1B: Transmission of genetic information from the gene to the protein Flashcards
(173 cards)
1
Q
Nucleotides
A
Monomers of nucleic acids, consists of sugar, nitrogenous base and phosphate group
2
Q
Types of Nucleotides
A
Thymine, Adenine, Guanine, Uracil
3
Q
Structure of Nucleotides
A
Phosphorus is linked at the 5 carbon of the sugar; Nitrogenous Base is linked to the 1 carbon of the sugar
4
Q
Pyrimidines
A
Single ring; Cytosine, Uracil, Thymine
5
Q
Purines
A
Two rings; Adenine, Guanine
6
Q
Nucleoside
A
Sugar + Nitrogenous Base
7
Q
Types of Nucleosides
A
Cytidine, Uridine, Adenosine
8
Q
DNA
A
Deoxyribonucleic Acid
9
Q
Double Helix
A
2 single strands of DNA wound around each other held together by hydrogen bonds
10
Q
Watson-Crick Model
A
Two linear strands running antiparallel and twisted in a right-handed spiral; bases are located inside of the helix
11
Q
Base Pairing Specificity
A
Nucleobases are connected via hydrogen bonds:
A2T
C3G
DNA with more G-C are more stable
12
Q
Function of DNA in transmission of Genetic Information
A
Complementary base pairing property allows for DNA replication and transmission of genetic information
13
Q
Central Dogma
A
DNA -> RNA -> Protein
14
Q
Denaturation of DNA
A
dsDNA comes apart due to heating or a change in pH
15
Q
Annealing of DNA
A
ssDNA joins again due to complementary nucleotide sequences and random molecular motion
16
Q
Hybridization of DNA
A
Denatures two different DNA sequences then uses ssDNA from each to anneal to dsdna
17
Q
Process of PCR
A
Denature -> Anneal -> Extend
18
Q
Mechanism of Replication
A
- Separation of Strands
2. Coupling of Free Nucleic Acids
19
Q
Enzymes of Replication
A
- DNA Gyrase
- Helicase
- SSB - Primase
- DNA Pol III
- DNA Pol I
- DNA Ligase
20
Q
Helicase
A
Unwinds double helix of DNA
21
Q
DNA Pol III
A
Binds one strand of DNA from an RNA primer, moves 3’ to 5’ producing a leading strand
22
Q
Primase
A
Produces RNA primers at the 5’ end, allowing for the synthesis of Okazaki fragments
23
Q
Okazaki Fragments
A
Short discontinued fragments of replication products on the lagging strand
24
Q
DNA Pol I
A
Removes RNA primers by the 5’ end to 3’ end
25
DNA Ligase
Seals the spaces in the strand between the Okazaki Fragments
26
Single-Strand Binding Protein
Responsible for keeping the DNA unwound after helicase unwinds the helix
27
DNA Gyrase
Uncoils DNA ahead of the replication fork
28
Semi-conservative nature of replication
Each DNA helix contains one parent strand and one new strand; older DNA has more methyl groups added so its always possible to determine which strand is older
29
Origin of Replication
Point at which replication begins; multiple points in eukaryotes and singular in prokaryotes
30
Telomerase
Replicates the end of DNA molecules which consist of telomeres that help keep genetic information and prevent it from being lost during replication
31
Repair during Replication
DNA Pol has proofreading activity (3'->5' exonuclease) which replaces incorrect nucleotides
DNA Pol I has 5'->3' exonuclease activity which allows for removal of incorrect nucleotides
32
Repair of Mutation
```
Mismatch
Base-Excision
Nucleotide-Excision
Nick Translation
SOS Response
```
33
Mismatch Repair
Enzymes recognize incorrectly paired bases and cuts out the stretch of DNA containing the mismatch; utilizes methylations to determine old from new strand
34
Base-Excision Repair
A single base is removed and replaced using DNA Pol and Ligase
35
Nucleotide-Excision Repair
Damaged nucleotide gets cut out and replaced (due to thymine dimers)
36
Nick Translation
RNA primers are replaced with DNA through 5' to 3' activity
37
SOS Response
When there is too much DNA for normal repair; the DNA Pol replicates over the damaged area as if it were normal
38
Triplet Code (Codon)
Sequence of nucleotides of mRNA that codes for amino acids; 3 nucleotides = single amino acid
39
Anticodon
3 bases at the end of tRNA (transfer anticodon) that correspond to the nucleotide triplet in mrNA during translation
40
Degenerate Code
Multiple 3 codon combinations code for the same amino acid (20 total); more than one codon codes for a given amino acid
41
Wobble Pairing
When two nucleotides in RNA molecules do not follow Watson-Crick base pairing rules
42
Types of Wobble Base Pairs
```
G-U
I-U
I-A
I-C
I=hypoxanthine
```
43
Missense Mutations
A new nucleotide changes the codon to produce a changed amino acid in protein
44
Nonsense Mutations
A new nucleotide changes the codon to a stop codon that prematurely truncates a protein
