L3 - Gene Expression Flashcards
1
Q
What does DNA polymerase use in DNA replication?
A
Uses parental DNA strand as a template
Ensure DNA is copied into DNA
2
Q
What does RNA polymerase use in transcription?
A
RNA polymerase uses parental DNA strand as a template to make an mRNA transcript
DNA is converted to RNA and RNA expresses the gene that is transcribed
3
Q
What happens in translation?
A
Mature mRNA transcript is converted into amino acids to form a polypeptide chain and subsequently a protein
4
Q
Where does transcription and replication occur?
A
Nucleus
5
Q
Where does translation occur?
A
Cytoplasm
6
Q
What combination of amino acids make up a protein sequence?
A
A combination of 20 amino acids
7
Q
What do amino acids form?
A
Proteins
8
Q
What element forms the basic structure of amino acids?
A
Carbon
9
Q
How do amino acids differ?
A
All different shapes and properties
10
Q
Draw the basic structure of an amino acid
A
11
Q
What is important about the R group on an amino acid?
A
- The R group is variable. It depends on the amino acid and confers the biochemical properties of the amino acid.
- Conveys different properties and structures of the protein
12
Q
What is the simplest amino acid? Why?
A
Glycine
The R group is a hydrogen
13
Q
What is an example of an amino acid which has a highly branched R group?
A
Methionine and lysine
14
Q
What amino acid is used for the start of translation?
A
Methionine
15
Q
Draw the structure of methionine
A
16
Q
Draw the structure of lysine
A
17
Q
Draw the structure of glutamine
A
18
Q
Draw the structure of phenylalanine
A
19
Q
Draw the structure of tyrosine
A
20
Q
Draw the structure of glycine
A
21
Q
Draw the structure of glutamate
A
22
Q
Draw the structure of valine
A
23
Q
Draw the structure of serine
A
24
Q
Why is lysine so important?
A
- Lysine is a highly positively charged amino acid
- Important for condensing the DNA information into a structure within the nucleus that allows it to be compacted and open up when required to be replicated or transcribed
25
What reaction is responsible for the bonding between two amino acids?
Condensation reaction
26
What type of bond is formed between two amino acids?
What molecule is removed?
Peptide bond
Water molecule
27
Draw an equation for the formation of a peptide bond between two amino acids
This forms a dipeptide
28
Where does the peptide bond form between two amino acids?
Between the carboxyl group of one amino acid and the amino group of the adjacent amino acid
29
What is meant by triplet code?
- A triplet is a codon or set of 3 bases
- The genetic code is a triplet code in which 3 nucleotides in RNA specify for 1 amino acid in proteins
- Each triplet on the DNA codes for a specific amino acid in RNA when translated
30
How many bases are needed per amino acid to ensure all 20 amino acids can be translated for?
3 bases coded for 1 amino acid
This combination would potentially give 64 amino acids
31
What is the codon for methionine?
AUG
32
What is important about methionine?
Will be at the start of every translation
The start codon
Going back this means a DNA codon can be identified as ATG
33
What are the 3 stop codons?
UAA, UAG AND UGA
34
Why is the genetic code degenerate?
There is more than one codon per amino acid with the exception of methionine
35
What is the maximum number of codons per amino acid?
6
36
What is partial degeneracy?
- This means the first 2 bases on the codon are the same, but the third is 1 of 3 possible bases
- This means the code translates for different amino acids
e.g. aspartimate and glutamate
37
What is complete degeneracy?
- This means the first two bases on the code and are the same, but the third is one of four possible bases
- All four possibilities code for the same amino acid
e.g. glycine
38
How can the 20 amino acids be grouped?
According to biochemical or structural properties
39
What are hydrophobic amino acids? Give examples
These amino acids repel water
E.g. valine, leucine, isoleucine, methionine and proline
40
What are nucleophilic amino acids? Give examples
Will donate an electron pair to form chemical bonds
E.g. Serine, threonine, cysteine
41
What are basic amino acids? Give examples
The R group is basic at a neutral pH
Contain nitrogen and bind protons to become positive
Are also nucleophilic
e.g. Histidine, lysine, arginine
42
What are acidic amino acids? Give examples
The R group is acidic at a neutral pH
Contain carboxylic acids and lose protons to become negative
E.g. aspartic acid and glutamic acid
43
Give examples of aromatic amino acids
Phenylalanine, tyrosine, and tryptophan
Absorb at 280nm
44
Give examples of amide amino acids
Glutamine and asparagine
45
Give examples of small amino acids
Glycine and alanine
46
Why can mutations be detrimental to the outcome of a protein?
Can lead the loss of function of proteins in mechanism which are essential to cellular functioning
47
Which amino acids can be sourced through diet?
Threonine, phenylalanine, tryptophan, valine, leucine, isoleucine, methionine, histidine, lysine
48
Which amino acids are 'non-essential' and sourced through bodily production?
Cysteine, alanine, glycine, serine, glutamine, asparagine, arginine, aspartic acid, glutamic acid and tyrosine
49
Draw the peptide for Met - Phe - Gly at pH 7
50
What must be identified after a gene has been sequenced?
The open reading frame (ORF)
51
How many possible reading frames are there for a region of DNA?
6 ( 3 in each direction for both strands)
52
Which strand of DNA is used as a template for RNA?
Dependent on which reading frame is open
53
Why are there 6 possible reading frames?
DNA is anti-parallel so there are 3 possible frames per strand
54
Define an open reading frame (ORF)
An open reading frame (ORF) is a run of codons that start with ATG and end with the termination codon TGA, TAA, or TAG
55
What should you never write out when learning an mRNA sequence?
Never right start or stop
Always write the correlating amino acid to codon
E.g. AUG is Met
56
What should be written at the start of an amino acid sequence?
N-Met
Signifies the start of the protein
57
What should be written at the end of an amino acid sequence?
-C
Signifies the end of the protein
58
What does -C mean at the end on an amino acid sequence?
The end of the sequence as the end codon does not encode for an amino acid. This is the carboxyl group of the proceeding amino acid that ends the protein
59
Can you read from the 2nd or 3rd reading frame?
Yes so long as there is a start and end codon
60
What happens if there is more than one potential reading frame?
The open reading frame is the frame which produces the longest peptide
61
What should you not write on the end of the polypeptide?
The 5' and 3' ends
62
What is meant by non-overlapping codons?
Adjacent codons do not overlap so no single base can take part in the formation of more than one codon
Codons are always read in a series of 3
63
What is meant by non-ambiguity?
The genetic code is non-ambiguous because while the same amino acid can be coded for by more than one codon, the same codon shall not code for two or more different amino acids
64
Why is the genetic code universal?
The same sequence of 3 bases encode the same amino acids in all life forms
65
Why does the genetic code have polarity?
Always read in the 5' to 3' direction
