Genetics exam 2

Proteins

Essential for all processes completed by living things

• purposes: Enzymes, structure, transport, communication, defense, movement, storage, hormones

amino acids

all proteins are polymers of

peptide bonds

what are proteins joined by?

The genetic code

Universal code for protein synthesis

• strong evidence that all living things share common evolutionary heritage

codons

what does the genetic code consist of

Degenerate

a single amino acid can be coded by multiple different codons

Unambiguous

Each codon always codes for the same single amino acid

• non overlapping

• each nucleotide is part of only one codon

Start and stop signals

specific three letter codes are always at the beginning and the end of a reading frame. Marks the beginning and the end of the amino acid chain (polypeptide)

reading Frame

• start codon at the beginning (AUG) which codes for MET

• atop codon at the end (UAA, UGA, AUG) which does not code for an amino acid

antiparallel

Remember: mRNA is

transcribed ____

5’ – 3’

codons are written from _____ to ______

tRNA

• binds amino acids and delivers them to a ribosome

isoaccepting tRNAs

Having different anticodons, but carry the same amino acids

translation

• the prices through which mRNA is used to assemble a protein

• Occurs at ribosomes (bond or unbound)

• Ribosomes attaches at the 5’ end of an mRNA strand and moves towards the 3’ end

• new amino acids are attached to the carboxyl end of the amino acid

the cap

what helps the ribosomes attach at the 5’ end

tRNA charging

tRNAs bind to amino acids

initiation

components for translation are assembled at the ribosome

Stages of translation

Amino acids are joined one at a time

Termination

protein synthesis halts at the termination codon

Aminoacyl- tRNA

What facilitates the attachment of the amino acid to the tRNA?

• Ensures the correct amino acid is attached to the correct tRNA

Anti- Codon

The complementary sequence to a codon

• tRNA matches to the codon in the mRNA then adds the amino acids to the sequence

16s RNA

what binds to the Shine- Delgarno sequence

Kozak sequence

Initiation in eukaryotes: recognition of start codon is completed by a consensus sequence known as____

12

how many initiation factors to eukaryotes use?

Poly A-tail

____ binds to cap- binding proteins, which enhances binding to the small subunit

Aminoacyl (A) site

where all tRNAs enter, except the initiator

peptide (P) site

Where the ignitor tRNA initially bonds

A site

charged tRNA binds to ___ site

GDP, EF-Tu-GDP

GTP is cleaves to form ____ and _____ is released

Translocation (elongation)

• Movement of the ribosome down the mRNA in 5’-3’ direction

• tRNA does not move, the ribosomes move around them

• tRNA that previously occupied the P site is now in the E site

• tRNA that previously occupied the A site is now in the P site

translocation

Ribosome: cytoplasm —> A site —> P site —> E site —> cytoplasm

Oncogenes

genes that drive uncontrolled cell division

• over expressed or constitutively expressed

constitutive expresson

continuous, unregulated production of a gene product (RNA or protein)

examples of constitutive expression (cancer development)

• MYC gene is over expressed in lymphomas and carcinomas

• BRAF gene is over expressed in melanoma

• KRAS gene is over expressed in lung and colorectal cancer

neurodegenerative disease

Dysregulation of transcription factors or RNA processing

• Amyloid-β is overproduced in Alzheimer’s disease, leading to plaque build up in the brain

α-synuclein is misfolded and accumulates in aggregates called Lewy bodies within cells in Parkinson’s Disease

any stage

gene products can be regulated at what stage?

Alteration of DNA or chromatin structure

• Gene availability and packaging

• DNA methylation

Transcription

• stops gene products form being produced

• Preserves energy in the cell

mRNA processing

• Modification of mRNA determines if RNA is allowed to move into the cytoplasm (eukaryotes)

• Changed to amino acid sequence

• Not an important point of control for prokaryotes

mRNA stability

• Faster mRNA degradation= less protein produced

• Reduces how much mRNA is available for translation

Translation

• complex process, lots of enzymes and factors involved

• Opportunities for control either each of those required elements

• Availability of amino acids

• Sequences in untranslated regions

Post- translation

• Changes to proteins after translation

• Protein stability

• Activity (enzymes and inhibitions)

operons

Bacteria genes are transcribed in ____

Promoter

region upstream of a gene where RNA Pol and transcription factors bind

mRNA molecule

Genes are transcribed together in a single _____

Operon

group of bacterial gene that are transcribed together, their promoter, and any other additional sequences

araC gene pGLO plasmid

• Regulatory gene

• Encodes the AraC repressor protein

pBAD promoter

landing site for RNA polymerase to transcribe downstream genes

gfp gene

• encodes green

• Fluorescent protein

amp (or bla) genre

encodes beta lactamase, an enzyme that breaks down ampicillin (an antibiotic)

