Topic 2 - Protein Synthesis (2.6 to 2.10) Flashcards
(101 cards)
1
Q
What is the genetic code
A
A set of rules that define how the four letter code of DNA is translated into 20 proteinogenic amino acids
1
Q
What is a triplet
A
A sequence of 3 DNA bases that are read together and determine 1 amino acid
2
Q
What is a codon
A
A triplet of bases in mRNA that
are complimentary to anticodons
3
Q
How many amino acids are there
A
There are 22 proteinogenic amino acids but only 20 in our genetic code
4
Q
What is a polypeptide
A
another name for a protein
5
Q
What are proteinogenic amino acids
A
Amino acids that are incorporated biosynthetically into polypeptides
6
Q
How is the genetic code degenerate
A
Most amino acids can be coded for by multiple triplets
7
Q
Why is the genetic code degenerate
A
There are only 20 proteinogenic amino acids in our genetic code but there are 64 possible triplet combinations
8
Q
What is partial degeneracy of triplets
A
Where the first two nucleotides are the same but the third is different
e.g uug and uua code for leucine (both start with uu)
9
Q
What is complete triplet degeneracy
A
Where any base can take the third position and still code for the same amino acid
10
Q
What is a transcription unit
A
Any section of DNA that is used to transcribe a polypeptide
11
Q
What are the 3 sections of a transcription unit
A
The promoter
The structural gene
The terminator
12
Q
What is the purpose of the promoter
A
RNA polymerase binds upstream to the promoter
This allows RNA polymerase to assemble RNA nucleotides.
13
Q
What is the structural gene
A
The part of the gene which is read and transcribed
14
Q
What part of the structural gene is ‘read’ and transcribed
A
The antisense strand (3’ to 5’)
This is because RNA polymerase places from 5’ to 3’ (starting at the 3’ end of the antisense strand and moving towards the 5’ end)
It reads up, and writes down
15
Q
What is the purpose of the terminator
A
It causes RNA polymerase to ‘break off’ which stops RNA nucleotides from being placed / forming phosphodiester bonds
16
Q
What happens during transcription
A
-DNA unzips and unwinds at one gene
-DNA helicase breaks the hydrogen bonds between complimentary nitrogenous bases
-RNA polymerase binds to the promoter region catalysing RNA nucleotides to line up on the template strand (antisense strand)
-Hydrolysis of phosphorylated molecules such as ATP occurs and the energy is used to form phosphodiester bonds between adjacent nucleotides
-RNA polymerase reaches the terminator region and transcription ends leaving a single strand of mRNA
17
Q
What does RNA polymerase do
A
It adds complimentary RNA nucleotides to the template strand (reads up writes down) and causes phosphodiester bonds to form between adjacent nucleotides
18
Q
**How are RNA nucleotides activated ** (check w sir)
A
Through phosphorylation (adding phosphate to the nucleotide)
19
Q
What is the sense strand (transcription)
A
This is the strand that is not used in transcription
5’ to 3’
The mRNA formed in transcription is a copy of the sense (or coding) strand
20
Q
What is formed in transcription
A
Pre-mRNA
21
Q
How is pre-mRNA made into mature-mRNA
A
The introns are removed through splicing and the exons are rearranged into any order
22
Q
Why can one gene code for multiple polypeptides
A
As the exons can be rearranged into any order
23
Q
What are Introns
A
Regions in mRNA that do not code for amino acids
24
What are Exons
Regions that code for amino acids
25
Where are the ribosomes located and what happens at them
In the cytoplasm
Translation occurs
26
How does mature-mRNA move to the ribosomes
It exits the nucleus via small nuclear pores and moves into the cytoplasm
It then binds to the small ribosomal subunit
27
What are ribosomes made of
Ribosomes are made from proteins
.
Two subunits
The small subunit (size 20s) binds to the mRNA and reads it
The large subunit (size 40s) contains 3 sites (P, A, E) which tRNA binds to. It also joins the amino acids to form a polypeptide
Total size in eukaryotes = 80s
28
What direction does the small ribosomal subunit read mRNA
In a 5' to 3' direction
29
What amino acid is coded for at the start codon of all eukaryotes
Methionine
30
What happens during translation
-The small ribosomal subunit attached to the mRNA and begins scanning it (until reaching the start codon)
-The tRNA carrying methionine (the start codon) forms a hydrogen bond with the complimentary mRNA codon at the p-site
-The large subunit joins the small subunit at the start codon (translation elongation can now occur)
-As tRNA occupies the p-site the 2nd tRNA molecule and its amino acid bind to the A-site
-A peptide bond forms between the amino acids and the polypeptide chain is transferred to the amino acid in the A site
-The tRNA molecule no longer holding an amino acid moves into the e-site, and the tRNA in the A-site moves into the P-site
-The ribosome moved down one codon in the 5' to 3' direction (towards the 3' end)
-tRNA in the E-site leaves and a new tRNA moves into the A-site
-This process is repeated and peptide bonds form between the amino acids
-the process ends when the A-site becomes occupied by a stop codon
The amino acid folds into a complex 3D polypeptide
31
What happens when the ribosomal a-site is occupied by a stop codon
A release factor protein is released which causes the ribosomal subunits to dissociate.
