1B: Transmission of genetic information from the gene to the protein Flashcards
Nucleotides
Monomers of nucleic acids, consists of sugar, nitrogenous base and phosphate group
Types of Nucleotides
Thymine, Adenine, Guanine, Uracil
Structure of Nucleotides
Phosphorus is linked at the 5 carbon of the sugar; Nitrogenous Base is linked to the 1 carbon of the sugar
Pyrimidines
Single ring; Cytosine, Uracil, Thymine
Purines
Two rings; Adenine, Guanine
Nucleoside
Sugar + Nitrogenous Base
Types of Nucleosides
Cytidine, Uridine, Adenosine
DNA
Deoxyribonucleic Acid
Double Helix
2 single strands of DNA wound around each other held together by hydrogen bonds
Watson-Crick Model
Two linear strands running antiparallel and twisted in a right-handed spiral; bases are located inside of the helix
Base Pairing Specificity
Nucleobases are connected via hydrogen bonds:
A2T
C3G
DNA with more G-C are more stable
Function of DNA in transmission of Genetic Information
Complementary base pairing property allows for DNA replication and transmission of genetic information
Central Dogma
DNA -> RNA -> Protein
Denaturation of DNA
dsDNA comes apart due to heating or a change in pH
Annealing of DNA
ssDNA joins again due to complementary nucleotide sequences and random molecular motion
Hybridization of DNA
Denatures two different DNA sequences then uses ssDNA from each to anneal to dsdna
Process of PCR
Denature -> Anneal -> Extend
Mechanism of Replication
- Separation of Strands
2. Coupling of Free Nucleic Acids
Enzymes of Replication
- DNA Gyrase
- Helicase
- SSB - Primase
- DNA Pol III
- DNA Pol I
- DNA Ligase
Helicase
Unwinds double helix of DNA
DNA Pol III
Binds one strand of DNA from an RNA primer, moves 3’ to 5’ producing a leading strand
Primase
Produces RNA primers at the 5’ end, allowing for the synthesis of Okazaki fragments
Okazaki Fragments
Short discontinued fragments of replication products on the lagging strand
DNA Pol I
Removes RNA primers by the 5’ end to 3’ end
DNA Ligase
Seals the spaces in the strand between the Okazaki Fragments
Single-Strand Binding Protein
Responsible for keeping the DNA unwound after helicase unwinds the helix
DNA Gyrase
Uncoils DNA ahead of the replication fork
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
Origin of Replication
Point at which replication begins; multiple points in eukaryotes and singular in prokaryotes
Telomerase
Replicates the end of DNA molecules which consist of telomeres that help keep genetic information and prevent it from being lost during replication
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
Repair of Mutation
Mismatch Base-Excision Nucleotide-Excision Nick Translation SOS Response
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
Base-Excision Repair
A single base is removed and replaced using DNA Pol and Ligase
Nucleotide-Excision Repair
Damaged nucleotide gets cut out and replaced (due to thymine dimers)
Nick Translation
RNA primers are replaced with DNA through 5’ to 3’ activity
SOS Response
When there is too much DNA for normal repair; the DNA Pol replicates over the damaged area as if it were normal
Triplet Code (Codon)
Sequence of nucleotides of mRNA that codes for amino acids; 3 nucleotides = single amino acid
Anticodon
3 bases at the end of tRNA (transfer anticodon) that correspond to the nucleotide triplet in mrNA during translation
Degenerate Code
Multiple 3 codon combinations code for the same amino acid (20 total); more than one codon codes for a given amino acid
Wobble Pairing
When two nucleotides in RNA molecules do not follow Watson-Crick base pairing rules
Types of Wobble Base Pairs
G-U I-U I-A I-C I=hypoxanthine
Missense Mutations
A new nucleotide changes the codon to produce a changed amino acid in protein
Nonsense Mutations
A new nucleotide changes the codon to a stop codon that prematurely truncates a protein
Initiation Codon
AUG (methionine); starts the translation process
Prokaryotes = Shine-Delgarno Sequence
Eukaryotes = Kozak Sequence
Termination Codon
End translation of the mRNA strand
UAA
UAG
UGA
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
tRNA
In the cytoplasm, directs translation of mRNA into proteins; contain anticodon
rRNA
Necessary for ribosome assembly, plays a role in mRNA binding to ribosomes and in translation, contains active site for catalysis (peptide bond formation)
Mechanism of Transcription
[Eukaryotes = Nucleus]
[Prokaryotes = Cytoplasm]
Initiation -> Elongation -> Termination
Initiation
RNA Pol binds to the promoter region of DNA
Elongation
Transcription factors unwind the DNA strand and allow RNA Pol to transcribe a strand of DNA into a strand of mRNA; C3G, A2U
Termination
RNA Pol reaches a terminator sequence and then releases the mRNA polymer and detaches from the DNA
Eukaryotic Structure
5’ UTR
Coding Sequence
3’ UTR
Coding Sequence
