Unit 1 Cells and Proteins: Key Area 2 - Protiens (Structure) Flashcards
What is a distinguishing feature of proteins?
There folded nature and ability to bind specifically to other molecules.
What are proteins polymers of?
Amino acids.
What are the 2 functional groups of amino acids?
The amine and acid group.
What does the wide range of functions carried out by proteins result from?
The wide range of functions carried out by proteins results from the diversity of R groups.
What determine the structure of the protein?
The sequence of amino acids.
What makes each amino acid different?
The R-group.
What are the 5 components of an amino acid?
The amine group, acid group, R-group, hydrogen atom and central carbon.
What are amino acids linked together by and what does this produce?
Peptide bonds which produces a polypeptide.
What are the 4 main R-groups of amino acids?
Polar, Hydrophobic, Acidic (Negatively charged), Basic (Positively charged).
What can the R-group of amino acids vary in?
Size, shape, charge, hydrogen bonding capacity and chemical reactivity. They can be as simple as hydrogen or as complex as a chain with rings.
What are the key features of an aAcidic R-group?
- Ends with a negatively charged group.
- Hydrophilic.
- Key component is a carboxylic acid group - COOH.
What are the key features of a Basic R-group?
- Ends with a positively charged group.
- Hydrophilic.
- Key component of their R-group is an amine group.
What are the key features of a Polar R-group?
- Slightly charged.
- Hydrophilic.
- Key component: carbonyl (CO), (OH) or amine (NH).
What are the key features of a Hydrophobic R-group?
- Hydrophobic.
- Do not have charged.
- Non-Polar.
- Key component is a hydrocarbon - CH3, long chain of CH and rings
What are the other levels of protein structure other than the sequence and binding of amino acids?
- Primary Structure
- Secondary Structure
- Tertiary Structure
- Quaternary Structure
What is the primary structure?
The primary structure is the sequence in which the amino acids are synthesised into the polypeptide.
What happens in the primary structure?
Amino acids link by peptide bonds to from a polypeptide.
Due to the make up of amino acids, what does the primary structure have?
A n-terminal and c-terminal.
What results in regions of a secondary structure?
Hydrogen bonding along the backbone of the protein strand results in regions of secondary structure.
What are the 3 types of secondary structure?
- Alpha Helix
- Beta Sheets
- Turns
How are Alpha Helix formed?
By twisting the polypeptide chain into a spiral/helix then stabilising with hydrogen bonds. Where the R-group sticks out.
What are the 2 types of beta sheet?
- Parallel: the chains run in the same direction.
- Anti-parallel: the chains run in opposite directions.
What is the structure of beta sheets like?
The beta sheet has parts of the chain running alongside each other, forming a sheet. The R-groups sit above and below the sheet.
What stabilises the alpha helix?
Hydrogen bonding.
What is the structure of turns like?
They reverse the direction of the polypeptide chain and the chain folds back on itself.
What is the tertiary structure?
The final folded shape of the polypeptide.
How Is the tertiary structure established?
By many different interactions between the R-groups of the amino acids.
What are the 5 R-group interactions of the tertiary structure?
- Hydrophobic Interactions.
- Ionic Bonds.
- London Dispersion Forces (LDFs).
- Hydrogen Bonds.
- Disulphides Bridges.
How does Hydrophobic Interactions in the tertiary structure work?
Amino acids tend to cluster together on the interior of a protein, away from the surface (and away from water).
How does Ionic Bonds in the tertiary structure work?
Occurs when atoms that are oppositely charged are held by an electrostatic attraction.
What happens to COOH and NH2 in Ionic Bonds in tertiary structure?
They become COO- and they are strongly charged and attracted to each other.
How does LDFs in the tertiary structure work?
Weak interactions between the electron clouds of atoms. These interactions may result in attraction or repulsion between states.
How does Hydrogen Bonds in the tertiary structure work?
One of the weaker interactions between amino acids. An electrostatic attraction which occurs between a hydrogen atom and an electronegative atom, such as oxygen or nitrogen.
How does Disulphide Bridges in the tertiary structure work?
A covalent bond between R-groups containing Sulphur (between two thiol- SH - group).
What is a prosthetic group?
