Exam 4 Quiz 3 Flashcards by Bella Forster

making protein involves

all 3 forms of RNA: mRNA, tRNA, rRNA

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mRNA

-uses the genetic code as their language
-reads as a series of triplets called codons
-each codon codes for a specific amino acid

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how many possible codons

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how many amino acids

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genetic code redundancy

more than 1 codon can code for the same amino acid

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wobble site

third site within the codon because it is not needed to define the amino acid

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start site

AUG

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stop codons

UAG
UAA
UGA

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why is reading frame important

the movement or shift down of only one codon can change the amino acid that it codes for changing the genetic code

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AUG in bacteria contains

formyl methionine

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tRNA

-transfer RNA
-73-93 nucleotides long
-single stranded with secondary structures
-modified bases

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why does tRNA have increased stability when compared to mRNA

through the single strands with secondary structures and the modified bases

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modified bases

pseudouridine, inosine, D=dihydrouridine, dimethyl guanosine

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clover leaf structure

structure of tRNA that is beneficial in that it prevents attack by ribonuclease becasue they typically attacked linear

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what forms the clover leaf structure

intra-strand base pairing

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functional importance of tRNA

-anti-codon area
-3’ acceptor end

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anti codon area

bases that recognize mRNA codons

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3’ acceptor end

-attaches 3 bases (cytosine, cytosine, adenine) to 3’ end
-termed CCA

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what adds CCA onto the 3’ end

CCA adding enzyme

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aminoacyl-tRNA synthase

adds amino acid onto the CCA

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rRNA

prime component of ribosomes

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ribosomes

-where translation occurs
-site of protein synthesis
-60% rRNA
-40% protein

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prokaryotic ribosomal subunits

70S total, 50S large, 30S small

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eukaryotic ribosomal subunits

80S total, 60S large, 40S small

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rRNA off of 50S subunit

5S and 23S rRNA

rRNA off of 30S subunit

16S rRNA

rRNA off of 60S subunit

5S, 5.8S, and 28S rRNA

rRNA off of 40S subunit

18S rRNA

translation initiation

small subunit is separated from large subunit

what keeps the two subunits separated

IF-3 initiation factor that is bound to the 30S subunit

5' untranslated region upstream of a gene has...

...Shine dalgarno sequence

Shine Dalgarno sequence

base pairs with the 3' end of the 16S rRNA which puts AUG into prime recognition

when AUG is in prime recognition then

AUG becomes available for recognition by the tRNA carriers: formyl methionine

what helps tRNA get into its place

IF-2

where does tRNA eventually need to get into

future P site

what is displaced that causes initiation

IF-1 displaces IF-3 which begins the process of initiation

when initiation begins, what is opened up

50S subunit is open, IF-2 then uses energy to pack the tRNA into the P site and then leaves

where do all incoming tRNA go?

A site, except tRNA 1 goes to P site

elongation factors

-EF-Tu -EF-Ts -23S rRNA -EF-G

EF-Tu

-helps bring in next tRNA with amino acid -if it fits anticodon loop then 16S + 23S interact and GTP locks in place -GTP becomes GDP

EF-Ts

turns GDP back into GTP

23S rRNA

-peptidyl transferase enzyme -RNA based -binds AA in P site -needs translation to occur in order to shift ribosome down 1 unit (requires energy)

EF-G

-helps move the ribosome down a unit -moves empty tRNA from P site to E site (to exit) -growing peptide then moves into P site to have empty A site to start process over again

why is translation efficient

-polycistronic sequences -multiple ribosomes can attach because of trasnlocation

polysomes

makes translation more efficient **not speific to eukaryotes

polysomes in prokaryotes

-combine transcription and translation to occur simultaneously

why can transcription and translation occur at the same time in eukaryotes?

-they have no nucleus -RNA polymerase

protein folding uses…

-chaperones -GroEL -GroES

chaperone proteins

-initiate folding -DNA K and DNA J are the main mechanisms used

DNA K and DNA J

ATP dependent enzymes

GroEL and GroES

make up a barrel structure that allows the protein to go through which forces proper protein folding (ATP dependent)

protein processing first codon

-first codon typically cleaved away BUT bactera tend to not cleave off all of their protein

what is left behind when bacteria doesnt cleave off all protein

formyl methionine

formyl methionine is

a great trigger four our immune response

why is formyl methionine a trigger for our immune response

our white blood cells ahve formyl methionine receptors to fight off/start an immune response against it

after prtein get made they go through

extra processing in the ER and golgi to attach sugars

glycosylation

sugaring process

most antibiotics are derived from

bacteria

antibiotics that inhibit protein synthesis

-Aminoglycosides -Tetracyclines -Chloramphenicol -Macrolides

what do all of those antibiotics target?

70S ribosome which is only effective against bacteria

how to we prevent the antibiotics from attacking the 70S in our mitochondria

by giving the antibiotic in smaller concentration doses so it does not interfere

Aminoglycosides

-obtained from streptomyces -streptomycin, gentamycin, tobramycin, neomycin -cyclohexane ring and 1 or more amino sugars -binds to 30S causing misreading of mRNA message -effective against gram - enteric -bacteriocidial

bacteriocidial

kill microorgansims

bacteriostatic

prevent reproduction of microorganisms

Tetracyclines

-broad spectrum -binds to 30S and inhibits enterance of tRNA onto A site -not used in kids or pregnant women -acne medicine and animal feel -bacteriostatic

chloramphenicol

-broad spectrum -obtained from streptomyces venezuelae -binds to 50S inhibits formation of peptide binds between AA -last resort antibiotic bc of bad side effects -used in 3rd world countries

side effects of chloramphenicol

aplastic anemia: low white, red, and platelet count which messes with bone marrow production

macrolides

-erythromycin, clarithromycin, azithromycin -lactone rings to one or more sugars -binds to 50S ribosomal subunit + prevents translocation of the ribosome: EFG is responsible

bacteria timing of transcription and translation

same time

eukarya timing of transcription and translation

sperate time

archaea timing of transcription and translation

seperate time

bacteria recognition of mRNA by small ribosomal subunit

shine dalgarno sequence

eukarya recognition of mRNA by small ribosomal subunit

5' cap

archaea recognition of mRNA by small ribosomal subunit

shine dalgarno sequence

bacteria coding of start codon

formyl methionine

eukarya coding of start codon

AUG mehtionine

archaea coding of start codon

AUG methionine

bacteria amount of transcription factors

fewest

eukarya amount of transcription factors

multi-subunit, a lot more complex

archaea amount of transcription factors

multi subunit but not complex

bacteria amount of termination factors

eukarya amount of termination facotrs

archaea amount of termination factors