45
Initiation Codon
AUG (methionine); starts the translation process
Prokaryotes = Shine-Delgarno Sequence
Eukaryotes = Kozak Sequence
46
Termination Codon
End translation of the mRNA strand
UAA
UAG
UGA
47
mRNA
Carries genetic information (in the form of codons) that corresponds to amino acids for protein synthesis
5' terminal is capped by a 7-methyl guanosine triphosphate cap; 3' end is added poly-A tail
48
tRNA
In the cytoplasm, directs translation of mRNA into proteins; contain anticodon
49
rRNA
Necessary for ribosome assembly, plays a role in mRNA binding to ribosomes and in translation, contains active site for catalysis (peptide bond formation)
50
Mechanism of Transcription
[Eukaryotes = Nucleus]
[Prokaryotes = Cytoplasm]
Initiation -> Elongation -> Termination
51
Initiation
RNA Pol binds to the promoter region of DNA
52
Elongation
Transcription factors unwind the DNA strand and allow RNA Pol to transcribe a strand of DNA into a strand of mRNA; C3G, A2U
53
Termination
RNA Pol reaches a terminator sequence and then releases the mRNA polymer and detaches from the DNA
54
Eukaryotic Structure
5' UTR
Coding Sequence
3' UTR
55
Coding Sequence
Where translation begins and ends; contains amino acid sequences for protein synthesis during translation
56
3' UTR
Contains crucial information for mRNA stability
57
Processing in Eukaryotes
1. Cap Addition
2. Polyadenylation
3. Splicing
58
Cap Addition
Addition of a 5' methyl guanosine cap that occurs during transcription; prevent chain degradation
59
Polyadenylation
A poly-A tail is added to the 3' end; enhances the stability of mRNA and regulates transport to cytoplasmic compartment
60
Splicing
Removes introns
61
Introns
Not expressed in proteins
62
Exons
Encoding sequences and they are reserved
63
Ribozymes
Ribonucleic Acid Enzymes; catalyzes biochemical reactions, join amino acids together and form protein chains; play a role in RNA splicing, viral replication and RNA biosynthesis
64
Spliceosomes
Splicing machines that remove and cut introns from pre-mRNA
65
snRNA
Small nuclear RNA, couples with snRNPs that 5' and 3' splice sites of introns
66
snRNPs
Combine of snRNA and protein factors that are essential in intron removal
67
Eukaryotic Ribosome
40S + 60S; 80S
68
Prokaryotic Ribosome
30S + 40S; 70S
69
General Ribosome Structure
mRNA binding site (small subunit); E site, P site and A site (large subunit)
70
P site
Binds to tRNA and extends amino acid chain
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A site
Binds to tRNA holding new amino acid
72
E site
When a stop codon is encountered, release factors are bound and the chain falls off
73
Post-Translational Modification
```
Glycosylation
Acetylation
Methylation
Sulfation
Phosphorylation
```
74
Post-Translational Modification
```
Glycosylation
Acetylation
Methylation
Sulfation
Phosphorylation
```
75
Chromosomal Proteins
Histones & Non-Histone
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Histones
Order & Package DNA into Nucleosomes; aids with gene regulation; allows DNA to fit inside the nucleus
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Non-Histones
Regulatory and Enzymatic Function
78
Single copy DNA
Holds most of the organisms genetic information; protein synthesis & gene expression; holds most of the protein-coding genes; low rates of mutation
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Repetitive DNA
Concentrated at centromeres, not translated, high rates of mutation
80
Moderate Repetitive DNA
Transcribed by RNA Pol I or III; contains protein-coding genes
81
Highly Repetitive DNA
Not transcribed; contains no genes
82
Highly Repetitive DNA
Not transcribed; contains no genes
83
Supercoiling
Compacts DNA so it doesn't get tangled onto itself
84
Positive Supercoil
Left Handed; difficult to unwind
85
Negative Supercoil
Right Handed; easier to unwind
86
Topoisomerases
Alter DNA topology to carry proper functions
87
Topoisomerase I
Remove DNA supercoils; break strands during recombination; condense chromosomes
88
Topoisomerase II
Cuts strands to manage DNA tangles and supercoils
89
Chromatin
Makes up the nucleus and function in gene expression and repression
90
Heterochromatin
Tightly packed; contains more DNA; late replication
91
Heterochromatin
Dense; Few or No Genes; Replicates Late; Not Transcribed
| Increased Acetylation & Decreased Methylation
92
Euchromatine
Loose; Lots of Genes; Replicates Early; Can be transcribed
| Increased Methylation & Decreased Acetylation
