17 Gene to Protein Flashcards
“___ are the links between genotype and phenotype”
Proteins
What does ’gene expression’ refer to?
The process by which DNA directs the synthesis of specific proteins.
What does ’alkaptonuria’ refer to?
A hereditary condition in which the body lacks an enzyme to break down ‘alkapton’ causing it the be present in urine, which appears black.
What does the ’one gene, one enzyme hypothesis’ refer to?
The idea that every gene codes for and thus leads to a phenotype by leading to the formation of an enzyme.
Note: this theory is disproven
What is did the ‘one gene, one enzyme hypothesis’ get replaced with?
The ‘one gene, one protein’ as some genes code for proteins other than enzymes
What does ’complete growth medium’ refer to?
A growth medium which includes salts, glucose and vitamins align with all 20 amino acids
What are the basic steps of the conversion of DNA to proteins?
Transcription, ‘RNA processing’ and Translation
What does ‘mRNA’ stand for?
Messenger RNA
What molecule does transcription form?
‘pre-mRNA’
What can pre-mRNA be called?
The ‘primary transcript’
What does ’primary transcript’ refer to?
The RNA formed directly by transcription i.e. the unprocessed pre mRNA
What are the bases of DNA?
A, C, T and G
What are the bases of RNA?
A, C, U and G
What is ‘U’ in terms of the RNA base?
Uracil, which replaces thymine
What is the DNA base that is replaced by uracil?
Thymine
What is the basic principle behind ’transcription’?
The information in the DNA is transferred to messenger RNA by the formation of an RNA strand that is complementary to the template strand.
Which strand of DNA is used as the ‘template strand’?
For any given gene, the same strand
is used as the template every time the gene
is transcribed.
For other genes on the same DNA molecule, however, the opposite strand may be the one that always functions as the template.
What is the basic principle behind ’translation’?
The information encoded in the mRNA is translated into a sequence of amino acids and thus a polypeptide
Where does ’transcription’ occur?
In a prokaryote in the cytoplasm.
In a eukaryote it occurs in the nucleus
Where does ‘RNA processing occur’?
Prokaryote: DOES NOT OCCUR
Eukaryote: nucleus
Where does ’translation’ occur?
Prokaryote/Eukaryote: cytoplasm (in ribosomes)
What does ’codon’ refer to?
A nucleotide triplet which codes for a specific amino acid etc.
What are the basic types of ‘codon’?
’Start codon’, ’Stop codon’ and those that code for amino acids.
What are the sequences of the ’start codons’?
AUG which codes for the amino acid ‘Met’ or acts as a start codon.
What are the sequences of the ’stop codons’?
UAA, UAG and UGA
What does ’reading frame’ refer to?
The frame of reference with with the triplet codons are interpreted.
For example _ACT_UAG_GCT
A point mutation would shift the farm of reference and thus lead to missense/nonsense
What are the stages of ’transcription’?
‘Initiation’,’elongation’ and ’termination’
In what direction is RNA formed an thus which direction does RNA polymerase move?
RNA is formed 5’ to 3’
Therefore the RNA polymerase must move 3’ to 5’ down the template strand so that the mRNA is antiparallel.
What is an important consideration when converting a DNA sequence to a series of amino acids?
DNA is typically read 5’ to 3’. However the RNA polymerase must form the mRNA so that it produced 5’ to 3’.
To ensure that the mRNA is antiparallel to the DNA the RNA polymerase must move down the template strand in a 3’ to 5’ direction.
Therefore if asked to translate a series of DNA to amino acids one must also read it 3’ to 5’
Also remember that the RNA formed is complementary (not identical) to the DNA. Thus ACT on the DNA would become UGC
What does ’triple code’ refer to?
The fact that each codon is a triplet of 3 nucleotides
Based on the fact that 3 nucleotides code for one amino acid, what property does DNA/RNA have?
It is a ’triplet code’
What happens during the ‘initiation’ stage of transcription?
RNA polymerase binds to the ‘promoter’, the DNA strands unwind, and the polymerase initiates RNA synthesis at the start point on the template strand.
Note that no primer is formed
Is a primer needed during translation?
Nope
What happens during the ‘elongation’ stage of transcription?
The polymerase moves downstream (3’ to 5’), unwinding the DNA and elongating the RNA transcript 5′ → 3′. In the wake of transcription, the DNA strands re-form a double helix.
What is the ’termination’ phase of transcription?
The RNA transcript is released, and the polymerase detaches from the DNA.
Transcription is complete
What does ’downstream’ refer to in the context of genetics?
In transcription and DNA replication it refers to the direction the RNA/DNA polymerase moves.
Therefore ‘downstream is 3’ to 5’
How is transcription guided?
The RNA polymerase binds to a special region on the template strand called the ‘promoter’
It then moves ‘downstream’ through the ’transcription unit’ which is the length of DNA which is actually transcribed
In prokaryotic transcription is reaches a region called the ’terminator’ which instructs it to stop. In eukaryotes termination is signalled differently.
What are the specific RNA polymerases used in transcription?
In prokaryotes there is only one generic polymerase that is used.
Eukaryotes have at least three types of RNA polymerase in their nuclei. The one used for mRNA synthesis is called RNA polymerase II. The other RNA polymerases transcribe RNA molecules that are not translated into protein.
What specifically happens during the ‘initiation phase’ of transcription?
The promoter of a gene includes the transcription start point (the nucleotide where RNA synthesis actually begins)
RNA polymerase binds in a precise location and orientation on the promoter to determine where transcription starts and which DNA strand is used as the template strand.