A prosthetic group is a non-protein unit tightly bound to a protein and necessary for its function.
What is an example of a prosthetic group?
The haem in haemoglobin. The ability of haemoglobin to bind oxygen is dependent on the non-protein haem group.
What can affect the interactions between R-groups?
Temperature and pH. Which is why pH and temperature can affect the structure and function of a protein.
What are the effects of temperature on the interactions between R-groups?
Increasing the temperature disrupts the interactions that hold the protein in shape. The protein begins to unfold, eventually being denatured.
What are the effects of pH on the interactions between R-groups
As pH increases or decreases from the optimum, the normal ionic interactions between charged groups are lost, which gradually changes the conformation of the protein until it becomes denatured.
What is a Ligand?
A ligand is a substance that can bind to a protein.
What R-groups can allow binding to ligand?
Those that are not involved in protein folding.
What will the binding sites have to the ligand?
Binding sites will have complementary shape and chemistry to the ligand.
What happens to a protein as a ligand binds to it?
As a ligand binds to a protein-binding site the conformation of the protein changes. This change in conformation causes a functional change in the protein.
What is an example of a drug that acts as a ligand and how does it work?
Nicotine by binding to a protein receptor called acetylcholine. Where nicotine is a very small molecule in comparison to the acetylcholine.
What is an allosteric enzyme?
An enzyme is an enzyme who’s activity is regulated by altering its conformation.
Where do allosteric interactions occur?
Between spatially distinct sites. Active site = substrate, Allosteric site = substance other than the substrate.
What do allosteric enzyme contain?
A second type of site called an allosteric site.
What do many allosteric proteins consist of?
Many allosteric proteins consist of multiple subunits (have quaternary structure).
What do modulators do?
Modulators regulate the activity of the enzyme when they bind to the allosteric site.
Following binding of a modulator what happens to the active site?
Following binding of a modulator, the conformation of the enzyme changes and this alters the affinity of the active site for the substrate.
What is the function of negative modulators?
To reduce the enzymes affinity for the substrate = decrease activity.
What is the function of positive modulators?
To increase the enzymes affinity for the substrate - increase activity.
What shows co-operativity?
Allosteric points with multiple subunits show co-operativity in binding, in which changes in binding at one subunit alter the affinity of the remaining subunits.
What does the binding of a substrate molecule to one active site of a allosteric enzyme do in terms of co-operativity?
Increases the affinity of the other active sites binding of subsequent substrate molecules.
Why is co-opoerativity of biological importance?
The activity of allosteric enzyme can vary greatly with small changes in substrate concentration.
What is an example of a molecule that shows co-operativity, why does it show this and how does it work?
Haemoglobin as it is made up of 4 polypeptide subunits, where each subunit contains a haem group. Where one of the subunits binds a molecule of oxygen, subsequently binding by other oxygen molecules is more likely. Where oxy - haemoglobin releases oxygen, the same process happens.
What is the influence of increasing temperature and reducing pH on affinity of haemoglobin?
Reduced pH and increased temperature in actively respiring tissues will reduce the binding of oxygen to haemoglobin, promoting increased oxygen delivery to tissue.
What is the influence of reducing temperature and increasing pH on affinity of haemoglobin?
A decrease in pH or an increase in temperature lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced.
What is phosphorylation?
The addition or removal of phosphate can cause reversible conformational change in proteins.
What is phosphorylation a common form of?
This is a common form of post-translational modification.
What is the function of protein kinases?
Protein kinases catalyse the transfer of a phosphate group to other proteins. Where the terminal phosphate of ATP is transferred to specific R groups.
What is the function of protein phosphates?
Protein phosphatase catalyses the transfer of a phosphate group from protein onto ADP to regenerate ATP.
What does phosphorylation bring about?
Phosphorylation brings about conformational changes, which can affect a protein’s activity.
What does phosphorylation regulate?
The activity of many cellular proteins, such as enzymes and receptors, is regulated by phosphorylation.
What does phosphorylation of some proteins do?
Some proteins are activated by phosphorylation while others are inhibited.
What can the addition of a phosphate group change in terms of charge and how does this affect the ionic interactions?
Adding a phosphatase group adds negative charges. Ionic interactions in the unphosphorylated protein can be disrupted and new ones created.
