B2 Chapter 1: Proteins Flashcards
What are 2 causes of a variation of proteins encoded by a single gene?
- Alternative splicing
- Post-translational modifications
Approximately how many amino acids form a polypeptide?
40 - 5 000
What is the approximate range of relative molecular mass of a polypeptide?
4 000 - 580 000
What is relative molecular mass?
The ratio of the sum of atomic masses within a molecule to the 1/12 the mass of a carbon-12 atom.
Name 10 major groups of proteins.
- Enzymes
- Structural proteins
- Adhesion proteins
- Signalling proteins
- Receptor proteins
- Transport proteins
- Motor proteins
- Immunoglobulins
- Storage proteins
- Gene regulatory proteins
What is the function of adhesion proteins?
To mediate the cell-cell or cell-extracellular matrix contact.
What is the function of signalling proteins?
To faciliate inter- and intracellular communication through being recognised by the relevant receptor molecules.
What is the function of receptor proteins?
To recognise specific signalling molecules in the extracellular or intracellular environment in order to faciliate communication.
Name two types of receptor proteins?
Not specific names, just types.
- Cell surface receptors
- Intracellular receptors
What is the function of transport proteins?
To facilitate transport of substances within, to, and from the cell. E.g., membrane transport proteins
What is the function of motor proteins?
Moving vesicles along mictrotubules to their destination to be released. Faciliates movement.
What is the function of Immunoglobulins?
Also known as antibodies, they recognise specific antigens on the surface of infected cells or foreign bacteria.
What is the function of storage proteins?
To bind to and store nutrients.
What is the function of gene regulatory proteins?
Bind to DNA to regulate gene expression.
What type of protein is ferritin?
Storage protein - specifically iron.
Give one example of a gene regulatory protein.
Lac repressor.
What are ligands?
An ion or molecule that binds to a specific associated protein at its binding site.
What is ‘Primary structure’?
In proteins
The amino acid sequence
What is a proteins secondary structure?
The stable three-dimensional arrangements stretches of a polypeptide makes. (alpha helices and beta sheets)
What is a proteins tertiary structure?
The arrangement of a proteins secondary structures.
What is a proteins Quarternary structure?
The arrangement of subunits of a multimeric protein.
What is the difference between a homomeric protein and a heteromeric protein?
A homomeric protein contains identical subunits.
A heteromeric protein contains different subunits.
If a protein is formed of 4 subunits that are all the same, how could you describe it?
Homotetrameric
What is a cytokine?
A type of signalling protein
What is a cofactor?
A non-protein group that is associated with a protein. Essential for the proteins function.
Give one example of a cofactor.
Haem in haemoglobin
If a protein is formed of only one polypeptide chain, how can it be described?
Monomeric
What is a protein domain?
Dictinct units within a protein that have particular function.
What are disulfide bridges?
Covalent bonds between two cysteine residues.
What is the function of disulfide bridges in a protein?
Stabilises the arrangement of the protein by holding sections together - within a subunit or between subunits.
Are alpha helices right handed or left handed?
Right handed
What are protein folds/motifs?
Extensive arrangements of a proteins secondary structures.
What is a β barrel?
A protein fold/motif in which β sheets wrap around to form a barrel-shaped structure where the inner surface is often hydrophobic.
What can a β barrel be used for?
To carry molecules.
What is a rossman fold/dinucleotide binding fold?
α helices arranged alternately on either side of β sheet
What are the repeating atoms in a polypeptide backbone?
N, C, C with O
What is the proper term for the central carbon atom within an amino acid?
α-carbon/ Cα
In an amino acid what is attached to the α-carbon?
Not including the carboxyl and amino group
A hydogren and the side chain of the amino acid/
What is on either end of a polypeptide?
Amino group (-NH2) / N-terminus
Carboxyl group (-COOH) / C-terminus
What is the convention when numbering amino acids in a polypeptide?
Start counting from N-terminus.
When would a protein go through conformational change?
When interacting with specific molecules or going through modificiation.
