Proteins & Enzymes Flashcards
What singular molecule makes up the primary structure of a protein? What joins these molecules together?
Amino acids are the basic unit of the primary structure of a protein, held together by peptide (covalent) bonds
How does the R group of an amino acid contribute to a proteins secondary structure?
It doesn’t
What is the difference between a nucleotide and a nucleoside?
A nucleotide is a deoxyribose sugar with an attached phosphate group, while a nucleoside is a deoxyribose sugar without one
Draw the general chemical structure of an amino acid.
H
|
NH2--C--COOH
|
RHow are amino acids classified?
They are classified by the properties of their R groups
What type of reaction forms the peptide bond used to join amino acids together?
A hydrolysis reaction, involving the removal of a water molecule
Between which molecules are the hydrogen bonds formed in the secondary structure of an alpha helix?
The carbonyl- oxygen (C=O) and the amyl- hydrogen (N-H)
The peptide bonds in an amino acids primary sequence are rigid and planar. What do these 2 terms mean?
The peptide bonds in an amino acids primary structure are unable to rotate and all lie in the same plane
Explain the difference between the cis and trans conformation. Which conformation do peptide bonds exhibit?
The trans conformation involves the central carbon atom of the amino acids being on opposite sides of the peptide bond, while the cis conformation involves the central carbons being on the same side - this would cause steric clashes, and so proteins adopt the trans conformation
What is the isoelectric point of a protein?
The pH at which the protein has no overall net charge
How many amino acids are there per turn in an alpha helix?
3.6 amino acids
What is stronger: a parallel or anti-parallel Beta sheet?
An anti-parallel beta sheet
How would you define the tertiary structure of a protein?
The way in which the secondary structure of a polypeptide chain is folded or arranged into a 3-dimensional figure
What distance are amino acids linked by hydrogen bonds?
4 amino acids away
How many amino acids are there per turn in an alpha helix?
3.6 amino acids
What is stronger: a parallel or anti-parallel Beta sheet?
An anti-parallel beta sheet
How would you define the tertiary structure of a protein?
The way in which the secondary structure of a polypeptide chain is folded or arranged into a 3-dimensional figure
What distance are amino acids linked by hydrogen bonds?
4 amino acids away
What type of bond is a peptide bond?
A covalent bond
Amino acids contain a central carbon atom? What bond joins the amino group, carboxyl group, R group, and hydrogen atom?
Covalent bonds
What is an amino acid residue?
An amino acid residue is what remains after an amino acid has been incorporated into a polypeptide sequence, defined by its R group
What does a low pH suggest about the amount of H+ ions in solution?
There is a relatively high amount
What peptide bond has partial double-bond characteristics? Why is this?
A C-N bond - due to its electron resonance
Why don’t peptide bonds exhibit cis- formation?
Due to steric clashes this configuration involves
Is the isoelectric point of acidic proteins greater or less than 7? What can you say about the charges of the amino acids of an acidic protein?
The isoelectric point of an acidic protein is less than 7 - the amino acids within its structure are mainly negatively charged - these amino acid tend to lose protons, giving them a negative charge, and making their external environment more H+ rich in the process
Is the isoelectric point of basic proteins greater or less than 7? What can you say about the charges of the amino acids of a basic protein? Why?
The isoelectric point of a basic protein is greater than 7 - the amino acids within its structure are mainly positively charged - they bind protons, giving the amino acid a positive charge, and meaning there are less protons in the external environment so it is less acidic (more basic)
Suggest 2 amino acid residues that are strong helix formers. Why is this?
Alanine and leucine - this is because they are small and hydrophobic
What is a Beta sheet?
A side-by-side arrangement of beta-strands
Describe the structures of fibrous and globular proteins.
- fibrous proteins are composed of long strands/sheets with a single type of recurring secondary structure
- globular proteins have a compact structure and are composed of several types of secondary structure
What type of protein is collagen? Describe its repeating sequence?
