Genetics Exam 4 (Ch 14,15,16)

Codon

a three-nucleotide sequence of DNA that codes for an amino acid

Start codon

AUG

What does AUG code for?

Methionine

Stop codons

UAA, UAG, UGA

Which amino acids do UAA, UAG, UGA code for

None

Reading frame

a linear sequence of codons in a nucleic acid defined by a start codon and a stop codon

Unambiguous

Each of the 61 triplets codes for one of 20 amino acids

Degenerate

Most amino acids are encoded by more than one codon

Universal

most living organisms use the same code

Commaless

There are no breaks between the codons in a reading frame

Non-overlapping

the triplets in a reading frame are in a tandem sequence and do not overlap.

What is flow of genetic information?

DNA-transcription-RNA-translation-protein

Where is a gene located?

locus on a chromosome

What is a substitution mutation?

when a base is replaced with a different base in DNA

What is the result of a substitution mutation

a permanent single-codon change in a protein-coding gene

What is the result of a silent substitution mutation

new codon codes for the same amino acid as the original codon

What is the result of a missense substitution mutation

the new codon codes for a different amino acid

What is the result of a nonsense substitution mutation

the new codon is a stop codon

What is the result of a nonsense substitution becoming a stop codon

a shorter polypeptide

How do mutations occur?

1) spontaneously 2) errors in DNA replication

Where do substitution mutations occur?

DNA

Mutations may be ___ or may be caused by __ in DNA replication. They occur in the ___ and are copied to ___ if they occur within genes.

spontaneous, errors, DNA, RNAs

2 multiple choice options

What are insertions?

a single base is added to the DNA sequence

What is the result of an insertion?

1) a frameshift mutation; a shift in the reading frame 2) all codons for insertion site are changed

What is the difference between an insertion and a substitution?

Insertion is adds base, substitution replaces a base

What is a deletion mutation?

the loss of a single base

Why do deletion mutations happen?

Errors in DNA replication

Insertion causes a ...

frameshift

Substitution causes change ...

in one codon

Deletions causes a ...

frameshift and shorter polypeptide

Basic requirements for Translation

1) mRNA 2) charged transfer RNAs 3) ribosome 4) no primers

Other requirements

1) initiation factors 2) elongation factors 3) energy sources 4) no primers

Transfer RNA (tRNA)

a single RNA with intramolecular base pairings

Which end of tRNA does the amino acid attach to

3' end

Which "arm" is the 3' end in the cloverleaf model

the acceptor arm

What does the anticodon loop base pair with?

a codon in an mRNA

The __ group of the ___ is covalently attached to the __ of a __

carboxyl, amino acid, 3' end, tRNA

The carboxyl group of the amino acid is __ attached to the _ end of a ___

covalently, 3', tRNA

What does a modified adenine result in?

Inosine

Where does inosine occur?

1rst base of anticodon

What can inosine pair with?

A, U, C

Codons specifying the same amino acid are __, resulting in a ___ genetic code

synonymous, degenerate

What is the Wobble Hypothesis? (Sotero definition)

the interaction between the third position of the codon in the mRNA and the first position of the anticodon in the tRNA

In what orientation do the mRNA codon and tRNA anticodon pair?

Anti-parallel; mRNA 5' -> 3', tRNA 3' -> 5'

3 multiple choice options

For example: AGG in the anticodon can pair with __ or __, which both code for the amino acid __

UCC, UCU, Serine

What tRNA binds to stop codons?

Stop codons do not have a tRNA

What binds to a stop codon at the A site?

release factor (RF1 or RF2)

Why does tRNA need to be charged?

to provide energy for the formation of a new peptide bond between amino acids in the ribosome

Which enzymes catalyze the charging of tRNAs?

Twenty different Aminoacyl tRNA synthases (one for each amino acid)

3 multiple choice options

Step 1 of charging tRNA:

amino acid activation

How is amino acid activated

amino acid is converted to an aminoacyladenylic acid

What is Step 1 of charging a tRNA considered?

energy-consuming step

Why is step 1 of charging a tRNA considered the energy-consuming step?

requires ATP

What is step 2 of charging a tRNA?

charging

What happens during the charging step of charging of a tRNA

aminoacyladenylic acid loses the AMP and the carboxyl group of the amino acid is attached to the 3' end of a tRNA

What is the result of the charging step of charging a tRNA?

an aminoacyl tRNA (a charged tRNA)

Step 2, in summary; the aminoacyladenylic acid __ the __ and the __ __ of the amino acid is attached to the __ end of a tRNA

The result is an ___ (a __ tRNA)

loses, AMP, carboxyl group, 3', aminoacyl tRNA, charged

Traits of the prokaryotic ribosome

1) large particle of rRNA and proteins 2) where translation occurs 3) two subunits: small and large

What is the unit that measures the rate at which particles sediment in a centrifugal field?

