1B: Transmission of genetic information from the gene to the protein Flashcards Preview

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Flashcards in 1B: Transmission of genetic information from the gene to the protein Deck (173):
1

Nucleotides

Monomers of nucleic acids, consists of sugar, nitrogenous base and phosphate group

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Types of Nucleotides

Thymine, Adenine, Guanine, Uracil

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Structure of Nucleotides

Phosphorus is linked at the 5 carbon of the sugar; Nitrogenous Base is linked to the 1 carbon of the sugar

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Pyrimidines

Single ring; Cytosine, Uracil, Thymine

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Purines

Two rings; Adenine, Guanine

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Nucleoside

Sugar + Nitrogenous Base

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Types of Nucleosides

Cytidine, Uridine, Adenosine

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DNA

Deoxyribonucleic Acid

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Double Helix

2 single strands of DNA wound around each other held together by hydrogen bonds

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Watson-Crick Model

Two linear strands running antiparallel and twisted in a right-handed spiral; bases are located inside of the helix

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Base Pairing Specificity

Nucleobases are connected via hydrogen bonds:
A2T
C3G
DNA with more G-C are more stable

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Function of DNA in transmission of Genetic Information

Complementary base pairing property allows for DNA replication and transmission of genetic information

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Central Dogma

DNA -> RNA -> Protein

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Denaturation of DNA

dsDNA comes apart due to heating or a change in pH

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Annealing of DNA

ssDNA joins again due to complementary nucleotide sequences and random molecular motion

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Hybridization of DNA

Denatures two different DNA sequences then uses ssDNA from each to anneal to dsdna

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Process of PCR

Denature -> Anneal -> Extend

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Mechanism of Replication

1. Separation of Strands
2. Coupling of Free Nucleic Acids

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Enzymes of Replication

1. DNA Gyrase
2. Helicase
-SSB
3. Primase
4. DNA Pol III
5. DNA Pol I
6. DNA Ligase

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Helicase

Unwinds double helix of DNA

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DNA Pol III

Binds one strand of DNA from an RNA primer, moves 3' to 5' producing a leading strand

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Primase

Produces RNA primers at the 5' end, allowing for the synthesis of Okazaki fragments

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Okazaki Fragments

Short discontinued fragments of replication products on the lagging strand

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DNA Pol I

Removes RNA primers by the 5' end to 3' end

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DNA Ligase

Seals the spaces in the strand between the Okazaki Fragments

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Single-Strand Binding Protein

Responsible for keeping the DNA unwound after helicase unwinds the helix

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DNA Gyrase

Uncoils DNA ahead of the replication fork

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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

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Origin of Replication

Point at which replication begins; multiple points in eukaryotes and singular in prokaryotes

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Telomerase

Replicates the end of DNA molecules which consist of telomeres that help keep genetic information and prevent it from being lost during replication

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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

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Repair of Mutation

Mismatch
Base-Excision
Nucleotide-Excision
Nick Translation
SOS Response

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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

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Base-Excision Repair

A single base is removed and replaced using DNA Pol and Ligase

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Nucleotide-Excision Repair

Damaged nucleotide gets cut out and replaced (due to thymine dimers)

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Nick Translation

RNA primers are replaced with DNA through 5' to 3' activity

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SOS Response

When there is too much DNA for normal repair; the DNA Pol replicates over the damaged area as if it were normal

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Triplet Code (Codon)

Sequence of nucleotides of mRNA that codes for amino acids; 3 nucleotides = single amino acid

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Anticodon

3 bases at the end of tRNA (transfer anticodon) that correspond to the nucleotide triplet in mrNA during translation

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Degenerate Code

Multiple 3 codon combinations code for the same amino acid (20 total); more than one codon codes for a given amino acid

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Wobble Pairing

When two nucleotides in RNA molecules do not follow Watson-Crick base pairing rules

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Types of Wobble Base Pairs

G-U
I-U
I-A
I-C
I=hypoxanthine

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Missense Mutations

A new nucleotide changes the codon to produce a changed amino acid in protein

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Nonsense Mutations

A new nucleotide changes the codon to a stop codon that prematurely truncates a protein

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Initiation Codon

AUG (methionine); starts the translation process
Prokaryotes = Shine-Delgarno Sequence
Eukaryotes = Kozak Sequence

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Termination Codon

End translation of the mRNA strand
UAA
UAG
UGA

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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

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tRNA

In the cytoplasm, directs translation of mRNA into proteins; contain anticodon

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rRNA

Necessary for ribosome assembly, plays a role in mRNA binding to ribosomes and in translation, contains active site for catalysis (peptide bond formation)

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Mechanism of Transcription
[Eukaryotes = Nucleus]
[Prokaryotes = Cytoplasm]