In translation, what occurs to EF-Tu, it’s attached GTP, and it’s attached tRNA when the EF-Tu binds to a ribosome?
The EF-Tu undergoes conformation chainge, hydrolyses the GTP to GDP causing the release of the tRNA, and EF-Tu to dissociate from the ribosome.
At cytolsolic 7.2 pH what occurs to the amino and carboxyl groups of an amino acid?
Name the overall process and then describe the process of each group.
They are ionised.
- The carboxyl group loses a proton and becomes negatively charged.
- The amino group gains a proton and becomes positively charged.
What type of reaction occurs in the formation of C-N peptide bonds between amino acids?
Condensation reaction
Water molecule is produced
What is a CO-NH group also known as?
A peptide group.
Formed through peptide bonding between amino acids.
What are the four chemically distinct groups amino acid side chains can be sorted into?
- Negatively charged (acidic)
- Positively charged (basic)
- Uncharged polar (no net charge but charge distributed unevenly in the side chain)
- Non-polar (charge is distributed evenly in the side chain)
What are the levels of protein heirarchy?
Give brief descriptions
- Primary | Amino acid sequence
- Secondary | Basic stable structures (alpha helix, beta pleated plates etc.)
- Tertiary | Three-dimernsional arrangements of secondary structures
- Quaternary | Closely associated polypeptide chains forming mutlimeric proteins
Why is the rotation of the polypeptide backbone limited?
Name the process that limits it and give brief outline of what this is.
Steric interference | Repulsive forces between atoms due to the space occupied by their electron clouds.
What would be required to overcome steric inteference?
Energy input
Name the two most common secondary structures in proteins.
- α helices
- β pleated sheets
Describe α helices
- Common secondary structures of proteins
- Right handed helical conformation
- Hydrogen bonds between N-H of one peptide group and C=O of fourth peptide group along
- R-chains point outwards
Desribe β pleated sheets
- Hydrogen bonding between adjacent strands
- Can run parallel or anti-parallel to one another
What bonds are involved in the formation of a proteins secondary structures?
Hydrogen bonding
In globular proteins what are the distinct regions of secondary structures linked by?
Random coils
What are the steps involved in X-ray crystallography?
- Protein is crystallised
- Protein crystal irradiated with beam of X-rays
- X-rays scattered by diffraction (more electrons = more scattering)
- Analysis of x-ray diffraction pattern
- Formation of electron density map
- Molecular model formation
What is a protein domain?
A distinct sub-structure composed of secondary structures. They are often linked by a flexible hunge, and have distinct functions that contribute to the overall protein function.
If a globular protein is within an aqueous environment, how would charged groups within the hydrophobic core stabilise themselves?
Through ionic interaction with oppositely charged groups.
What non-covalent and covalent bonds are involved in stabilising teritary structure?
Non-Covalent
- Hydrogen bonds
- Hydrophobic interactions
- Ionic bonds
Covalent
- Disulfide bonds/bridges
What are disulfide bridges?
A covalent bond between 2 sulfur atoms within cysteine side chains.
In what circumstance would polypeptide residues tolerate unfavourable conditions?
If the overall stability of the polypeptide is improved.
What are cofactors?
Non-protein molecules that associate with proteins and are essential for their function.
In terms of quaternary structure of a protein, what is the difference between homomeric and heteromeric proteins?
Homomeric proteins are formed of identical subunits.
Hetermomeric proteins have non-identical subunits.
In multimeric proteins, what types of proteins are often found to contain covalent disulfide bonds?
Secreted and extracellular proteins.
Non-covalent interactions between surfaces of subunits drive what protein heirarchal structure?
Quaternary
What is the function of a chaperone protein?
To help large, or multiple domain contaning proteins to fold into the correct conformation by:
- Preventing innaportpriate interactions by aggreagrating between the protein and other molecules, or between the protein molecules themselves.
- Recover and refold misfolded proteins
What is the name of the the type of enzymez that breaks down polypeptides?