Where translation begins and ends; contains amino acid sequences for protein synthesis during translation
3’ UTR
Contains crucial information for mRNA stability
Processing in Eukaryotes
- Cap Addition
- Polyadenylation
- Splicing
Cap Addition
Addition of a 5’ methyl guanosine cap that occurs during transcription; prevent chain degradation
Polyadenylation
A poly-A tail is added to the 3’ end; enhances the stability of mRNA and regulates transport to cytoplasmic compartment
Splicing
Removes introns
Introns
Not expressed in proteins
Exons
Encoding sequences and they are reserved
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
Spliceosomes
Splicing machines that remove and cut introns from pre-mRNA
snRNA
Small nuclear RNA, couples with snRNPs that 5’ and 3’ splice sites of introns
snRNPs
Combine of snRNA and protein factors that are essential in intron removal
Eukaryotic Ribosome
40S + 60S; 80S
Prokaryotic Ribosome
30S + 40S; 70S
General Ribosome Structure
mRNA binding site (small subunit); E site, P site and A site (large subunit)
P site
Binds to tRNA and extends amino acid chain
A site
Binds to tRNA holding new amino acid
E site
When a stop codon is encountered, release factors are bound and the chain falls off
Post-Translational Modification
Glycosylation Acetylation Methylation Sulfation Phosphorylation
Post-Translational Modification
Glycosylation Acetylation Methylation Sulfation Phosphorylation
Chromosomal Proteins
Histones & Non-Histone
Histones
Order & Package DNA into Nucleosomes; aids with gene regulation; allows DNA to fit inside the nucleus
Non-Histones
Regulatory and Enzymatic Function
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
Repetitive DNA
Concentrated at centromeres, not translated, high rates of mutation
Moderate Repetitive DNA
Transcribed by RNA Pol I or III; contains protein-coding genes
Highly Repetitive DNA
Not transcribed; contains no genes
Highly Repetitive DNA
Not transcribed; contains no genes
Supercoiling
Compacts DNA so it doesn’t get tangled onto itself
Positive Supercoil
Left Handed; difficult to unwind
Negative Supercoil
Right Handed; easier to unwind
Topoisomerases
Alter DNA topology to carry proper functions
Topoisomerase I
Remove DNA supercoils; break strands during recombination; condense chromosomes
Topoisomerase II
Cuts strands to manage DNA tangles and supercoils
Chromatin
Makes up the nucleus and function in gene expression and repression
Heterochromatin
Tightly packed; contains more DNA; late replication
Heterochromatin
Dense; Few or No Genes; Replicates Late; Not Transcribed
Increased Acetylation & Decreased Methylation
Euchromatine
Loose; Lots of Genes; Replicates Early; Can be transcribed
Increased Methylation & Decreased Acetylation
Euchromatin
Loose; Lots of Genes; Replicates Early; Can be transcribed
Increased Methylation & Decreased Acetylation
Telomere
Highly conserved DNA sequence located at the end of linear eukaryotic chromosomes; TTAGGG repeated sequence
Centromere
DNA sequence
Centromere
Made of heterochromatic DNA; center of chromosomes; microtubule spindle fibers attached
Centromere
Made of heterochromatic DNA; center of chromosomes; microtubule spindle fibers attached
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
Repressor
Reduces transcription
Inducer
Increases transcription
Inducer
Increases transcription
Jacob-Monod Model
Binding site for the lac repressor is near the transcription start site; operator prevents the repressor from binding
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
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
Repressor
Reduces transcription by binding to the operator blocking RNA Pol binding to the promtor
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
Gene Repression [Bacteria]
Inhibition of gene expression by changing regulatory protein activity
Repressor
Reduces transcription by binding to the operator and block the activity of RNA Pol
Inducer
Increases transcription
Jacob-Monod Model
Binding site for the lac repressor is near the transcription start site; operator prevents the repressor from binding
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
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
Repressor
Reduces transcription by binding to the operator blocking RNA Pol binding to the promtor
Gene Repression [Bacteria]
Inhibition of gene expression by changing regulatory protein activity; through the use of a repressor
Gene Repression [Bacteria]
Inhibition of gene expression by changing regulatory protein activity; through the use of a repressor
Transcriptional Regulation
Involves transcription factors through use of enhancers and silencers
Enhancers
Increases transcription upon binding
Silencers
Decreases transcription upon binding
DNA Binding Proteins
Polymerases, Nucleases, Histones; SSBP
DNA Binding Proteins
Polymerases, Nucleases, Histones; SSBP