This releases the amino acid chain
32
What is the structure of a ribosome (subunits)
Small subunit
Large subunit
E P A
The tRNA complimentary to the mRNA start codon binds to the P site
The rest of the tRNA initially binds to the A-site
33
What two groups do amino acids always contain
A carboxylic acid group (COOH), and an amine group (NH2)
R group
34
What does amphoteric mean
They can both accept and donate hydrogen ions
35
Why are amino acids amphoteric
They have both an acidic carboxyl group and a basic amine group
36
What does the amino acids 'R' Group determine
It determines how the amino acids interact with each other
This determines the secondary and tertiary structure of the protein
37
Which amino acid is the only one to contain sulphur
Cystine
38
Why is cystine (the amino acid) important
It can form a di-sulphide bridge (bond) with other cystines
This is the strongest bond in a protein
The more di-sulphide bridges a protein has the harder it is to denature
39
What is a dipeptide
The molecule formed when two amino acids react together
40
What type of reaction creates a dipeptide
A condensation reaction
41
What is a peptide bond
The bond formed when two amino acids react with each other.
The bond occurs between the carboxyl group of 1 amino acid and the amine group of another (OH from the carboxyl is removed and 1H from the amine is removed to make water)
O H
|| |
C - N
(Between two amino acids)
42
What is a carboxyl group
COOH
43
What is an amine group
NH2
44
What reaction breaks peptide bonds
Hydrolysis
45
What is a polypeptide
A chain of 3 or more amino acids
46
What are the 4 structures of a protein
Primary Structure
Secondary structure
Tertiary structure
Quaternary structure
47
What is the primary structure of a protein
The specific sequence of an amino acids that are held together by peptide bonds
(forming a polypeptide)
48
What is / happens in the secondary structure of a protein
This structure is where the folding of the polypeptide begins
The way the polypeptide folds (alpha helix or beat-pleated sheet) depends on where hydrogen bonds form (between peptide bonds)
49
What is an alpha helix and when is it formed
It is a single stranded helix
It forms in the secondary structure of a protein when hydrogen bonds form between every 4th peptide bond
50
What is a beta-pleated sheet and when is it formed
A folded polypeptide chain, resulting in two (or more) parallel strands
Hydrogen bonds form between opposite peptide bonds (in the secondary structure)
51
What is the tertiary structure and what happens in it
It is the third structure of a protein where folding continues
This folding / bending depends on interactions between the R groups and the attraction of different amino acids
The different bonds (e.g hydrogen , covalent, disulphide, ionic) determine how the amino acid folds
52
What is the quaternary structure of a protein
In this structure multiple polypeptide chains join together.
These chains are kept together by different bonds, such as hydrogen bonds or disulphide bonds
53
Which structure do some proteins not have
Not all proteins have the quaternary structure
54
What is the structure of an RNA nucleotide
A nucleotide containing Ribose sugar, a phosphate group and a nitrogenous base
55
What nitrogenous bases are present in RNA
Adenine
Uracil (replaces thymine)
Cytosine
Guanine
56
What is tRNA and where does it come from
Transfer RNA is a carrier of amino acids that is complementary to a codon of mRNA
It comes from the cytoplasm
57
What is the structure of tRNA
tRNA is a monomer made of RNA nucleotides.
It has an anti codon which is complimentary to mRNAs codons
It also has a specific amino acid attachment site, that allows it to form ester bonds with a specific amino acid
58
What are the differences in tRNA and mRNA structure
mRNA has a linear structure while tRNA has a 3d folded structure
mRNA is made of more nucleotides than tRNA
tRNA has a site for an amino acid
mRNA has no hydrogen bonds in its structure but tRNA does
59
Name a protein with a quaternary structure
Hemoglobin
60
What are globular proteins
Spherically folded proteins that are soluble in water
61
Why are globular proteins soluble in water
They have hydrophilic R groups on the surface and these groups interact with the water
Most of their hydrophobic groups are found on the inside
62
What type of protein is Haemoglobin
It is a globular protein
It has a quaternary structure, consisting of 4 subunits.
2 alpha subunits
2 beta subunits
63
Why can oxygen bind to heamoglobin
Each hemoglobin subunit contains 1 haem group
This group contains a singular Fe 2+ ion in its center that 1 oxygen can bind to
This means that each heamoglobin molecule can carry 4 oxygen
64
Why are enzymes and hormones globular proteins
Enzymes and hormones are transported around the body in transport mediums
To be carried in a transport medium they must be soluble
Globular proteins are soluble
65
What are fibrous proteins
Insoluble proteins with a long rope-like structure
They are often used for structural roles in organisms (e.g collagen and keratin)
66
Why are fibrous proteins insoluble
They have a high number of hydrophobic R groups on the surface of the protein.
