms when double stranded
hairpins
37
RNA structure
Single-stranded
Helical
Can form double helix with RNA or DNA
Self-complementary regions of DNA usually exist in the right-handed A-form
Unpaired nucleotides form bulges or internal loops
38
What is the sequence of information processing in genetic copying
DNA -> RNA -> Protein
39
The base complementary of the double helix allows each strand to act as a _________ for the synthesis of the other
template
40
What is the nucleophile and electrophile in the nucleotides
3' - OH acts as the nucleophile which attacks the alpha phosphate
41
_____ encodes the sequence of proteins and then ____ is used as an intermediate produced by transcription
DNA
RNA
42
What is the three sequences of strands when creating new genetic informaiton
mRNA (5'-GCU-3')
template DNA (3'CGA-5')
coding DNA (5'-GCT-3')
43
What starts transcription
-DNA bind the RNA polymerase enzyme and direct it to the start site
-The promoter directs RNA polymerase to start synthesis
44
How is transcription ceased
-Repressor bind promoter sequence and block transcription (operator sites)
45
What is the start codon for prokaryotic and eukaryotic cells
prokaryotic: fMeT
eukaryotic: H2N-Met
46
What are the 5 characteristics of the genetic code
3 nucleotides encode 1 AA
Codons are read sequentially
Genetic code is degenerate (some AA have more than one codon)
Genetic Code contains start and stop signals for protein synthesis
Genetic code is universal
47
What encapsulates the genetic code
tRNA
48
Each tRNA contains a template recognition site an _________ and carried one specific amino acid
Anticodon
49
What is polycistronic
More than one protein are encoded by a single mRNA
50
What is monocistronic
mRNA encodes for one AA
Have a cap and poly A tail
Eukaryotes
51
The non-coding intervening sequences are called what
Introns
52
What is recombinant DNA technology
Segments of DNA are detected, rearranged, added, deleted, introduced into the genomes of other cells
53
What are 4 important products if recombinant DNA technology that are in therapeutic use
Human insulin
Therapeutic growth factors
Therapeutic monoclonal antibodies
Blood clotting factors
Therapeutic interferons
Vaccines
54
What are the 6 steps of cloning
-Vector carding piece of DNA
-Cutting DNA of interest using restriction endonueases
-Joining two pieces of DNA covalently
-Introducing recombinant DNA into a host cell
-Selectivity propagating transformed cells
-Identifying host cells that contain recombinant DNA
55
If two pieces of DNA were cleaved with the same restriction enzyme they can be ___________
Recombined
56
What do vectors do
They allow a piece of DNA to be propagated
57
What are plasmids
Cloning vectors
Occur in bacteria
Exchanged between bacteria
Extrachromosomal circular DNA
Self-replicating
Resistance to antibiotic drug
58
pBR has _____ antibiotic resistance genes, inserting a gene into one of them will disrupt its antibiotic resistance
two
59
Bacteria that contains a plasmid is sensitive to what and if it does not contain a plasmid it is sensitive to what
with: sensitive to Amp and Tet
w/o: sensitive to Amp
60
What is a bacteriophage
viruses that infect bacteria
61
What is bacteria artificial chromosomes (BAC)
circular pieces of DNA and contain bacterial origin of replication
62
What are yeast artificial chromosomes (YAC)
used to introduce DNA into yeast cells as hosts
63
Rank the size of bacteriophage, bacteria artificial chromosomes (BAC), yeast artificial chromosomes (YAC)
bacteriophage < BAC < YAC
64
Mammalian genes contain _______ and cannot be processed by bacteria
introns
65
what is cDNA
complementary DNA
66
If a mixture of mRNA is used as a starting material, a library of _______ can be made
cDNA
67
What is southern blotting
use DNA to probe / detect DNA
68
What is northern blotting
use nucleic acids (DNA and RNA) to probe / detect RNA
69
What is western blotting
use antibodies to detect proteins
70
What ingredients are needed for di-dioxy-sequencing
DNA template
DNA polymerase
Primer
dNTPs
ddNTPs
71
What is the process of ddNTP sequencing
-3’-OH of ribose attacks alpha phosphate of next nucleotide for chain elongation
-ddNTPs lack the 3’-OH when ddNTPs are used and reaction stops
72
How much variations is found in human genomes
0.1%
73
Groups of genes inherited together are called
Haplotypes
74
Oligonucleotides up to ______ long can be synthesized
120 bp
75
What are the ingredients of PCR reaction
Amplified DNA
Primers
