Chapter 17 - From Gene to Protein Flashcards
What is gene expression, and what two stages does it include?
The process by which DNA directs protein synthesis.
The two stages are
- Transcription
- Translation
Briefly describe the differences in the transcription/translation process for the synthesis of DNA for Prokaryotes and Eukaryotes
Prokaryotes
mRNA produced by transcription is immediately translated without processing.
Eukaryotes
Nuclear envelope separates transcription from translation
Eukaryotic RNA transcripts are modified through RNA processing to yield finished mRNA
What is a codon?
- The flow of information from gene to protein is based on a triplet code:
- A series of non-overlapping, 3-nucleotide “words” called codons.
- These triplets are the smallest units of uniform length that can code for all amino acids
- Each codon specifies the amino acid to be placed at the corresponding position along a polypeptide (protein).
Why do we use triplets for codons (or 3 nucleotides per codon in otherwords) ?
There are 4 nucleotides (A,G,T,C)
There are 20 amino acids
It must be a combination of more than one nucleotide that specifies one amino acid
Could a codon be 2 nucleotides long? if grouped in pairs there are 42 = 16 combinations… not enough combinations
With triplets there are 43 = 64 combinations More than enough combinations for all 20 amino acids.
Experimentation confirmed that codons are triplets of nucleotides
During transcription, one of the two DNA strands, called the ____________ ________ provides a template for odering the sequence of nuecleotides in an RNA transcript
Template strand
During translation (protein building) the mRNA base triplets (codons) are read in what direction on the carbon?
During translation, codons are read in the 5’ to 3’ direction
*Extra: The 5’ and 3’ mean “five prime” and “three prime”, which indicate the carbon numbers in the DNA’s sugar backbone. The 5’ carbon has a phosphate group attached to it and the 3’ carbon a hydroxyl group. This asymmetry gives a DNA strand a “direction”.
How do we read DNA ?
During translation, codons along an mRNA molecule are read by translation machinery in the 5’ to 3’ direction.
Each codon specifies the addition of one of the 20 amino acids
For example, UGG particular position on the DNA strands results in the placement of the amino acid Tryptophan (Trp) at the corresponding position of the polypeptide to be produced.
Why is genetic code redundant but not ambiguous?
Redundant……
because an amino acid can be specified by more than 1 codon.
Not Ambiguous…..
because no codon specifies more than one amino acid.
In order for a specified polypeptide to be produced, codons must….
*Also review cracking the code Image*
….be read in the correct reading frame (correct groupings)
Transcription is the first stage of gene expression, briefly describe how it begins.
RNA synthesis is catalyzed by RNA polymerase, which pries the DNA strands apart and hooks together the RNA nucleotides
RNA synthesis follows the same base-pairing rules as DNA, except uracil substitutes for thymine
- The DNA sequence where RNA polymerase attaches is called the promoter; in bacteria, the sequence signaling the end of transcription is called the terminator*
- The stretch of DNA that is transcribed is called a transcription unit*
What is the DNA sequence where RNA polymerase attached to called? and what is the sequence signalling end of transcription?
Promoter
The DNA sequence where RNA polymerase attaches is called the promoter
Terminator
in bacteria, the sequence signaling the end of transcription is called the terminator
What is the stretch of DNA that is transcribed called?
Transcription Unit
What are the three (3) stages of transcription? (brief description)
1. Initation & RNA Polymerase Binding
- Promoters signal the initiation of RNA synthesis
- Transcription factors mediate the binding of RNA polymerase and the initiation of transcription
- Completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a transcription initiation complex
- A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes
2. Elongation of RNA strand
As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time.
Transcription progresses at a rate of 40 nucleotides per second in eukaryotes.
A gene can be transcribed simultaneously by several RNA polymerases.
