Biology II- Genetics (cont.)

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Extranuclear genes

genes outside the nucleus; located in mitochondria and chloroplast

1952

Hershey and chase did an experiment on viruses where they could tell that DNA is the genetic material in cells and not protein

1953

Watson, Crick, Franklin and Wilkins write about the structure of DNA; received the Nobel Prize in 1960

Nucleic acid (DNA)

made form nucleotides which are constructed from phosphate, sugar and nitrogenous bases (A,T, G, C)

DNA

has a phosphate, sugar backbone double stranded rung shaped base, and is twisted into a helix
strands held together by weak bonds of hydrogen bases

Bases are made of purines

2 rings made of Adenine(A) and Guanine(G)

Bases are made of pyrimidines

1 ring made of Thymine(T) and Cytosine(C)

Base pairings

A-T, G-C; 5 prime end has free phosphates; 3 prime end has sugar; replication is always ordered as '5' before '3'

DNA replication

DNA is unwound and replication happens in both directions; happens during the S phase

replication fork

DNA separation point

RNA polymerase

makes RNA molecules; protein involved in DNA replication

DNA polymerase

makes DNA molecules

Primase

makes primer; An enzyme that joins RNA nucleotides to make the primer.

Helicase

unwinds the double helix

Single strand binding

proteins that stabilize the unwound DNA

Anti parallel

the strands of DNA go in opposite directions; 5 prime end matches with 3 prime end

Primer formation

primase (RNA polymerase) makes a short strand of RNA primer to help the building of the DNA copy

Elongation

nucleoside triphosphate creates and attaches appropriate base by using DNA polymerase

Leading strand

the top strand of original DNA; a simple process of laying down a primer and DNA polymer which houses up appropriate nucleotides
DNA is then built

Lagging strand

DNA strand built in the opposite direction
it creates a section then leaps to the other end to finish

Onizaki fragments

has multiple primers to create DNA

After Elongation

the primers (RNA) is removed and replaced by DNA polymerase; gap left from RNA replacement so DNA ligase stitches the fragments together

DNA repair: Nuclease

removes damaged or incorrect nucleotide

DNA repair: DNA polymerase

replaces the removed and damaged DNA

DNA repair: DNA ligase

knits the new DNA to the existing DNA

Telomeres

non-coding DNA strands at the end of chromosomes( not part of gene) protects chromosomes from deterioration

Protein Synthesis

the change from genes(DNA) to proteins

Transcription: first step to Protein Synthesis

the making of a messenger RNA(mRNA) form a DNA template
takes place in the nucleus and makes a pre-mRNA

Translation: second step to Protein Synthesis

makes a polypeptide chain from a mRNA template
changes a nucleotide code into a polypeptide code
takes place at the ribosome in the cytoplasm

polypeptide

a long chain of amino acids

Transcription and Translation

this mRNA processing makes the real mRNA

RNA bases

Adenine, Guanine, Cytosine, Uracil

Transcription makes

strands of RNA that are complementary to the DNA bases

RNA is translated from

codons(sequence of 3 nucleotides [Amino acid codes]) to amino acids

First stage: Transcription in prokaryotes-Initiation

Promoter-DNA sequence that signals the start of transcription
RNA polymerase binds to the promoter, it then unwinds the DNA

Second stage: Transcription in prokaryotes- Elongation

RNA polymerase adds nucleotides (A, G, U, C); continues to unwind DNA; Builds the RNA in the 5 prime-3prime pattern; no primers are needed for the process; makes many mRNA's on one DNA strand

Last stage: Transcription in prokaryotes- Termination

the DNA sequence polymerase drops off, then the creation of the mRNA is done

Transcription in eukaryotes- Initiation

Transcription factors are necessary to RNA polymerase to bind to promoters
i.e. TATA Box, Transcription Initiation Complex

TATA Box transition factor

DNA promoter sequence

Transcription Initiation Complex

RNA polymerase and Transcription factors attach to this

Transcription in eukaryotes- Elongation

has more than one type of RNA polymerase

Transcription in eukaryotes- Termination

polyadenylation signal- DNA sequence that ends transcription
is code for many A's (adenines) in a row
the RNA is cut from the polymerase and becomes pre-mRNA

RNA processing

alternations of the ends of the pre-mRNA
5prime end has '5' cap added for modified G nucleotide
3 prime end has a poly-A tail added to it; sometimes has hundreds of Adenine nucleotides

RNA splicing

the cut and paste of RNA molecules

RNA and DNA are non-coding

meaning they will not be translated to proteins

introns

non-coding RNA ends

exons

coded RNA ends

Alternative splicing

one gene can have a piece of many different polypeptides

mRNA

messenger RNA made during transcription and used during translation

tRNA

transfer RNA; has amino acid binding site on one end and anti-codon on the other end; brings amino acids to the polypeptide

rRNA

ribosomal RNA; makes up the ribosome

Aminoacyl tRNA synthase

the attachment of an amino acid to the RNA with the assistance of ATP and enzymes; is a tRNA wit an amino acid attached to it

Ribosomes

enzymes that have two sub-units; a large sub-unit and a small sub-unit; each has a binding site; the large and small sub-units stay separate until translation begins

Ribosome large sub-units

has three binding sites; A-aminoacyl tRNA, P-peptidyl tRNA, E-exit

Ribosomes small sub-unit

has a binding site fro mRNA

Translation- Initiation

the mRNA, tRNA, and both ribosomal units come together; creates a translation initiation complex

initiator tRNA

binds to a "start" codon (AUG) and always methionine

Translation- Elongation

amino acids are added to the mRNA chain one by one
A new tRNA binds to the A-site of the ribosomal, the amino acid binds to the chain in the P-site, the tRNA moves to the next site, and the old tRNA is kicked off; this process goes in one direction

Translation- Termination

stop codon(UAG, UAA, or UGA) begins at this point; the release factor binds to the stop codons and the whole translation initiation complex falls apart

Modification to polypeptides

folding occurs; some things may be added or removed from the chain; some polypeptides are targeted for specific locations; polypeptide initiates binding of ribosomes to Rough ER; polypeptide then ends up in ER

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