Nucleotides
Tac Polymerase
Thermocycler (PCR machine)
76
What are the three steps in the cycle of PCR
Strand separation (highest temp)
Annealing of primers (lowest temp)
DNA synthesis (intermediate temp)
77
What is RT-PCR
Reverse transcriptase using mRNA to get cDNA
78
What is the procedure of site directed mutagenesis
Grow plasmid containing gene
Isolate plasmid
Separate strands of plasmid
Hybridize strands
Synthesize strands
Introduce DNA into bacteria clone
Harvest plasmid with mutated gene
79
In E. Coli what is the start site
Ori C
80
How many origins of replication are in eukaryotes
multiple
81
4 processes of pre-priming complex
DnaA binding to OriC
helicase DnaB separates strands
DNA topoisomerase II relieving topological stress
Primase DnaG synthesizing RNA primer
82
What does helicase do
separates strands
83
What does DNA polymerase do
proofreading activity
84
What does RNA polymerase do
can start process without a primer
85
What does primase do
RNA primer to start DNA synthesis
86
What are Okazaki fragments
they help lagging strand by being small pieces so it can start backwards
87
What does single strand binding proteins do (SSB)
separation of strands generates naked single strand which are protected by that
88
What does DNA polymerase I do
removal RNA and replacement with DNA
89
5' -> 3' endonuclease activity
remove bases in forward direction
90
3' -> 5' endonuclease activity
remove bases in backward direction for proofreading
91
What does DNA topoisomerase II do
relieves topological stress produced by strand seperation
92
What does ligase do
joins together the gaps between Okazaki fragments
93
The synthesis of leading and lagging strands are synthesized by two subunits in the same direction how does this work
The lagging strand is looped around to align with the leading strand
94
When does termination of DNA replication occur
When the two replication forks meet ter sites
95
In eukaryotes DNA is what
linear (causing shortening of DNA in synthesis)
96
What are telomeres and what do they do
Consist of repetitive DNA
Telomerase is reverse transcriptase and uses its own terminal RNA template
97
Similarities between RNA synthesis and DNA replication
RNA made 5' to 3'
Nucleophilic attack of 3'-OH on 5'-phosphate of incoming base
DNA strands must be opened to synthesize
98
Differences between RNA synthesis and DNA replication
No primer required
No proofreading occurs
99
What enzyme catalyzes RNA synthesis
RNA polymerase
100
What are the three stages of transcription
Initation
Elongation
Termination
101
What are two ways in which termination can occur
dependent on rho protein or independent of rho proteins
102
What are the key differences between eukaryotic and prokaryotic transcription
-Eukaryotes have a nucleus
-Eukaryotes transcription in nucleus, prokaryotes in cytosol
-Eukaryotes transcription and translation are separated in space and time which allows mRNA to be modified
-Prokaryotes transcription and translation occur in the same compartment simultaneously
103
Which eukaryotic RNA polymerase synthesizes mRNA
Type 2
104
Initial binding of transcription factors leads first to the formation of a _______ complex
Closed
105
Proteins with help add activity facilitate the formation of a transcription bubble causing a __________ complex
Open
106
What is the complex order for initiation
Closed -> open -> elongation complex
107
Pol II has a ______________ domain that becomes phosphorylated during transcription initiation
Carboxyterminal this then forms a elongation complex
108
What are the 4 processes in mRNA processing
5’ cap added
Introns spliced out
Poly A tail added
RNA editing at certain bases
109
How is the 5’ cap added
5’ to 5’ linkage instead of 5’ to 3’ linkage
110
Splicing is directed by __________ __________ and can occur either before or after the cleavage and polyadenylation steps
Splice signals
111
Synthesis of the cap is carried out be enzymes tethered to the carboxyterminal domain of ________
POL II
112
Most introns begin with a ___ and end with an _____
GU
AG
113
U1 and U2 are RNA compounds of _________ which contain both RNA and proteins
snRNP (small nuclear ribonucleoproteins)
114
The 2’-OH of the A in the branch site is the attacking __________ in the first reaction. It attacks the phosphorus at 3’-OH of G at the 5’ splice site. This process yields the loop intermediate called what
Nucleophile
Lariate intermediate
115
The complex of mRNA and snRNP is known as a ____________
Splicesome