Post-Transcriptional Control
Modification of normal nucleotides occurs to control the structure of tRNAs and rRNAs:
Splicing, Cap & Tail, Methylation
Splicing
Introns are removed and exons remain
5’ Cap & 3’ Poly-A Tail
Protects RNA from degradation
Cancer
A result of failure of normal cellular controls; divides without regulation; stimulates angiogenesis; they avoid apoptosis
Oncogenes
Genes that have the potential to cause cancer; speeds up cell division
Proto-oncogenes
A normal gene that can become an oncogene due to mutations or increased expression
Antioncogene (Tumor Suppressor Genes)
Protects cells from cancer; they dampen or repress the regulation of the cell cycle or promote apoptosis
Antioncogene (Tumor Suppressor Genes)
Protects cells from cancer; they dampen or repress the regulation of the cell cycle or promote apoptosis
Regulation of Chromatin Structure
Modified via methylation, acetylation, phosphorylation
Regulation of Chromatin Structure
Modified via methylation, acetylation, phosphorylation
Nucleosome
Repeating subunit that is made of histones
Histones
H1, H2A-H2B [tetramer], H3 -H4 [tetramer]
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
Non-Coding RNAs
Not translated into a protein; regulate RNA Splicing, DNA replication and Gene regulation
Non-Coding RNAs
Not translated into a protein; regulate RNA Splicing, DNA replication and Gene regulation
Recombinant DNA
DNA composed of nucleotides from two different sources
DNA Cloning
Introduces a fragment of DNA into a vector plasmid
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
Vector Components
OoR, Fragment of Interest, One Gene for Ab Resistance so that the colony could be selected after replication
DNA Libraries
Large collections of known DNA sequences
Genomic Libraries
Large fragments of DNA (coding and noncoding regions of the genome)
Generation of cDNA
mRNA is purified and converted back to DNA by reverse transcriptase
cDNA Library
Consists of cloned cDNA inserted into particular host cells
DNA Hybridization
Joining of complementary base pair sequences from two different strands of DNA
Polymerase Chain Reaction (PCR)
Amplifies the size of DNA from a small piece of DNA; 3 steps: Denature, Anneal, Elongate
Polymerase Chain Reaction (PCR)
Amplifies the size of DNA from a small piece of DNA; 3 steps: Denature, Anneal, Elongate
Agarose Gel Electrophoresis
Separates DNA molecules by size
Southern Blotting
Detects presence and quantity of various DNA strands in a sample
Southern Blotting
Detects presence and quantity of various DNA strands in a sample
DNA Sequencing
Using ddNTPs (dideoxyribonucleotides) which terminate the DNA chain because they lack a 3’ Hydroxyl Group
DNA Sequencing
Using ddNTPs (dideoxyribonucleotides) which terminate the DNA chain because they lack a 3’ Hydroxyl Group; sequence read directly from gel
Gene Therapy
A method of curing genetic deficiencies by introducing a functional gene with a viral vector
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
Knockout Mice
Created by deleting a gene of interest
Knockout Mice
Created by deleting a gene of interest
Northern Blotting
Determines size and sequence information of mRNA; utilizes radiolabeled RNA
RT-qPCR
mRNA is reverse transcribed followed by quantitative PCR
Western Blotting
Quantifies the type and size of a protein
Location of the expression
Uses fluorescent protein marker
Location of the expression
Uses fluorescent protein marker
Stem Cells
Cells that have the ability to differentiate into other specialized cells; divides to produce more stem cells
Stem Cells in Humans
Found in Bone Marrow, Adipose Tissue and Blood
Function of Stem Cells
Self-renewal, differentiation into specialized cells
Hierarchy of Stem Cells
Totipotent -> Pluripotent -> Multipotent -> Oligopotent -> Unipotent
Hierarchy of Stem Cells
Totipotent -> Pluripotent -> Multipotent -> Oligopotent -> Unipotent
Totipotency
Ability to divide and produce all of the differentiated cells in an organism
e.g. Zygotes & Spores
Pluripotency
Ability to differentiate into any of the three germ layers (endoderm, mesoderm, ectoderm)
e.g. Blastocyst
Multipotency
Describes progenitor cells which have the gene activation potential to differentiate into multiple but limited cell types
e.g. Hematopoietic Stem Cells
Oligopotency
Describes progenitor cells to differentiate into a few cell types
e.g. Lymphoid/Myeloid Stem Cells
Unipotency
One stem cell that differentiates into only one cell type
Unipotency
One stem cell that differentiates into only one cell type
e.g Hepatoblast (become hepatocytes)
Unipotency
One stem cell that differentiates into only one cell type
e.g Hepatoblast (become hepatocytes)
Medical Applications of DNA Technology
Diagnose Genetics & Infectious Diseases
Development of Vaccines
Therapeutic Hormones
Human Gene Therapy