In bacteria, the RNA polymerase itself specifically recognizes and binds to the promoter. In eukaryotes, a collection of proteins called ‘transcription factors’ mediate the binding of RNA polymerase and the initiation of transcription. The complex of transcription factors and RNA polymerase II bound to the promoter is called a transcription initiation complex.
Once the appropriate transcription factors are firmly attached to the promoter DNA and the polymerase is bound in the correct orientation, RNA nucleotides the enzyme unwinds the two DNA strands and starts transcribing the template strand.
What does ’promotor’ refer to?
The region of DNA that the RNA polymerase binds to. This initiates transcription and is found in eukaryotes and prokaryotes
What does ’terminator’ refer to?
The DNA sequence found in bacteria which acts as the signal to stop transcription
What does ’transcription unit’ refer to?
The actual region of the template strand which is transcribed
What is the DNA sequence from which transcription is initiated called?
The ‘promotor’
What is the region of DNA which in bacteria signals the termination of transcription called?
The ’terminator’
What is the actual region of the template strand which is transcribed called?
The ’transcription unit’
What is an example of a specific promoter region?
The ’TATA’ box which is used in many eukaryotic genes as the promotor region and consists of the nucleotide sequence ‘TATA’ i.e. thymine, adenine etc.
How is the binding of the RNA polymerase to the promoter mediated?
In bacteria the RNA polymerase recognises and binds directly to the promoter region.
In eukaryotes ’transcription factors’ bind to the promotor region and in turn bind to the polymerase. This complex of a polymerase and its ’transcription factors’ is called a ’transcription initiation complex’
What does ’transcription factor’ refer to?
The proteins which in eukaryotes bind to the promoter region and in turn the polymerase to mediate the attached of the polymerase to the promotor
What are those things which bind to the promoter region so that the polymerase can be attached?
’Transcription factors’
What does ’transcription initiation complex’ refer to?
A polymerase and its bound transcription factors.
What is a polymerase and its bound transcription factors called?
A ’transcription initiation complex’
What is typical transcription rate in eukaryotes?
Around 40 nucleotides per second
How can the transcription rate be increased?
A single gene can be transcribed simultaneously by several molecules of RNA polymerase following each other, with each forming an individual RNA strand
The congregation of many polymerase molecules simultaneously transcribing a single gene increases the amount of mRNA transcribed from it, which helps the cell make the encoded protein in large amounts.
Therefore it is particularly useful in secretory cells.
How is transcription terminated?
In bacteria, transcription proceeds through a terminator sequence in the DNA. The transcribed terminator (an RNA sequence) functions as the termination signal causing the polymerase to detach from the DNA and release the transcript, which requires no further modification before translation.
In eukaryotes, RNA polymerase II transcribes a sequence on the DNA called the ‘polyadenylation signal sequence’, which codes for a polyadenylation signal (AAUAAA) in the pre-mRNA.
This triggers proteins to cut the RNA strand free form the polymerase and thus transcription is complete
How does RNA transcription termination work in eukaryotes?
The polymerase transcribes a region called the ‘polyadenylation signal sequence’ which codes for the ‘polyadenation signal’ (AAUAAA) which terminates transcription
What does ’polyadenation signal sequence’ refer to?
The region of DNA which codes for the ‘polyadenation signal’ (AAUAAA) which terminates transcription
What does ’polyadenation’ refer to?
AAUAAA which when transcribed stops transcription.
What is the first step of RNA processing?
Each end of the RNA molecule is modified in a particular way.
At the 5’ end a ‘5’ cap’ is added which consists of a modified form of a guanine (G) nucleotide.
At the 3’ end an enzyme adds 50-250 adenine nucleotides to form a ‘poly-A tail’
What does ’5’ cap’ refer to?
The modified guanine nucleotide added to the 5’ (start) of the pre-mRNA
What does ’poly-A tail’ refer to?
The long sequence of adenine nucleotides added to the end of the pre-mRNA
What is the function of the 5’ cap and the poly-A tail?
They seem to facilitate the export of the mature mRNA from the nucleus.
They help protect the mRNA from degradation by hydrolytic enzymes.
They help ribosomes attach to the 5’ end of the mRNA once the mRNA reaches the cytoplasm.
What regions does a pre-mRNA molecule after the 5’ cap and poly-A tail have been added?
In order from 5’ to 3’:
5’ Cap 5’ UTR Start codon ‘Protein coding segment’ Stop codon 3’ UTR which includes the ‘polyadenylation signal’ Poly-A tail
(UTR = untranslated region)
What does ’protein coding segment’ refer to?
The actual region of mRNA which will become proteins although it does included introns which will be spliced out.
After the addition of the 5’ cap and poly-A tail, what happens in RNA processing?
‘RNA slicing’
How long is a typical protein?
400 amino acids long
What does ’UTR’ refer to?
Untranslated region
Put simply, what happens during RNA splicing?
The non-coding ‘intron’ segments are cut out to leave a continuous stream of coding ‘exons’
This remaining block of ‘exons’ is called the ‘coding segment’
What does ’exon’ refer to?
The region of the pre-mRNA that is left in after splicing and thus remains to code for a protein.
What does ’intron’ refer to?
The region of pre-mRNA that is spliced out of the pre-mRNA during RNA splicing
What is the region of RNA which is left in after splicing called?
The ‘exon’
What is the region of RNA which is cut out during splicing called?
Intron
What is the continuous coding sequence formed after RNA processing called?
The ‘coding segment’