Initiation -> Elongation -> Termination

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Initiation

RNA Pol binds to the promoter region of DNA

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Elongation

Transcription factors unwind the DNA strand and allow RNA Pol to transcribe a strand of DNA into a strand of mRNA; C3G, A2U

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Termination

RNA Pol reaches a terminator sequence and then releases the mRNA polymer and detaches from the DNA

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Eukaryotic Structure

5' UTR
Coding Sequence
3' UTR

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Coding Sequence

Where translation begins and ends; contains amino acid sequences for protein synthesis during translation

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3' UTR

Contains crucial information for mRNA stability

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Processing in Eukaryotes

1. Cap Addition
2. Polyadenylation
3. Splicing

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Cap Addition

Addition of a 5' methyl guanosine cap that occurs during transcription; prevent chain degradation

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Polyadenylation

A poly-A tail is added to the 3' end; enhances the stability of mRNA and regulates transport to cytoplasmic compartment

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Splicing

Removes introns

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Introns

Not expressed in proteins

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Exons

Encoding sequences and they are reserved

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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

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Spliceosomes

Splicing machines that remove and cut introns from pre-mRNA

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snRNA

Small nuclear RNA, couples with snRNPs that 5' and 3' splice sites of introns

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snRNPs

Combine of snRNA and protein factors that are essential in intron removal

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Eukaryotic Ribosome

40S + 60S; 80S

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Prokaryotic Ribosome

30S + 40S; 70S

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General Ribosome Structure

mRNA binding site (small subunit); E site, P site and A site (large subunit)

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P site

Binds to tRNA and extends amino acid chain

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A site

Binds to tRNA holding new amino acid

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E site

When a stop codon is encountered, release factors are bound and the chain falls off

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Post-Translational Modification

Glycosylation
Acetylation
Methylation
Sulfation
Phosphorylation

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Post-Translational Modification

Glycosylation
Acetylation
Methylation
Sulfation
Phosphorylation

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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

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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

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Moderate Repetitive DNA

Transcribed by RNA Pol I or III; contains protein-coding genes

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Highly Repetitive DNA

Not transcribed; contains no genes

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Highly Repetitive DNA

Not transcribed; contains no genes

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Supercoiling

Compacts DNA so it doesn't get tangled onto itself

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Positive Supercoil

Left Handed; difficult to unwind

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Negative Supercoil

Right Handed; easier to unwind

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Topoisomerases

Alter DNA topology to carry proper functions

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Topoisomerase I

Remove DNA supercoils; break strands during recombination; condense chromosomes

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Topoisomerase II

Cuts strands to manage DNA tangles and supercoils

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Chromatin

Makes up the nucleus and function in gene expression and repression

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Heterochromatin

Tightly packed; contains more DNA; late replication

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Heterochromatin

Dense; Few or No Genes; Replicates Late; Not Transcribed
Increased Acetylation & Decreased Methylation

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Euchromatine

Loose; Lots of Genes; Replicates Early; Can be transcribed
Increased Methylation & Decreased Acetylation

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Euchromatin

Loose; Lots of Genes; Replicates Early; Can be transcribed
Increased Methylation & Decreased Acetylation

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Telomere

Highly conserved DNA sequence located at the end of linear eukaryotic chromosomes; TTAGGG repeated sequence

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Centromere

DNA sequence

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Centromere

Made of heterochromatic DNA; center of chromosomes; microtubule spindle fibers attached

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Centromere

Made of heterochromatic DNA; center of chromosomes; microtubule spindle fibers attached

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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

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Repressor

Reduces transcription

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Inducer

Increases transcription

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Inducer

Increases transcription

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Jacob-Monod Model

Binding site for the lac repressor is near the transcription start site; operator prevents the repressor from binding

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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

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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

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Repressor

Reduces transcription by binding to the operator blocking RNA Pol binding to the promtor

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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

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Gene Repression [Bacteria]

Inhibition of gene expression by changing regulatory protein activity

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Repressor

Reduces transcription by binding to the operator and block the activity of RNA Pol

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Inducer

Increases transcription

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Jacob-Monod Model

Binding site for the lac repressor is near the transcription start site; operator prevents the repressor from binding

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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

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Repressor

Reduces transcription by binding to the operator blocking RNA Pol binding to the promtor

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Gene Repression [Bacteria]

Inhibition of gene expression by changing regulatory protein activity; through the use of a repressor

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Gene Repression [Bacteria]

Inhibition of gene expression by changing regulatory protein activity; through the use of a repressor

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Transcriptional Regulation

Involves transcription factors through use of enhancers and silencers

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Enhancers

Increases transcription upon binding

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Silencers

Decreases transcription upon binding

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DNA Binding Proteins

Polymerases, Nucleases, Histones; SSBP

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DNA Binding Proteins

Polymerases, Nucleases, Histones; SSBP

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Post-Transcriptional Control

Modification of normal nucleotides occurs to control the structure of tRNAs and rRNAs:
Splicing, Cap & Tail, Methylation