93
Euchromatin
Loose; Lots of Genes; Replicates Early; Can be transcribed
| Increased Methylation & Decreased Acetylation
94
Telomere
Highly conserved DNA sequence located at the end of linear eukaryotic chromosomes; TTAGGG repeated sequence
95
Centromere
DNA sequence
96
Centromere
Made of heterochromatic DNA; center of chromosomes; microtubule spindle fibers attached
97
Centromere
Made of heterochromatic DNA; center of chromosomes; microtubule spindle fibers attached
98
Operon
Determines whether a gene is on or off through use of a repressor, inducer etc; the genes down the operon are either expressed together or not at all
99
Repressor
Reduces transcription
100
Inducer
Increases transcription
101
Inducer
Increases transcription
102
Jacob-Monod Model
Binding site for the lac repressor is near the transcription start site; operator prevents the repressor from binding
103
Jacob-Monod Model
Binding site for the lac repressor is near the transcription start site; operator prevents the repressor from binding; when lactose binds to repressor; genes for galactosidase are transcribed
[R]==========[o][s]============
R= Regulatory Gene
O= Operator
S= Structural Gene
104
Jacob-Monod Model
Binding site for the lac repressor is near the transcription start site; operator prevents the repressor from binding; when lactose binds to repressor; genes for galactosidase are transcribed
[R]==========[O][S]============
R= Regulatory Gene
O= Operator
S= Structural Gene
105
Repressor
Reduces transcription by binding to the operator blocking RNA Pol binding to the promtor
106
Jacob-Monod Model [Prokaryotes]
Binding site for the lac repressor is near the transcription start site; operator prevents the repressor from binding; when lactose binds to repressor; genes for galactosidase are transcribed
[R]==========[O][S]============
R= Regulatory Gene
O= Operator
S= Structural Gene
107
Gene Repression [Bacteria]
Inhibition of gene expression by changing regulatory protein activity
108
Repressor
Reduces transcription by binding to the operator and block the activity of RNA Pol
109
Inducer
Increases transcription
110
Jacob-Monod Model
Binding site for the lac repressor is near the transcription start site; operator prevents the repressor from binding
111
Jacob-Monod Model
Binding site for the lac repressor is near the transcription start site; operator prevents the repressor from binding; when lactose binds to repressor; genes for galactosidase are transcribed
[R]==========[o][s]============
R= Regulatory Gene
O= Operator
S= Structural Gene
112
Jacob-Monod Model
Binding site for the lac repressor is near the transcription start site; operator prevents the repressor from binding; when lactose binds to repressor; genes for galactosidase are transcribed
[R]==========[O][S]============
R= Regulatory Gene
O= Operator
S= Structural Gene
113
Repressor
Reduces transcription by binding to the operator blocking RNA Pol binding to the promtor
114
Gene Repression [Bacteria]
Inhibition of gene expression by changing regulatory protein activity; through the use of a repressor
115
Gene Repression [Bacteria]
Inhibition of gene expression by changing regulatory protein activity; through the use of a repressor
116
Transcriptional Regulation
Involves transcription factors through use of enhancers and silencers
117
Enhancers
Increases transcription upon binding
118
Silencers
Decreases transcription upon binding
119
DNA Binding Proteins
Polymerases, Nucleases, Histones; SSBP
120
DNA Binding Proteins
Polymerases, Nucleases, Histones; SSBP
121
Post-Transcriptional Control
Modification of normal nucleotides occurs to control the structure of tRNAs and rRNAs:
Splicing, Cap & Tail, Methylation
122
Splicing
Introns are removed and exons remain
123
5' Cap & 3' Poly-A Tail
Protects RNA from degradation
124
Cancer
A result of failure of normal cellular controls; divides without regulation; stimulates angiogenesis; they avoid apoptosis
125
Oncogenes
Genes that have the potential to cause cancer; speeds up cell division
126
Proto-oncogenes
A normal gene that can become an oncogene due to mutations or increased expression
127
Antioncogene (Tumor Suppressor Genes)
Protects cells from cancer; they dampen or repress the regulation of the cell cycle or promote apoptosis
128
Antioncogene (Tumor Suppressor Genes)
Protects cells from cancer; they dampen or repress the regulation of the cell cycle or promote apoptosis
129
Regulation of Chromatin Structure