3. Termination of Transcription
The mechanisms of termination are different in bacteria and eukaryotes
In bacteria, the polymerase stops transcription at the end of the terminator
In eukaryotes, the polymerase continues transcription after the pre-mRNA is cleaved from the growing RNA chain; the polymerase eventually falls off the DNA
What is the first stage of transcription? Be descriptive
1. Initation & RNA Polymerase Binding
- Promoters signal the initiation of RNA synthesis
- Transcription factors mediate the binding of RNA polymerase and the initiation of transcription
- Completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a transcription initiation complex
- A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes
What is the second stage of transcription? Be descriptive
2. Elongation of the RNA Strand
- As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time.
- Transcription progresses at a rate of 40 nucleotides per second in eukaryotes.
- A gene can be transcribed simultaneously by several RNA polymerases.
What is the third stage of transcription? be descriptive..
3. Termination of Transcription
- The mechanisms of termination are different in bacteria and eukaryotes
- In bacteria, the polymerase stops transcription at the end of the terminator
- In eukaryotes, the polymerase continues transcription after the pre-mRNA is cleaved from the growing RNA chain; the polymerase eventually falls off the DNA
What is RNA processing?
Each end of a pre-mRNA molecule is modified in a particular way:
The 5′ end receives a modified nucleotide 5′ cap and the 3′ end gets a poly-A tail.
These modifications share several functions:
- They seem to facilitate the export of mRNA
- They protect mRNA from hydrolytic enzymes
- They help ribosomes attach to the 5′ end
Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions, what is this called? and what is the counterpart to this?
Introns
Non-coding regions
Exons
Regions that are expressed
What is RNA Splicing?
RNA Splicing
removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence.
*exons exit the nucleus
What the hell is a spliceosome?
Spliceosomes
in some cases, RNA splicing is carried out by spliceosomes. Spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites.
Some genes can encode more than one kind of polypeptide (depending on which segments are treated as exons during RNA splicing) what are these variations called?
Alternative RNA splicing
Because of alternative splicing, the number of different proteins an organism can produce is much greater than its number of genes.
Proteins often have a modular architecture consisting of discrete regions called _________.
In many cases, different exons code for different domains in a protein
_________ __________ may result in the evolution of new proteins.
Proteins often have a modular architecture consisting of discrete regions called Domains.
In many cases, different exons code for different domains in a protein
Electron shuffling may result in the evolution of new proteins.
After mRNA has been transcribed, spliced and modified, it is ready to produce protein. What happens to the mRNA to begin translation?
mRNA is shuttled out of the nucleus into the cytoplasm where it will bind to a ribosome and start Translation…
Translation is RNA-directed synthesis of a polypeptide. A cell translates an mRNA message into protein with help of _ _ _ _ _ _ _ _ _ _ _ (_ _ _ _) ?
Translation is RNA-directed synthesis of a polypeptide. A cell translates an mRNA message into protein with help of Transfer RNA (tRNA)
Describe tRNA
Molecules of tRNA are not identical:
- Each carries a specific amino acid on one end
- Each has an anticodon on the opposite end from the amino acid
- the anticodon on the tRNA base-pairs with a complementary codon on mRNA
For translation of the RNA to be accurate, what two steps are required?
1. A correct match between tRNA and an amino acid, done by the enzyme aminoacyl-tRNA synthetase
2. A Correct match between the tRNA anticodon and an mRNA codon.
In terms of codons, what is a wobble?
Wobble
Flexibile pairing at the third base of a condon. Allows some tRNA’s to bind to more than one codon.
What is the relationship of Ribosomes to the process of translation?
Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis
The two ribosomal subunits (large and small) are made of:
- Proteins and
- Ribosomal RNA (rRNA)
A ribosome has three binding sites for tRNA, what are they?
A Site
holds the tRNA that carries the next amino acid to be added to the chain.
P Site
holds the tRNA that carries the growing polypeptide chain.
E Site
is the exit site, where the discharged tRNA’s leave the ribosome.
What are the three stages of translation? (with a brief description of each)
1. Initiation of Translation
- Initiation stage of translation brings together mRNA, tRNA with the first amino acid, and the two ribosomal subunits
2. Elongation of polypeptide chain
- During the elongation stage, amino acids are added one by one to the preceding amino acid.
