1 - Protein Structure Flashcards
What is the primary structure of a protein?
The specific amino acid sequence in the polypeptide chain, held together with peptide bonds.
What is the secondary structure of a protein? Give 2 examples of secondary structures?
Local folded structures that form from a polypeptide due to interactions between amino acids, usually hydrogen bonds.
Alpha helix and beta sheet
What is the tertiary structure of a protein?
The 3D shape of a protein made up of multiple secondary structures (alpha helices and beta sheets)
What different interactions/bonds hold the tertiary structure?
Hydrophobic interactions
Hydrophilic interactions
Disulphide bridges
Hydrogen bonds
Ionic bonds
What is protein quaternary structure?
The arrangement of folded protein subunits which come together to a multi-subunit complex.
What interactions/bonds hold the secondary structure?
Hydrogen bonds
Give some roles of proteins in biochemical processes.
Enzymes
Transporters/channels
Structural support
Motion/contraction
Immune protection
Receptors
Ligands in cell signalling
Amino acids in a protein are joined by ………….. bonds, these are a type of …………… bond which produces a …………………….
Peptide, covalent, polypeptide
What groups are found on the central carbon of an amino acid?
Amino group (NH2)
Carboxyl group (COOH)
Hydrogen atom (H)
Distinctive side chain (R group)
Which groups change when an amino acid is ionised? What do they change to?
NH2 group becomes NH3+ (basic)
COOH becomes COO- (acidic)
Why is the acid-base behaviour determined by the R groups when amino acids are joined to become a polypeptide?
The NH3+ and COO- groups are joined as peptide bonds, they are only free at the ends.
It is the amino acid R groups that determine the acid-base properties
What is an amino acid residue?
What remains of an amino acid after it has been joined by peptide bonds
Define aliphatic
Linear chemical structure
Define aromatic
Ring chemical structure (based on benzene)
What are the positively charged amino acids?
Lysine
Arginine
Histidine
What are the negatively charged amino acids?
Glutamate
Aspartate
If the pH of the solution is less than the pK, the group will be …….
Protonated
If the pH of the solution is larger than the pK value the group will be ……
Deprotonated
True or false, peptide bonds are planar?
Why?
True
The C-N bonds has partial double bond characteristics due to delocalised electrons. It cannot rotate.
What is the difference between cis and trans peptide bonds?
Which of these is the only one to be exhibited in nature?
Trans peptide bonds have the alpha carbons (and R groups) on opposite sides of the peptide.
Cis peptide bonds have the alpha carbons and R groups on the same side.
Only trans peptide bonds are found in vivo.
What is the isoelectric point (pI) of a protein?
The pH at which there is no overall net charge
Basic proteins have a pI > 7
Acidic proteins have a pI < 7
What is a conjugated protein? Give an example.
A protein with covalently linked chemical components other than amino acids.
Lipoproteins, glycoproteins etc
Describe the structure of an alpha helix
A right handed helix of amino acids. Held together by hydrogen bonds, H bonds form between a C=O group and an -NH group 4 residues away
- 6 amino acids per turn
- 54 nm length added per amino acid
Describe the structure of a beta strand
Fully extended confirmation with 0.35 nm between adjacent amino acids
R groups alternate between opposite sides of the chain
B sheets are made up of arrangement of ……………, if the strands run in the same direction they are ………, if strands run in opposite directions they are ………
B strands, parallel, antiparallel
B sheets can be mixed with parallel and antiparallel
Give an example of:
- A protein with tertiary structure only
- A protein with quaternary structure
- myoglobin (single subunit)
- haemoglobin (multi-subunit)
What is a fibrous protein, give an example?
Long strands or sheets of a single repeating secondary structure
Used in support, shape and protection
E.g. collagen
What is a globular protein, give an example?
Compact protein with several types of secondary structures (alpha helix and beta sheet)
Used in enzymes and regulation
E.g. carbonic anhydrase
Describe the structure of collagen
Triple helix of collagen chains, contain glycine-X-X arrangement of amino acids. Stabilised by H bonds.
Collagen fibrils form from cross linking of collagen molecules
Hydrophobic side chains fold so they are …………, polar, charged chains are near the ……………
The exception is ………. proteins which are opposite
Buried inside the protein
Surface of the protein
Membrane proteins- hydrophobic exterior and hydrophilic channel
Disulphide bonds are formed between ……… residues
Cysteine
What are Van der Waals forces?
Dipole-dipole interactions due to small transient dipoles from movement of electrons
What is protein denaturation and what can cause it?
Disruption of protein structure
Caused by breaking of forces:
- heat - increases vibration
- pH - alters ionisation state of amino acids
- detergents - disrupts hydrophobic interactions
What is Creutzfelt-Jakob Disease? What causes it?
Rare and fatal condition causing severe brain damage.
Caused by misfolded proteins building up (prions) which cluster in plaques and kill brain cells.
What are amyloid fibres?
Misfolded insoluble form of a soluble protein.
High level of beta sheets
Stabilised by hydrophobic interactions
Accumulate in tissues, causing disease