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Splicing

Introns are removed and exons remain

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5' Cap & 3' Poly-A Tail

Protects RNA from degradation

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Cancer

A result of failure of normal cellular controls; divides without regulation; stimulates angiogenesis; they avoid apoptosis

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Oncogenes

Genes that have the potential to cause cancer; speeds up cell division

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Proto-oncogenes

A normal gene that can become an oncogene due to mutations or increased expression

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Antioncogene (Tumor Suppressor Genes)

Protects cells from cancer; they dampen or repress the regulation of the cell cycle or promote apoptosis

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Antioncogene (Tumor Suppressor Genes)

Protects cells from cancer; they dampen or repress the regulation of the cell cycle or promote apoptosis

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Regulation of Chromatin Structure

Modified via methylation, acetylation, phosphorylation

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Regulation of Chromatin Structure

Modified via methylation, acetylation, phosphorylation

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Nucleosome

Repeating subunit that is made of histones

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Histones

H1, H2A-H2B [tetramer], H3 -H4 [tetramer]

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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

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Non-Coding RNAs

Not translated into a protein; regulate RNA Splicing, DNA replication and Gene regulation

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Non-Coding RNAs

Not translated into a protein; regulate RNA Splicing, DNA replication and Gene regulation

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Recombinant DNA

DNA composed of nucleotides from two different sources

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DNA Cloning

Introduces a fragment of DNA into a vector plasmid

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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

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Vector Components

OoR, Fragment of Interest, One Gene for Ab Resistance so that the colony could be selected after replication

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DNA Libraries

Large collections of known DNA sequences

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Genomic Libraries

Large fragments of DNA (coding and noncoding regions of the genome)

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Generation of cDNA

mRNA is purified and converted back to DNA by reverse transcriptase

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cDNA Library

Consists of cloned cDNA inserted into particular host cells

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DNA Hybridization

Joining of complementary base pair sequences from two different strands of DNA

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Polymerase Chain Reaction (PCR)

Amplifies the size of DNA from a small piece of DNA; 3 steps: Denature, Anneal, Elongate

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Polymerase Chain Reaction (PCR)

Amplifies the size of DNA from a small piece of DNA; 3 steps: Denature, Anneal, Elongate

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Agarose Gel Electrophoresis

Separates DNA molecules by size

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Southern Blotting

Detects presence and quantity of various DNA strands in a sample

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Southern Blotting

Detects presence and quantity of various DNA strands in a sample

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DNA Sequencing

Using ddNTPs (dideoxyribonucleotides) which terminate the DNA chain because they lack a 3' Hydroxyl Group

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DNA Sequencing

Using ddNTPs (dideoxyribonucleotides) which terminate the DNA chain because they lack a 3' Hydroxyl Group; sequence read directly from gel

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Gene Therapy

A method of curing genetic deficiencies by introducing a functional gene with a viral vector

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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

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Knockout Mice

Created by deleting a gene of interest

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Knockout Mice

Created by deleting a gene of interest

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Northern Blotting

Determines size and sequence information of mRNA; utilizes radiolabeled RNA

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RT-qPCR

mRNA is reverse transcribed followed by quantitative PCR

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Western Blotting

Quantifies the type and size of a protein

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Location of the expression

Uses fluorescent protein marker

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Location of the expression

Uses fluorescent protein marker

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Stem Cells

Cells that have the ability to differentiate into other specialized cells; divides to produce more stem cells

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Stem Cells in Humans

Found in Bone Marrow, Adipose Tissue and Blood

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Function of Stem Cells

Self-renewal, differentiation into specialized cells

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Hierarchy of Stem Cells

Totipotent -> Pluripotent -> Multipotent -> Oligopotent -> Unipotent

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Hierarchy of Stem Cells

Totipotent -> Pluripotent -> Multipotent -> Oligopotent -> Unipotent

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Totipotency

Ability to divide and produce all of the differentiated cells in an organism
e.g. Zygotes & Spores

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Pluripotency

Ability to differentiate into any of the three germ layers (endoderm, mesoderm, ectoderm)
e.g. Blastocyst

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Multipotency

Describes progenitor cells which have the gene activation potential to differentiate into multiple but limited cell types
e.g. Hematopoietic Stem Cells

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Oligopotency

Describes progenitor cells to differentiate into a few cell types
e.g. Lymphoid/Myeloid Stem Cells

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Unipotency

One stem cell that differentiates into only one cell type

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Unipotency

One stem cell that differentiates into only one cell type
e.g Hepatoblast (become hepatocytes)

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Unipotency

One stem cell that differentiates into only one cell type
e.g Hepatoblast (become hepatocytes)

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Medical Applications of DNA Technology

Diagnose Genetics & Infectious Diseases
Development of Vaccines
Therapeutic Hormones
Human Gene Therapy