Modified via methylation, acetylation, phosphorylation
130
Regulation of Chromatin Structure
Modified via methylation, acetylation, phosphorylation
131
Nucleosome
Repeating subunit that is made of histones
132
Histones
H1, H2A-H2B [tetramer], H3 -H4 [tetramer]
133
DNA Methylation
Blocks promoter so that no transcription factors can bind for gene expression to occur (works as a repressor); plays a role in cell differentiation and embryonic development
134
Non-Coding RNAs
Not translated into a protein; regulate RNA Splicing, DNA replication and Gene regulation
135
Non-Coding RNAs
Not translated into a protein; regulate RNA Splicing, DNA replication and Gene regulation
136
Recombinant DNA
DNA composed of nucleotides from two different sources
137
DNA Cloning
Introduces a fragment of DNA into a vector plasmid
138
Restriction Enzyme (Endonuclease)
Cuts a plasmid and DNA fragment to leave them with sticky ends; joining fragment to plasmid it can be introduced into a bacterial cell and permitted to replicate
139
Vector Components
OoR, Fragment of Interest, One Gene for Ab Resistance so that the colony could be selected after replication
140
DNA Libraries
Large collections of known DNA sequences
141
Genomic Libraries
Large fragments of DNA (coding and noncoding regions of the genome)
142
Generation of cDNA
mRNA is purified and converted back to DNA by reverse transcriptase
143
cDNA Library
Consists of cloned cDNA inserted into particular host cells
144
DNA Hybridization
Joining of complementary base pair sequences from two different strands of DNA
145
Polymerase Chain Reaction (PCR)
Amplifies the size of DNA from a small piece of DNA; 3 steps: Denature, Anneal, Elongate
146
Polymerase Chain Reaction (PCR)
Amplifies the size of DNA from a small piece of DNA; 3 steps: Denature, Anneal, Elongate
147
Agarose Gel Electrophoresis
Separates DNA molecules by size
148
Southern Blotting
Detects presence and quantity of various DNA strands in a sample
149
Southern Blotting
Detects presence and quantity of various DNA strands in a sample
150
DNA Sequencing
Using ddNTPs (dideoxyribonucleotides) which terminate the DNA chain because they lack a 3' Hydroxyl Group
151
DNA Sequencing
Using ddNTPs (dideoxyribonucleotides) which terminate the DNA chain because they lack a 3' Hydroxyl Group; sequence read directly from gel
152
Gene Therapy
A method of curing genetic deficiencies by introducing a functional gene with a viral vector
153
Transgenic Mice
Mice integrated with a gene of interest into the germ line or embryonic stem cells of a developing mouse; can be mated to select for transgene
154
Knockout Mice
Created by deleting a gene of interest
155
Knockout Mice
Created by deleting a gene of interest
156
Northern Blotting
Determines size and sequence information of mRNA; utilizes radiolabeled RNA
157
RT-qPCR
mRNA is reverse transcribed followed by quantitative PCR
158
Western Blotting
Quantifies the type and size of a protein
159
Location of the expression
Uses fluorescent protein marker
160
Location of the expression
Uses fluorescent protein marker
161
Stem Cells
Cells that have the ability to differentiate into other specialized cells; divides to produce more stem cells
162
Stem Cells in Humans
Found in Bone Marrow, Adipose Tissue and Blood
163
Function of Stem Cells
Self-renewal, differentiation into specialized cells
164
Hierarchy of Stem Cells
Totipotent -> Pluripotent -> Multipotent -> Oligopotent -> Unipotent
165
Hierarchy of Stem Cells
Totipotent -> Pluripotent -> Multipotent -> Oligopotent -> Unipotent
166
Totipotency
Ability to divide and produce all of the differentiated cells in an organism
e.g. Zygotes & Spores
167
Pluripotency
Ability to differentiate into any of the three germ layers (endoderm, mesoderm, ectoderm)
e.g. Blastocyst
168
Multipotency
Describes progenitor cells which have the gene activation potential to differentiate into multiple but limited cell types
e.g. Hematopoietic Stem Cells
169
Oligopotency
Describes progenitor cells to differentiate into a few cell types
e.g. Lymphoid/Myeloid Stem Cells
170
Unipotency
One stem cell that differentiates into only one cell type
171
Unipotency
One stem cell that differentiates into only one cell type
| e.g Hepatoblast (become hepatocytes)
172
Unipotency
One stem cell that differentiates into only one cell type
| e.g Hepatoblast (become hepatocytes)
173
Medical Applications of DNA Technology
Diagnose Genetics & Infectious Diseases
Development of Vaccines
Therapeutic Hormones
Human Gene Therapy
