Topic 2 - Protein Synthesis (2.6 to 2.10) Flashcards
What is the genetic code
A set of rules that define how the four letter code of DNA is translated into 20 proteinogenic amino acids
What is a triplet
A sequence of 3 DNA bases that are read together and determine 1 amino acid
What is a codon
A triplet of bases in mRNA that
are complimentary to anticodons
How many amino acids are there
There are 22 proteinogenic amino acids but only 20 in our genetic code
What is a polypeptide
another name for a protein
What are proteinogenic amino acids
Amino acids that are incorporated biosynthetically into polypeptides
How is the genetic code degenerate
Most amino acids can be coded for by multiple triplets
Why is the genetic code degenerate
There are only 20 proteinogenic amino acids in our genetic code but there are 64 possible triplet combinations
What is partial degeneracy of triplets
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)
What is complete triplet degeneracy
Where any base can take the third position and still code for the same amino acid
What is a transcription unit
Any section of DNA that is used to transcribe a polypeptide
What are the 3 sections of a transcription unit
The promoter
The structural gene
The terminator
What is the purpose of the promoter
RNA polymerase binds upstream to the promoter
This allows RNA polymerase to assemble RNA nucleotides.
What is the structural gene
The part of the gene which is read and transcribed
What part of the structural gene is ‘read’ and transcribed
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)
What is the purpose of the terminator
It causes RNA polymerase to ‘break off’ which stops RNA nucleotides from being placed / forming phosphodiester bonds
What happens during transcription
-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
What does RNA polymerase do
It adds complimentary RNA nucleotides to the template strand (reads up writes down) and causes phosphodiester bonds to form between adjacent nucleotides
**How are RNA nucleotides activated ** (check w sir)
Through phosphorylation (adding phosphate to the nucleotide)
What is the sense strand (transcription)
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
What is formed in transcription
Pre-mRNA
How is pre-mRNA made into mature-mRNA
The introns are removed through splicing and the exons are rearranged into any order
Why can one gene code for multiple polypeptides
As the exons can be rearranged into any order
What are Introns
Regions in mRNA that do not code for amino acids
What are Exons
Regions that code for amino acids
Where are the ribosomes located and what happens at them
In the cytoplasm
Translation occurs
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
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
What direction does the small ribosomal subunit read mRNA
In a 5’ to 3’ direction
What amino acid is coded for at the start codon of all eukaryotes
Methionine
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
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
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
What two groups do amino acids always contain
A carboxylic acid group (COOH), and an amine group (NH2)
R group
What does amphoteric mean
They can both accept and donate hydrogen ions
Why are amino acids amphoteric
They have both an acidic carboxyl group and a basic amine group
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
Which amino acid is the only one to contain sulphur
Cystine
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
What is a dipeptide
The molecule formed when two amino acids react together
What type of reaction creates a dipeptide
A condensation reaction
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)
What is a carboxyl group
COOH
What is an amine group
NH2
What reaction breaks peptide bonds
Hydrolysis
What is a polypeptide
A chain of 3 or more amino acids
What are the 4 structures of a protein
Primary Structure
Secondary structure
Tertiary structure
Quaternary structure
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)
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)
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
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
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
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
Which structure do some proteins not have
Not all proteins have the quaternary structure
What is the structure of an RNA nucleotide
A nucleotide containing Ribose sugar, a phosphate group and a nitrogenous base
What nitrogenous bases are present in RNA
Adenine
Uracil (replaces thymine)
Cytosine
Guanine
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
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
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
Name a protein with a quaternary structure
Hemoglobin
What are globular proteins
Spherically folded proteins that are soluble in water
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
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
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
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
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)
Why are fibrous proteins insoluble
They have a high number of hydrophobic R groups on the surface of the protein.
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)
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
What are enzymes
Enzymes are biological catalysts
They lower the activation energy of reactions and are not used up
what type of proteins are enzymes
They are globular proteins
This means they are soluble in water and can be transported in blood
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
Who is Herman Emil Fischer
The man who came up with the lock and Key hypothesis
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
How many amino acids is the active site made of
6 to 10 amino acids
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
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
What two factors can cause enzymes to denature
High temperatures (above their optimal temperature)
A change in pH away from their optimal pH
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
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
What bonds hold the substrate to the enzyme
Weak non-covalent bonds (such as hydrogen bonds and and ionic bonds
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)
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)
What happens when the enzymes product is released
The enzyme returns to its original state and binds to a new substrate
What are catabolic enzymes
enzymes that break down substrates
What are anabolic enzymes
Enzymes that build up substrates
What is a conjugate protein
A protein containing at least one prosthetic group
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
What factors affect the rate of reaction (enzymes)
pH
Temperature
Substrate concentration
Enzyme concentration
What is proteolysis
Process where old / denatured enzymes are broken down into amino acids
How is enzyme concentration naturally increased
By increasing the rate of transcription
How is the concentration of enzymes naturally decreased
By increasing the rate of enzyme degradation (proteolysis)
Why are enzymes degraded
If they have an abnormal shape
If they are old
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
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
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
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
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
What does it mean if the active sites are saturated
All the active sites are occupied
Do competitive inhibitors completely stop a reaction
No
They only have a temporary effect, and substrate may still bind instead of the inhibitor
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
