Final - Transcription, Translation

_________ contain the information for all the proteins produced by an organism (not just enzymes)

Genes

___________ code for proteins

Genes

_____________ are made up of several different polypeptide chains, each of which is a product of a different gene

Proteins

What is the Metabolic Pathway for arginine synthesis?

Precursor ---> Ornithine ----> Citrulline ---> Arginine

Different enzymes catalyze each step in the metabolic pathway for _________

Arginine

___________ is the process of synthesizing mRNA from the DNA template

Transcription

____________ is the process of synthesizing proteins from mRNA sequence

Translation

What enzyme is responsible for transcribing mRNA from the DNA template (template strand)?

RNA polymerase

RNA polymerase synthesizes mRNA from DNA in the ______________direction

5' to 3'

After an mRNA is made in the cell nucleus, it is transported to the cytoplasm. Name the organelle and molecule that handles the process of translating the mRNA code into a protein

Organelle - RER

Molecule - Ribosome

Ribosomes transcribe (read) mRNA in the ___________ Direction

3' to 5'

The ___________ states that 1 gene can make multiple mRNA --> proteins

Central dogma theory

What is the order of the central dogma theory

1. DNA --> transcribed to

2. mRNA --> translated to

3. Proteins

True or False:

The arrows used in the Central dogma theory represent the flow of information between molecules, not the conversion of one molecule to another

True

What is a penotype and genotype?

Phenotype --> descriptive physical traits

Genotype --> sequence of amino acids (the code)

Where does Translation and Transcription occur in Prokaryotes and Eukaryotes?

Translation

1. Bacteria (prokaryotes) - cytoplasm

2. Eukaryotes - cytoplasm

Transcription

1. Bacteria - cytoplasm

2. Eukaryotes - Nucleus

__________ and ___________ link genotype and phenotype

- Transcription

- Translation

Difference in genotype cause difference in __________

Phenotype

True or False:

A small change in DNA sequence produces a large change in phenotype

True

How many amino acids are there?

20

What is a Codon

3 base (nucleotide) genetic code in an amino acid sequence

What direction are codons written in?

5 prime to 3 prime

What makes codons redundant?

Some amino acids consist of more than one codon

Give an example of redundant codons

Stop codon

- UAA

- UAG

- UGA

All amino acids except ____________ and _____________ are coded for by more than one codon

- Methionine (AUG)

- Tryptophan

The __________ codon initiates protein synthesis in translation

Start Codon (AUG)

The ___________ codon signals termination of protein synthesis

Stop Codon (UAA, UAG, UGA)

What happens to the amino acid sequence once a Stop is read

The ribosome denatures

_______________ allows one tRNA to read more than one codon (accounts for the redundancy of the genetic code)

Wobble pairing

True or False:

Translation of a codon is complete when a peptide bond forms between the amino acid originally carried by the tRNA and the growing polypeptide

True

Ribosomes synthesize proteins in a 3-step sequence in Translation. Explain the 3-step sequence

1. aminoacyl - aminoacyl tRNA attaches to the A site

2. Peptidyl - peptide bonds form between the tRNAs in site A and P

3. Exit - tRNA in the E site exits the ribosome

- tRNA from site P goes into E and A goes into P leaving A empty for another aminoacyl

__________ creates anti-codons

tRNA

________________ transfers amino acids during protein synthesis

tRNA

True or False:

Wobble pairing explains only how one tRNA can read more than one codon, not how one amino acid can be specified by more than on codon

True

________________ mutation replaces one base (nucleotide) from the amino acid sequence of mRNA

Substitution

When does a Substitution mutation usually occur?

When the first or second base of a codon is replaced with a different base

What happens when the third base of a codon in mRNA gets replaced by a different base?

Usually, nothing happens, and the sequence remains the same due to the redundancy of codons

________________ mutation is the Insertion or deletion of a base (nucleotide)

Frameshift

What effect does a Frameshift mutation have on the amino acid sequence?

Inserting or deleting a base from the sequence cause the entire sequence to shift over by one

- this is usually deleterious

What are all the Point Mutations and what effect does each have on the amino acid sequence?