67
What is the structure of collagen
Collagen is made of 3 polypeptide chains wound into a triple-helix
Every 3rd amino acid is glycine, so the strands of the triple helix are held tightly by hydrogen bonds.
Covalent bonds (cross links)
68
What is glycine
glycine is the amino acid with the smallest R group - only 1 H atom
This means it can for strong hydrogen bonds with itself - and keep a structure tight
69
What are enzymes
Enzymes are biological catalysts
They lower the activation energy of reactions and are not used up
70
what type of proteins are enzymes
They are globular proteins
This means they are soluble in water and can be transported in blood
71
Why are enzymes needed
Certain reactions in the body have a higher activation energy than energy that is available
If the body temperature was increased to supply the kinetic for a reaction energy **lipids and proteins** in your cell would denature
Using enzymes lowers the activation without increasing the body temperature
72
Who is Herman Emil Fischer
The man who came up with the lock and Key hypothesis
73
What is the Lock and key Hypothesis
A theory that states
Only enzymes that have and active side with a complimentary shape to a substrate, can form an enzyme-substrate complex
74
How many amino acids is the active site made of
6 to 10 amino acids
75
What deterimes the shape of an enzymes active side
The tertiary structure of a protein
Amino acid R-groups interact with each other and fold into complex 3D shapes. This folding determines the active sites shape
76
What deterimes which enzymes can bind to which substrates
The shape of the active site and the specific amino acid R groups in the active site
77
What two factors can cause enzymes to denature
High temperatures (above their optimal temperature)
A change in pH away from their optimal pH
78
What happens when an enzyme denatures
Bonds in the tertiary structure are broken so:
Its active site changes shape and is no longer complementary to a substrate
This process is irreversible
79
What is the Induced fit model
A theory that:
When in the presence of a substrate, there are subtle change sin the amino acid r-groups, causing a precisce conformation of the enxyme that excatly fits the substrate
80
What bonds hold the substrate to the enzyme
Weak non-covalent bonds (such as hydrogen bonds and and ionic bonds
81
what happens when the substrate colloded with and binds to the enzyme
After it form an ESC the substrate is converted into a product and an enzyme product complex is formed (EPC)
82
Why can the product be released (from an enzyme)
The product is a slightly different shape to the substrate, so the induced fit is undone and the product is released (as is not complementary)
83
What happens when the enzymes product is released
The enzyme returns to its original state and binds to a new substrate
84
What are catabolic enzymes
enzymes that break down substrates
85
What are anabolic enzymes
Enzymes that build up substrates
86
What is a conjugate protein
A protein containing at least one prosthetic group
87
How does increasing only substrate concentration affect the rate of reaction
As there are more substrate molecules in a given volume.
More enzymes and substeates collide so more ESCs can form
This means more substrate is converted into product - so the rate of reaction increases
Eventually all the active sites (of enzymes) are occupied by substrate
No new ESCs form, so the Rate of Reaction stays the same
88
What factors affect the rate of reaction (enzymes)
pH
Temperature
Substrate concentration
Enzyme concentration
89
What is proteolysis
Process where old / denatured enzymes are broken down into amino acids
90
How is enzyme concentration naturally increased
By increasing the rate of transcription
91
How is the concentration of enzymes naturally decreased
By increasing the rate of enzyme degradation (proteolysis)
92
Why are enzymes degraded
If they have an abnormal shape
If they are old
93
How does increasing enzyme concentration affect the rate of reaction
It causes it to increase
Enzymes decrease activation energy
There are more enzymes so more active sites for substrate to bind to
More ESCs are formed, so more product is released
Eventually the increase stops
The substrate molecules are all occupied in the active site or have been converted into products
94
How does the induced fit model explain activation energy
The enzyme puts a strain on the bonds in the substrate
This makes it easier for the substrate to break and form new bonds
95
What is a competitive inhibitor (enzymes)
A molecule with the same shape as a substrate.
The enzyme can bind to the inhibitor instead of the substrate, reducing the rate of reaction
96
What is a non-competitive inhibitor
An inhibitor which binds to the allosteric site of an enzyme
It binds at the same time as the substrate and causes the active site to denature
This stops the reaction from occuring
97
What happens when increasing substrate in the presence of competitive inhibitors
The effectiveness of the inhibitors will reduce as they have to compete with more substrate
98
What does it mean if the active sites are saturated
All the active sites are occupied
99
Do competitive inhibitors completely stop a reaction
No
They only have a temporary effect, and substrate may still bind instead of the inhibitor
100
How does pH have an effect on the rate of reaction (enzymes)
All enzyme reactions have an optimal charge
Deviations in pH cause the concentration of H+ ions to change.
This can cause the rate of collisions to decrease slightly
Extreme pH changes can cause hydrogen bonds to break