ori

origin of replication allows bacteria to makes copies of plasmid

regulator proteins

Regulator genes make____

regulator genes

• controls the expression of genes within an operon

• increases or decreases transcription

• Affects operon function, but is not part of the operon itself

• has its own promotor for the operon

• Regulator proteins bind to a region of the operon known as the operator

• determines if transcription can take place

negative control

• regulatory protein is repressor

• inhibits transcription

Positive control

• regulatory protein is an activator

• increases transcription

inducible operons

• transcription is normally off, something must induce transcription

• can be turned on

Repressible operons

• transcription is normally on, something must repress

• Can be turned off

proteins

essential for all processes completed by living things

• enzymes, structure, transport, communication, defense, movement, storage, hormones

amino acids

all proteins are polymers of _____. joined by peptide bonds t from a polypeptide chain

a.a

primary structure for proteins

degenerate (the genetic code)

a single amino acid can be coded by multiple different codons

unambiguous (genetic code)

each codon always codes for the same single amino acid

non overlapping (genetic code)

each nucleotide is part of only one codon

start and stop signals

specific three letter codes are always at the beginning and the end of a reading frame; marks the beginning and end of the Aino acid chain (polypeptide)

5’- 3’

codons are written form____ as they would appear in mRNA code

antiparallel

mRNA is transcribed as_____

tRNAs

binds amino acids and delivers them to a ribosome

• 
  

isoaccepting tRNAs

have different anticodons, but carry the same amino acid

translation

the process through which mRNA is used to assemble a protein

• occurs at the ribosomes (bound or unbound)

• New amino acids are attached to the carboxyl end of the amino acid

5’, 3’

Ribosomes attach at the ____ end of an mRNA strand and moves towards the _____ end. (Translation)

tRNA charging, initiation, elongation, termination

order of translation stages

tRNA charging

tRNA binds to amino acids

initiation

components for translation are assembled at the ribosome

elongation

amino acids are joined one at a time

termination

proteins synthesis halts at the termination code

CCA, 3’

all tRNA have a _____ sequence at the ____ end, where the carboxyl group is attached

Aminoacyl-tRNA

20 different enzymes, each specific for one amino acid

• recognizes all tRNA that would accept that amino acid

• Binds to the acceptor stem of the tRNA

tRNA charging

Aminoacyl-tRNA syntheses facilitates the attachment of the amino acid to the tRNA

• ensures the correct amino acid is attachment to the correct tRNA

anti- codon

the complementary sequence to a codon

• tRNA matches to the codon in the mRNA then adds the amino acid to the sequence

components needed for initiation

• mRNA

• small and large subunits of the ribosome

• initiation factors

• initiator tRNA with MET attached

• GTP

steps in initiation

1. mRNA binds to the small subunit of the ribosome

2. Initiator tRNA binds to the mRNA through base pairing between initiator codon and anticodon

3. Large ribosomal subunit joins the initiation complex

imitation of bacteria

• the small subunit (30s) binds to the mRNA

• mRNA can only bond when the subunits are separate

• initiation factors 3 (IF-3) binds to the small subunit to block binding of the large subunit during initiation

• initiation factor 1 (IF-1) enhances the dissociation between subunits

• 16s rRNA binds to the Shine- Dalgarno sequence in the bacterial mRNA

16s

____ rRNA binds to the Shine- Dalgarno

initiation in eukaryotes

• no Shine Dalgarno sequence for rRNA to bind

• small subunit of eukaryotic ribosome, initiation factors, and initiation tRNA work together to recognize 5’ cap and bind to it.

• Recognition of start codon is completed b y a consensus sequence knows as the Kozak sequence.

requirements for elongation

• 70S initiation complex

• tRNAs charges with their amino acids

• elongation factors

• GTP

C terminus

polypeptide chain grows by adding amino acids to the _____ terminus

start

N terminus = ____

end

C terminus = ____

E site

when amino acid is removed, tRNA exits through the _____. (elongation)

A site, P site, and E site

in elongation, ribosomes have 3 sites occupied by amino acids

A site (aminoacyl)

where tRNAs enter, except the initiator

P site (peptidyl)

where the initiator tRNA initially binds

GTP and ATP

provides energy during translation

isoaccepting tRNAs

two tRNAs that have different anticodons but carry the same amino acids are called____

3

how many codons function as stop codons

multiple codons can code for the same amino acids

the genetic code is described as degenerate because

each nucleotide is part of only one codon

what does it mean that the genetic code is nonoverlapping?

3’ CCA end

the amino acid attaches to the tRNA at the:

Small subunit binds mRNA → initiator tRNA pairs with start codon → large subunit joins

Which sequence of events correctly describes translation initiation in

bacteria?

Shine delgarno sequence

in bacteria, the 16s rRNA recognizes the