1. Frameshift

- creates a shift in the sequence that is almost always deleterious

2. Nonsense

- causes a change in the sequence that results in an early Stop codon

- Is usually deleterious

3. Missense (substitution mutation)

- change in the sequence can be deleterious, neutral or beneficial

4. Silent

- change in the DNA causes no change to the amino acid sequence making it neutral

DNA mutations are permanent changes in an organisms DNA. In other words, a permanent change in ________________

Genotype

What comes from a mutation? Are mutations always bad?

- Mutations create new alleles

- Can be beneficial (evolution), deleterious (denature), or neutral (no change)

True or False:

The point mutations, Missense, Nonsense, Frameshift and Silent can and do occur in DNA sequences that do not code for proteins

False, these mutations ONLY change the protein-coding portions of a gene

Chromosome mutation changes the structure or number of chromosomes permanently. How does this happen? Are chromosome mutations always bad?

- Chromosome mutations result when a mistake is made in moving chromosomes into daughter cells during mitosis or meiosis

- Can be beneficial, neutral or deleterious

_____________ are nonfunctional alleles resulting from mutations

Null Alleles

A __________ is an individual that carries a mutation

Mutant

Chromosomes of cancer cells exhibit deleterious chromosome mutation that includes ______________, ____________, _____________, _______________ and _____________

ADDIT

- Aneuploidy

- Deletions

- Duplications

- Inversions

- Translocations

How do you know which strand of DNA is the Template strand and which is the coding Strand

The sequence is placed after the TATA box on the template strand 3' to 5'

What makes up a Holoenzyme (RNA polymerase)

Sigma + Core

The ____________ enzyme locates and attaches to the TATA box to begin protein synthesis

Sigma

The Sigma enzyme binds to the _____________ to recognize sites where transcription should begin

Core Enzyme

____________ promote the start of transcription (binding sites for _____________)

- Promoters (TATA box)

- RNA polymerase

The ribosome on the ____________ strand reads the DNA template 5' to 3' to make mRNA while the ribosome on the ____________ strand reads mRNA 3' to 5' to make proteins

- Template

- Coding

The _____________ strand of DNA is transcribed while the _____________ strand is translated

- Template

- Coding

Multiple ribosomes can translate (read) mRNA (5' to 3') at a time in _________________ (speeds up protein production)

Only 1 ribosome can translate (read) mRNA (5' to 3') at a time in ________________ (slows down protein production)

- Bacteria (prokaryotes)

- Eukaryotes

A __________________ is formed by RNA polymerase after base pairing occurs

Phosphodiester bond (linkage)

___________ has a single RNA polymerase while ___________ have at least 3 distinct types of RNA polymerase (I, II, III)

- Bacteria (prokaryotes)

- Eukaryotes

Transcription:

______________ performs template-directed-synthesis in the 5' to 3' direction

RNA polymerase

Production of RNA lengthens in the _____________ phase of bacteria

Elongation

True or False:

Like DNA polymerase, RNA polymerase proofreads and corrects errors during synthesis

True

Unlike __________________, RNA polymerase does not require a primer to begin transcription

DNA polymerase

How do DNA polymerase and RNA polymerase compare and contrast?

What is the process of Initiating transcription in Bacteria?

1. Sigma binds to promoter region of DNA

2. RNA polymerase opens the DNA helix and transcription begins

3. Sigma is released from the core enzyme, RNA synthesis continues from DNA

In bacteria, transcription stops when RNA polymerase transcribes a DNA sequence called a ______________ signal

Transcription-termination

The formation of a __________ causes transcription to end in bacteria. How?

Hairpin

How does Transcription differ in eukaryotes and prokaryotes (bacteria)?

Eukaryotes

- Transcription occurs in the Nucleus

- Transcription produces pre-mRNA that contains exons and Introns

- After Transcription termination, the pre-mRNA needs extensive modifications before protein synthesis

- 5' Cap, poly(A) tail, and General transcription factors are used in RNA processing to mature pre-mRNA into mRNA for protein synthesis

Bacteria (Prokaryotes)

- Transcription occurs in the Cytoplasm

- After transcription termination, mRNA goes straight into protein synthesis (no 5' Cap, poly(A) tail or transcriptive factors)

How does Translation compare and contrast in eukaryotes and prokaryotes (bacteria)?