Proteases
How is a polypeptide prepared for its breakdown?
The covalent attachment of ubiquitin (protein)
What are proteases?
Proteolytic enzymes that break down proteins by catalysing the cleavage of peptide bonds.
Name two reasons proteases would break down a protein within a cell.
- If the protein is no longer needed by the cell.
- If the protein has been misfolded.
What is the danger of misfolded proteins? What do they do and why do they do this?
They tend to aggregate together to form more stabile formations.
Where may misfolded proteins have less chance of being broken down?
Outside of the cell.
Which proteins are fully functional upon release from the ribsosome and subsequent folding has occured?
Proteins that function within the cytosol.
What type of eukaryotic proteins require post-translational modification?
- Those synthesised in the RER
- Proteins to be secreted
- Those to be incorporated into the lumen
For eukaryotic proteins, where does post translational modifications occur?
The lumen of the endoplasmic reticulum.
Are covalent post-translational modifications of proteins reversible or irreversible?
Irreversible.
Name two covalent post-translational modifications of proteins and describe the mechanism. What are each of the products of these mechanisms used for?
- Protein glycosylation | The formation of a glycoprotein by the attachment of short sugar chains through reaction with, either the -NH2 group of the protein or the -OH group of an amino acid side chain. Glycoproteins are incorporated into cell membranes for cell communication, or secreted out of the cell to be used elsewhere.
- Protein lipidation | Lipid groups being covalently attached to the protein to form a lipid-linked protein. The lipid part anchors the protein into membranes, with the properties of the attached lipid determining which sheet of the membrane the protein will be located.
What are zymogens?
Proteins that are secreted in an inactive form.
What type of reaction occurs to zymogens, and to what bonds does it occur, for them to become active?
Hydrolysis of specific peptide bonds (proteolytic cleavage)
Why may some proteins secreted from the cell in an inactive form?
To prevent damage or interaction within the cell.
What is chromatography?
A process of separating constituent parts of a mixture (mobile phase) depending on how quickly they travel through a column containg the stationary phase material.
Name three types of chromatrography and what each is based on.
- Ion exchange chromatography | relative charge
- Hydrophobic interaction chromatography | relative hydrophobicity
- Gel filtration/size exclusion chromatography | relative size
What are enzymes?
Proteins that act as biological catalysts.
What are some common protein-binding ligands?
4 are listed
- cofactors
- small organic or inorganic molecules
- ions
- macromolecules
What type of interactions facilitate protein-ligand interactions?
Non-covalent
What must be compatible for a protein-ligand interaction?
Their chemical and physical properties.
What is site-directed mutagenesis (SDM)?
A technique used to study protein function and demonstrate the relationshio between a proteins structure and function.
Uses recombiant DNA texhniques to slectively replace the of interest residue with a critically different amino acid, allowing assessment of the importance of the initial amino acid by comparison of the mutated protein and the wild type protein.
What are conserved domains?
Areas of homologous amino acid sequences within proteins found across species that have been conserved through evolution.
What do homologous proteins share?
A common ancestor.
Why can enzymes be reused?
They are unaltered by reactions.
What is the lock and key hypothesis?
The idea that the specificity of the substrate and the active site of the enzyme act in a lock and key manner. (they dont really)
Why may an enzyme catalysed reaction not be reversible?
If the product do not bind as easily to the enzyme as the substrate once did.
What mayd ifferent enzymes show different levels of specificity for?
- The substrate
- The types of reactions
What must be overcome for a chemical reaction to occur?
An energy barrier.
What is an enzymes catalytic power?
The measure of its ability to speed up a reaction.
How do enzymes catalyse chemical reactions in terms of energy?
Enzymes offer an alternative pathway with less required energy to be expended in order to reach the transition state / they decrease the energy barrier.
In a chemical reaction between two reactants, what is the transition state?
The unstable intermediate.
What can influence the rate of enzyme-catalysed reactions occuring in a cell?
4 listed
- Temperature
- pH
- presence of cofactors
- presence of inhibitors