Collagen is a fibrous protein, and is characterised by a glycine-X-Y repeating sequence
What bond joins collagen molecules into its triple helical arrangement? What type of bond is then responsible for cross-linkage of collagen to form collagen fibrils?
Hydrogen bonds join individual collagen molecules to form the collagen triple helix - covalent bonds then cause cross-linkage between collagen molecules to form collagen fibrils
Describe 2 tertiary structures commonly found in globular proteins.
Domains - part of a polypeptide chain that folds into a specific shape - often has a specific functional role
Motif - folding patterns containing 1 or more element(s) of secondary structure
What residues do disulphide bonds form between?
They form between cysteine residues
Between what specific molecules are hydrogen bonds formed between?
An electronegative atom and a hydrogen atom bound to another electronegative atom
What type of bonds form between charged atoms?
Electrostatic interactions
How do van der Vaal’s forces form?
They form due to dipole-dipole interactions
What conformation is used to describe a normally folded, fully-functioning protein?
It’s native conformation
What word is used to describe alteration of a proteins structure from its native state?
Denaturation
What specifically does denature get a protein mean?
Breaking or disturbing the forces that hold the protein together (e.g. hydrogen bonds or van der Vaal’s forces) in its native state, via pH or heat for example
Where is all the information needed for the folding of a protein contained?
In its primary structure
What is protein folding in initially driven by?
It’s most stable conformation
What is an amyloid fibre?
A misfiled, insoluble protein that is normally soluble
What is the activation energy?
The minimum amount of energy needed in a reaction for substrate/reactants to begin a chemical reaction
List and describe 2 ways in which you can increase the rate of a reaction.
- increase concentration of substrate - increases the chance of a molecular collision
- increase temperature - increases the number of molecules with the activation energy
What is the transition state?
A high energy intermediate with the highest energy potential along the reaction co-ordinate
How do enzymes affect the rate of a reaction?
They reduce the activation energy of the substrates required to instigate a reaction
What is the active site of an enzyme?
The site where substrate binds and where chemical reactions occur
What term is used to describe the shape/structure of an active site and the shape/structure of its ligand?
Complementary
What does the ‘induced fit’ theory suggest?
That an enzymes active site and its ligand are only truly complementary after the ligand has bound the enzyme
What structures bind substrates to their active site? Why these structures?
Non-covalent bonds - these ensure they are not as strongly bound so the enzyme and substrate can eventually dissociate
What is the Vo?
The initial velocity of a reaction
What is the Vmax?
The maximal rate of reaction where all enzyme active sites are saturated with substrate
What is Km?
The substrate concentration that gives exactly half the maximal velocity (Vmax) - it gives an indication of a enzymes affinity to its substrate
How can Vo (the initial velocity of a reaction) be calculated? What is this equation known as?
Vmax / km + (substrate) - the Michaelis-Menten equation
What does the Michaelis-Menten Model propose?
The Michaelis-Menten model proposes that a specific complex forms between the enzyme and substrate, and is a necessary intermediate in the reaction
What does a high Km suggest about an enzyme?
The enzyme has a low affinity for it’s substrate
What is the rate of an enzyme catalysed reaction proportional to?
The concentration of the enzyme
What plot can the Michaelis-Menten equation be re-arranged to show? What type of plot is this?
The Lineweaver-Burk Plot - this is a linear plot
What 3 ways can an enzyme inhibitor block an enzyme?
- irreversible
- reversible (competitive)
- reversible (non-competitive)
How does an irreversible enzyme inhibitor function?
They bind very tightly to the enzyme via covalent bonds
How does the binding of competitive and non-competitive reversible enzymes differ?
Competitive inhibitors bind the enzyme at its active site, while non-competitive inhibitors bind at allosteric sites other than the active site
How does a competitive enzyme affect a Lineweaver-Burk Plot? How does a non-competitive enzyme affect a Lineweaver-Burk Plot?
A competitive enzyme will move the plot above the normal plot about the Y-axis - a non-competitive enzyme will move the plot above the normal plot about the X-axis
How does a competitive inhibitor affect the Vmax and Km?