Svedberg unit (S)

What does the Svedberg unit (S) rate depend on?

1) weight 2) shape 3) size

The Svedberg unit (S) is used for measuring ...

1) large molecules 2) large cell components 3) ribosomes 4) organelles

What are the step of initiation of translation in prokaryotes?

1) mRNA binds to the small ribosomal subunit with the AUG codon positioned on the P site

2) f-Met-tRNA binds to the AUG codon

3) the large ribosomal subunit joins the complex

What are the step of initiation of translation in eukaryotes?

1) mRNA binds to the small ribosomal subunit with the AUG codon positioned on the P site

2) the large ribosomal subunit joins the complex

What is the result of initiation in prokaryotes

the creation of the 70s initiation complex for elongation

What does translation initiation require

1) GTP for energy 2) initiation factors (IF proteins)

What are the three sites in the ribosome

1) peptydyl (P) 2) aminoacyl (A) 3) exit (E)

What is the first amino acid formed in prokaryotes

formyl-methionine

In elongation, what facilitates the binding of the second tRNA to the second codon at the A site?

EF-Tu (an elongation factor) + GTP

What happens between the amino acid on the first tRNA and the second tRNA?

they form a dipeptide

After bonding with the first and second amino acid, what happens to the mRNA?

it's shifted to place the second codon in the P site and the third codon to the A site

What does tRNA do after the third codon is shifted into the A site?

the tRNA carrying the third amino acid binds to the third codon on the A site

What happens to the dipeptide on the second tRNA after the third amino acid is bound to the third codon?

it's transferred to form a tripeptide attached to the third tRNA

Where does the second tRNA move to once the tripeptide is formed?

it moves to the E site; aided by EF-G and GTP

Once the second tRNA moves to the E site the third codon move to the ...

P site

How does translation terminate?

1) a STOP codon moves to the A site of the ribosome 2) No tRNAs bind to stop codons 3) release factors 1 or 2 (RF1/RF2) releases polypeptide chain 4) RF3 releases the polypeptide chain from the last tRNA 5) RF3 triggers dissociation of the entire ribosome complex

RF3 is __ dependent

GTP

In prokaryotes, transcription and translation happen

simultaneously

What do the mechanisms of gene regulation determine?

1) Where a gene is expressed 2) When a gene is expressed 3) How much a gene is expressed

What is every gene in regard to RNA

an RNA-coding region (a transcribed region) of DNA

3 multiple choice options

What regions are not transcribed

regulatory regions

What are transcription factors

DNA-binding proteins that recognize specific sequences within the regulatory region(s) near the gene

Transcription factors bind to DNA?

YES!!!

1 multiple choice option

What do transcription factors recognize at regulatory regions?

specific sequences

What do transcription factor do at regulatory region(s)

activate or repress transcription

What regulates genes in prokaryotes?

the operon

What is the operon? (Sotero definition)

a cluster of structural genes with related functions under the control of a common regulatory system

What is an operon? (Simple definition)

cluster of genes controlled by one promoter

What are operons key to in prokaryotes

helping control protein production

What do operons respond to?

Changes in the environment

Do prokaryotes prefer lactose or glucose?

glucose

What do the structural genes under lac operon control

What does lactose isomerize into

allolactose

2 multiple choice options

The operon inducer is

allolactose

What happens to the lac operon if glucose and lactose are present?

allolactose will bind to lac repressor inhibiting it from binding to the operator, no cAMP, RNA polymerase performs insignificant transcription

Lactose and glucose are present; lac operon is ...

OFF

2 multiple choice options

Lactose is absent, glucose is present; lac operon is ...

OFF

3 multiple choice options

Lactose and glucose are absent; lac operon is

OFF

3 multiple choice options

Lactose is present, glucose is absent; lac operon is

ON

3 multiple choice options

What happens to the lac operon if only lactose is present?

allolactose will bind to lac repressor inhibiting it from binding to the operator, high cAMP, RNA polymerase can perform transcription

2 multiple choice options

What is the relationship between cAMP and glucose?

Inverse relationship; the absence of glucose induces the activity of the enzyme adenylate cyclase which catalyzes the hydrolysis of ATP into cAMP + PP

2 multiple choice options