Eukaryotes

- Translation occurs in the Cytoplasm

- The start codon (AUG) in a part of the Kodak sequence

Prokaryotes

- Translation occurs in the Cytoplasm

- The start codon (AUG) is placed after the Shine Dalgarno sequence

Where does RNA processing in Eukaryotes occur?

Nucleus

The _____________ signals transcription termination

Poly(A) Signal

Proofreading is done by ____________ during ______ synthesis

- RNA polymerase

- RNA synthesis

What happens after transcription termination?

mRNA is ready for Translation to begin

- right away in bacteria

- after extensive modifications in eukaryotes

Instead of using the Sigma enzyme, eukaryotic RNA polymerases recognize promoters (TATA box) using ___________________________

General transcription factors

Why are the 5' Cap and Poly(A) tail in RNA processing (after transcription) important and where are they located?

5' Cap

- located on the 5' end of the strand

- protects the 5' end from being denatured (attacked by enzymes)

- Enables ribosomes to bind to the mRNA

Poly(A) tail

- located on the 3' end of the strand

- protects the 3' end from being denatured

- required for ribosomes to start translation

What does the 5' Cap and poly(A) tail consist of?

5' Cap -

poly(A) tail - a string of Adenines

True or False:

With the addition of the 5' Cap, poly(A) tail and completion of RNA splicing, the processing of the pre-mRNA is finally complete

True

_______________sometimes begins translating mRNA before its transcription is complete

Bacteria

Why can Bacteria transcribe and translate at the same time?

Bacteria has no nuclear envelope to separate the 2 processes

After the 5' Cap is added to the 5' end of the strand (In eukaryotes), ____________ occurs

RNA Splicing

What happens during and after RNA spiling?

During - Introns are cut out of pre-mRNA

After - Exons are joined together by bonds to form the final mature mRNA

What ribozyme and molecule are responsible for RNA splicing?

Ribozyme - Spliceosome

Molecule - snRNA

____________ are transcribed regions that removed from final mRNA

Introns

___________ are the transcribed regions retained in mature mRNA

Exons

True or False:

5' and 3' Untranslated regions (UTRs) are a part of the pre-mRNA

True

Why are the 5' and 3' Untranslated regions (UTRs) important?

essential for mRNA stability and function in protein synthesis

What are the 3 phases of protein synthesis (translation)?

1. Initiation - Initiating translation

2. Elongation - extending the polypeptide chain (amino acid sequence)

3. Termination - terminating translation

3 phases of protein synthesis:

___________________ is the process of assembling a ribosome (small subunit, large subunit, tRNA)

Initiating translation

The initiation of translation is a ____________, unlike the initiation of transcriptions that is at a ________________

- Start codon (AUG)

- Promoter (TATA box)

The ___________ phase extends the polypeptide chain by adding amino acids

Elongation

What happens in the Elongation Phase of translation?

1. An aminoacyl tRNA attaches to the A site

2. Peptide bond forms between the tRNA in A site and P site

3. Translocation occurs

What happens during Translocation in the Elongation phase?

The tRNA from A site transfers to P site and P transfers to E site, leaving the A site empty for another aminoacyl to attach

How does protein synthesis end? (translation)

Once a Stop codon (UAA, UGA, UAG) is found, a release factor fills the A site and translation terminations occurs

3 phases of protein synthesis:

What happens once a Stop codon (UAA, UAG, UGA) is found in the mRNA sequence?

Termination

- A release factor attaches to the A site, breaks the peptide bonds

- Polypeptide and tRNAs are released

- Ribosome subunit separates

True or False:

Stop codons can be found anywhere in the sequence

False, they can only be found in the 3' region (not the very end of an mRNA)

Is the ribosome an Enzyme or a Ribozyme?

The ribosome is a ribozyme (not a protein-based enzyme)

While Elongation is the same in Eukaryotes and prokaryotes, Initiation and termination are much more complex in ______________

Eukaryotes

Protein folding is guided and accelerated by proteins called ________________

Molecular chaperones

True or False:

Proteins are not fully formed and functional at the end of translation

True