3. Termination
- Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome.
- The A site accepts a protein called a release factor
- The release factor causes the addition of a water molecule instead of an amino acid.
- This reaction releases the polypeptide, and the translation assembly then comes apart.
What is the first stage of translation? How does this proceed….
1. Ribosome Association and Initiation of Translation
- Initiation stage of translation brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits
1) First, a small ribosomal subunit binds with mRNA and a special initiator tRNA
2) Then, the small subunit moves along the mRNA until it reaches the start codon (AUG)
3) Proteins called initiation factors bring in the large subunit that completes the translation initiation complex
Go through the process of the second stage of translation
2. Elongation of polypeptide chain
During the elongation stage, amino acids are added one by one to the preceding amino acid.
Each addition involves proteins called elongation factors and occurs in three steps:
- Codon recognition,
- Peptide bond formation and
- Translocation
What is the third stage of translation? go through the process
3. Termination
Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome.
The A site accepts a protein called a release factor
The release factor causes the addition of a water molecule instead of an amino acid.
This reaction releases the polypeptide, and the translation assembly then comes apart.
What two populations of ribosomes are evident in the cells?
Free Ribosomes
(in the cytosol)
Free ribosomes mostly synthesize proteins that function in the cytosol.
Bound ribosomes
(attached to the ER)
Make proteins of the endomembrane system and proteins that are secreted from the cell.
*Both types are identical and can interchange
How do proteins enter the endoplasmic reticulum?
A signal-recognition particle (SRP) binds to the signal peptide
The SRP brings the signal peptide and its ribosome to the ER
What are mutations and point mutations?
Mutations
changes in the genetic material
Point mutations
are chemical changes in just one base pair of a gene
Point mutations (chemical changes in just one base pair of a gene) can be divided into what two general categories?
1. Base-pair substitutions
- A base-pair substitution replaces one nucleotide and its partner with another pair of nucleotides.
- Can result in 3 different outcomes:
- Silent mutations have no effect on the amino acid produced by a codon because of redundancy in the genetic code
- Missense mutations still code for an amino acid but not necessarily the right amino acid.
- Nonsense mutations change an amino acid codon into a stop codon, nearly always leading to a non-functional protein
2. Base-pair insertions or deletions
- Insertions and deletions are additions or losses of nucleotides pairs in a gene.
- These mutations have a disastrous effect on the resulting protein more often than substitutions do.
- Insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation.
Within point mutations, the primer category it is divided into is called “base-pair substituions”. A base-pair substitution replaces one nucleotide and its partner with another pair of nucleotides, there is three outcomes.
What is the first outcome?
Silent mutations
have no effect on the amino acid produced by a codon because of redundancy in the genetic code
Within point mutations, the primer category it is divided into is called “base-pair substituions”. A base-pair substitution replaces one nucleotide and its partner with another pair of nucleotides, there is three outcomes.
What is the second outcome?
Missense mutations
still code for an amino acid but not necessarily the right amino acid.
Within point mutations, the primer category it is divided into is called “base-pair substituions”. A base-pair substitution replaces one nucleotide and its partner with another pair of nucleotides, there is three outcomes.
What is the third outcome?
3. Nonsense mutations
change an amino acid codon into a stop codon, nearly always leading to a non-functional protein
Base-pair insertions or deletions are additions or losses of nucleotides pairs in a gene. Insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation.
What are the three possibilities?
- Frameshift causing immediate nonsense (1 base-pair insertion)
- Frameshift causing extensive missense (1 base-pair deletion)
- No frameshift, but one amino acid missing (3 base-pair deletion)
What happens if a single nucleotide in a DNA template strand changed?
The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein.
What is a Gene? (be specific)
Gene
In summary, a gene can be defined as a region of DNA that can be expressed to produce a final functional product, either a polypeptide or an RNA molecule
