CHEM 41 DNA TRANSLATION

Translation

Process of translating mRNA to a sequence of amino acids during protein synthesis

Peptide bonds

Link amino acids in a polypeptide chain

5’ to 3’

Genetic code is written in a typical convention of _____ to _____

Codon

Triple of bases

Reading frame

Established by AUG

Frame shift mutation

Reading frame shifts due to mutation (deletion or addition of DNA bases)

AUG

Initiation codon

Commaless

Genetic code is _____, meaning bases are not skipped

Non-overlapping

Genetic code is _____, which means no single base can take part in the formation of more than one codon

Degeneracy

Also known as redundancy of genetic code

several

Degeneracy of genetic code allows for _____ codons to code for the same amino acids

Stop codons

UGA, UAA, UAG

Met (AUG) and Trp (UGG)

Only _____ and _____ have a single codon

resistance against DNA mutations

Degeneracy of genetic code provides _____ against ______

Conservative substitution

Amino acid with different base but similar properties is caused by ______

Quasi-universal

Genetic code features and translation applies to prokaryotes and eukaryotes across all species

anticodon, H-bonding

Codon in mRNA is complementary to _____ sequence in tRNA via _____

parallel

Alignment of RNA sequences (mRNA and tRNA) is _____

cloverleaf or cruciform

Secondary structure of tRNA achieved by complementary base pairing

T arm (loop)

tethers tRNA to ribosome

D arm (loop)

identification of tRNA by aminoacyl synthethase

aminoacyl-tRNA synthethase

Enzyme that attaches the appropriate amino acid on tRNA to the 3’-OH end

Acceptor stem

Amino acid binding site via ester bond

3’-OH

The amino acid binds to the ____ of the acceptor stem

Wobble base pair

Noncanonical (non-Watson and Crick) base pairing of third codon base with its anticodon

inosinate (I)

Some tRNAs contain _____ which is flexible and can H-bond with U, C, and A

Aminoacylation or charging of tRNA

Cleavage of a triphopshate group

aminoacyl-tRNA synthethases

Enzyme that catalyzes amino acid activation and linkage

Structural basis of genetic code

amino acid recognition and tRNA loading by aminoacyl-tRNA transferase is the _____

ribosomes

Molecular machines responsible for protein synthesis

rRNA and protein

Comprise ribosomes

larger and more complex

Eukaryotic ribosomes are _____ and _____ than prokaryotic ribosomes

80S

Prokaryotic ribosome : 70S :: Eukaryotic ribosome : _____

E (exit site), P (peptidyl site), A (aminoacyl site)

Three sites in the ribosome

Exit site (E)

Accomodates deactylated/”spent” tRNA

Peptidyl site (P)

Accomodates tRNA attached to growing peptide chain

Aminoacyl site (A)

Accomodates aminoacyl-tRNA

Initiation factors (IFs)

Proteins that initiate translation

Shine-Dalgarno site

Short, purine-rich initiation sequence upstream of AUG in prokaryotic mRNA (-7 to -4)

initiation complex

Large prokaryotic ribosomal subunit (50S) associates to form _____

transcription

Translation can occur simultaneously with _____ in prokaryotes

5’ cap

In eukaryotes, the small ribosomal subunit binds to the _____

5’ cap

Prokaryotes : Shine-Dalgarno site :: Eukaryotes : ____

one amino acid

Polypeptide chain extends by _____ residue per cycle

fMet (formylmethionine)

Eukaryotes : Met :: Prokaryotes : _____

amino group, carbonyl group

_____ of next AA attacks _____ of previous AA, forming a peptide bond

release factor

Protein that binds at A-site which releases the completed polypeptide and dissociates the ribosome into subunits

sites of regulation

Amino acids containing N, O, or S act as _____

formyl group, methyl, or additional residues

Enzymatic removal acts on _____, _____, or _____

Acetylation

addition of an acetyl group (-COCH₃)

Glycosylation

Sugars added to specific amino acids

N-linked

Sugar added to Asn

O-linked

Sugar added to Ser or Thr

Kinases

Enzyme that transfers phosphates

isoprenyl group

Addition of _____ from intermediates of cholesterol synthesis pathway

farsenyl group

3 isoprenyl groups attached together

disulfide linkage

Two Cys residues form a _____

pre in preproenzyme

signal sequences within enzyme’s AA sequence that direct it to its proper cellular location

pro in preproenzyme

enzyme is inactive and requires cleavage or other modifications to be activated

also called zymogen

Virus

Small collection of genetic material surrounded by a protein coat (capsid); exceptions to the central dogma

RNA

Majority of virsues contain _____ except adenoviruses

replicate by themselves

Viruses cannot ______

proofreading activity

Known viral RNA replicases lack _____

synthesis of RNA strand

RNA replicase catalyzes _____ of _____ strand

mutation and evolution

RNA viruses undergo very rapid _____ and _____

Retrovirus

Type of virus that creates a DNA copy of its RNA genome

Reverse transcription

The process of synthesizing DNA from an RNA template

dsDNA

Reverse transcriptase catalyzes synthesis of _____from the ssRNA genome

RNA-dependent DNA synthesis

Reverse transcriptase first makes the DNA strand complementary to the viral RNA template

RNA degradation

Reverse transcriptase degrades viral RNA in the DNA-RNA hybrid

DNA-dependent DNA synthesis

Reverse transcriptase completes the synthesis of the other DNA strand, forming the dsDNA copy

tRNA primer, high error rate, and high mutation/evolution rate

Reverse transcriptase uses _____ and lacks 3’ to 5’ proofreading like RNA pol; leading to _____ and _____

integrase

Enzyme that integrates the dsDNA copy into the host cell’s genome

proviral DNA

passed onto succeeding generations and can be transcribed upon meeting certain conditions

Coronavirus

Virus with spike proteins that have a crown-like appearance

positive-sense ssRNA genome, RNA-dependent RNA synthesis

Coronavirus contains a _____ genome and utilize _____ synthesis

Ribosomal frameshifts

Involves altering the reading frame by shifting one nucleotide to the left and enables the coronavirus to encode more proteins

Lytic and lysogenic cycles

Two cycles observed in bacteriophages

Lytic cycle

New copies of the virus are actively made and causes lysis of the host sell after replication

Lysogenic cycle

Integration of viral genome into host cell’s genome and replicated alongside it

dormant

In the lysogenic cycle, the virus remains _____ until certain conditions are met in the lytic cycle

Zoonotic disease

Infectious disease that jumps from an infected animal to a human