Gene Expression

Topoisomerase enzyme (DNA rep)

relax’s/ relieves by reducing the degree of supercooling in the DNA strand

Helicase (DNA rep)

untwists and separates the 2 parental strands at the replication fork

RNA primer (DNA rep)

lays RNA so DNA nucleotide can be added to the 3’ end

DNA polymerase lll (DNA rep)

adds nucleotides to DNA templates

DNA polymerase l (DNA rep)

replaces RNA primer with DNA nucleotides. And fills the gaps between Okazaki fragments on the lagging strand.

Okazaki fragments (DNA rep)

fragments of DNA that conform on the lagging strand

leading strand (DNA rep)

synthesized continuously 5’ —> 3’ direction as strands unravel

lagging strand (DNA rep)

synthesized discontinuously, built away

Ligase (DNA rep)

acts as the glue that links okazaki fragments with primers

Single strand binding proteins (SSB’s)

help stabilize parental strands

Direction of template strand

3’ —> 5’

transfer RNA (tRNA)

is responsible for carrying amino acids to the ribosome during translation and transferring them on to the growing polypeptide (amino acid) chain.

messenger RNA (mRNA)

is an RNA copy of a gene that carries the instructions for producing a specific protein from the nucleus to the ribosome.

ribosomal RNA (rRNA)

Ribosomal RNA (rRNA) is a structural component of ribosomes that assists with translation of messenger RNA .

Central Dogma

DNA-->RNA-->Protein

• describes the flow of information

Transcription

process by which RNA polymerase synthesizes an mRNA copy of the target gene.

(Transcription) Step 1: Initiation

• TF (transcription factors) recognize a key area within the promoter region. TATA box

• TF mediate the binding of RNA polymerase to the promoter

• The assembly of the Transcription Initiation Complex (TIC) is complete

(Transcription) Step 2: Elongation

• RNA polymerase pries DNA strands apart, reading the DNA template in a 3’ to 5’ direction

• Transcription of the DNA template begins

• RNA polymerase adds nucleotides to the 3’ end of a growing chain producing a transcription unit

(Transcription) Step 3: Termination

• RNA polymerase transcribes the polyadenylation signal sequence

• A short distance after transcribing AAUAAA, the pre-mRNA is cleaved and freedom from the DNA template

Prokaryotic transcription occurs in the ________

cytoplasm

• don’t have introns (non-protein coding) sequences in their DNA, so prok mRNA is immediately available for translation by ribosomes.

Eukaryotic transcription occurs in the ______

nucleus

• do have intron sequences in their DNA , so euk mRNA has to be processed before it can leave the nucleus to be translated.

splicing

is to prevent extra amino acids from being translated into the polypeptide, bc that would change the folding of the protein therefore, changing the function

(Translation) Step 1: Initiation

• mRNA leaves the nucleus through nuclear pore and arrives at bound or unbound ribosome

• Translation Initiation Complex (TIC) forms at P site from mRNA, 2 ribosomal subunits, and tRNA carrying methionine

(Translation) Step 2: Elongation

• At site A a codon receives tRNA with anticodon

• Enzymes help form peptide bond btw amino acids of tRNA molecules

• tRNA at P-site rotates to E-site leaving an amino acid & detaching from ribosome

(Translation) Step 3: Termination

• tRNA enters at A rotates to P —> E repeatedly until stop codon is reached

• Release factor binds and molecules detach from one another. New protein is released into cell.

__________ couple transcription and translation

prokaryotes

___________ transcription and translation are separated because eukaryotes have nuclei.

eukaryotic

introns

extrons

RNA processing stages

Stage 1: Splicing

Stage 2: Alteration of ends

During stage 2 of RNA processing (alteration of ends), what is added to the 5’ end ?

guanine methyl cap

During stage 2 of RNA processing (alteration of ends), what is added to the 3’ end ?

poly A tail (200-250) adenine nucleotides

RNA processing sequence

1. snRNA base pair at specific sites along the intron

2. SnRNPs and other proteins form a molecular complex (spliceosome)

3. Pre-mRNA begins being spliced

4. RNA is cut - releasing intron while splicing exons together

5. Spliceosome comes apart, mRNA contains exons - now to be altered

6. 5’ cap consisting of modified guanine nucleotide (GTP) is added to the 5’ end of pre-mRNA

7. string of (50-250) adenines are added to 3’ end to form poly A tail. pre-mRNA is called mature mRNA and may leave the nucleus safely.

Purpose of translation

make protein

(Translation) When mRNA leaves the nucleus goes to

a ribosome

(Translation) Bound ribosome

attached to ER, used if protein is outside of a cell

(Translation) Unbound ribosome

freely in cytoplasm, used if protein is inside the cell

(Translation) trucks in amino acids in translation

tRNA

(Translation) 2 attachment site on tRNA

(Translation) Specifies the sequence in which tRNA lands on the mRNA

codon

The ____ of the mRNA binds to the _____ on the tRNA

codon

anticodon

Determines the ultimate shape and function of a protein

sequence of amino acids

Point mutations

• only affect one gene

• Occur during DNA synthesis

• 2 types: substitution or frameshift

Chromosomal mutations

• affect big sections

• More detrimental

• Occurs during meiosis

Substitution mutation

Type of mutation where the original nucleotide is replaced by a different nucleotide

3 types:

• silent

• missense

• nonsense

Silent substitution mutation

A change in a single nucleotide that doesn’t result in a change in amino acid sequence (neutral)

Missense mutation

A change in single nucleotide that results in a change in a single amino acid sequence

Nonsense mutation

A change in a single nucleotide that results in a premature stop-codon in the mRNA sequence

• negative impact on protein

• Won’t fold or function properly bc lack of amino acids

Frameshift mutation

Mutation where the addition or removal of a single nucleotide changes the reading frame for the protein. Always negative effect

2 types:

• insertion

• deletion

Insertion mutation

Mutation where an insertion of a single nucleotide into the DNA sequence changes entire amino acid sequence. Protein won’t fold or function properly

Deletion mutation

Mutation where a deletion of a single nucleotide into the DNA sequence changes entire amino acid sequence. Protein won’t fold or function properly

Sickle Cell Anemia

• caused my missense mutation in hemoglobin gene

Practice FRQ: Describe what happening between steps 1 & 2?

tRNA anticodon #3 and #4 occupy the P and A site. There is a condensation reaction between amino acid 3 and amino acid 4 to build a peptide bond.