The Km increases - the Vmax is unaffected
How does a non-competitive inhibitor affect Vmax and Km?
It lowers the Vmax - Km is unaffected
How do enzymes catalyse a reaction?
They lower the activation energy required for the reaction to occur
What are the 2 overall ways you can regulate a proteins activity?
- change gene expression of the protein
- directly affect an enzyme (either its structure or substrate concentration etc)
What is an isoenzyme? Give an example.
An isoenzyme is an enzyme that carries out the same reaction as another, only it has different kinetic properties (e.g. different Km) - an example includes glucokinase and hexokinase
What is product inhibition?
Product inhibition involves the accumulation of the product of a reaction, where the product eventually begins to inhibit the rate of reaction
What type of relationship to allosteric enzymes show between their rate of reaction and substrate concentration?
A sigmoidal relationship
What are the 2 states that an enzyme can exist in?
A high affinity R state
A low affinity T state
What is the difference between an allosteric activator and an allosteric inhibitor?
An allosteric activator increases the proportion of enzyme is the high affinity R state, while an allosteric inhibitor decreases the proportion of enzyme in the low affinity T state
Where do allosteric activators and inhibitors bind?
They bind at allosteric sites, seperate to the active site of the enzyme
What is an allosteric enzyme?
Allosteric enzymes are enzymes that can change their conformation upon binding of an effector (allosteric activator/inhibitor) which results in a change in binding affinity at the enzymes active site
What is the role of phosphofructokinase? What molecules can act as allosteric activators/inhibitors?
Phosphofructokinase controls the rate of glycolysis -
- allosteric activators include AMP & fructose 2,6 bisphosphate
- allosteric inhibitors include ATP, citrate, & H+ (hydrogen)
What type of bonding is phosphorylation?
Covalent bonding
What enzyme catalyses phosphorylation? What is its method of action?
Protein kinases catalyse phosphorylation - these transfer the terminal phosphate from ATP and add it to the -OH group of a serine, tyrosine, or threonine residue
What enzymes are responsible for reversing phosphorylation?
Protein phosphatases reverse the effects of protein kinases, by catalysing the hydrolytic removal of phosphoryl groups from proteins
What makes protein phosphorylation so effective?
The rate of phosphorylation/dephosphorylation can be easily adjusted - phosphorylation can also allow for amplification effects, which amplify the effects of an initial signal by several orders of magnitude
How may phosphorylation affect a proteins structure?
Phosphorylation adds 2 negative charges, which can have huge effects on protein structure and properties - phosphoryl groups can also make hydrogen bonds, again changing a proteins properties
Glycogen synthesis and breakdown are reciprocally regulated. What does this mean?
Glycogen is broken down by the same signals that inhibit its synthesis
What is a zymogen?
An inactive precursor of an enzyme
Name a specific body response that is directly the result of a series of proteolytic activations.
The blood-clotting cascade
What is A1-antitrypsin? What specific enzyme does it inhibit which when active produces conditions similar to emphysema?
A1-antitrypsin is a 53kDa enzyme that inhibits the activity of various proteases - one such protease is elastase, which is responsible for the destruction of alveolar walls - a deficiency in A1-antitrypsin therefore can lead to conditions in the lungs resembling emphysema
Describe how trypsin produces chymotrypsin.
Trypsin cleaves an inactive zymogen (chymotrypsinogen) into chymotrypsin
What type of bond is a disulphide bond?
A covalent bond
Name 2 acidic amino acids.
- glutamate
- aspartate
Name 3 basic amino acids.
- lysine
- arginine
- histidine
What are the 2 stereoisomers of proteins? Which one exists in the environment?
L and D - L is what exists in the environment
Why doesn’t the D stereoisomer of amino acids exist in the environment?
D would cause incorrect folding
What is a stereoisomer?
Molecules with the same molecular formula but which differ in their 3D arrangement
List 5 hydrophobic amino acids.
- alanine
- glycine
- valine
- leucine
- isoleucine
