Protein Structure & Function Flashcards
What happens to an amino acid in solution?
Both the amino and carboxyl groups ionise
NH3+
COO-
Groups created
What is the charge on a zwitterion (ignoring the presence of the amino acid R group)?
No overall net charge
Out of the NH2 and COOH groups of the amino acid, which is basic and which is acidic?
NH2 = basic
COOH = acidic
What is meant by terms acidic and basic in terms of protein transfer?
Acidic = Proton donor Base = proton acceptor
Classification of an amino acid is dependent on the amino acid’s…
R group
Negatively charged groups are acidic or basic?
Acidic
Positively charged groups are acidic or basic?
Basic
What does pKa give an indication of?
How likely something is to ionise
The pKa value is equal to…
The pH at which the…
protonated form = deprotonated form
What is the relationship between the pH of a solution and the pKa of a BASIC amino acid?
If the pH < the pKa of a amino acid, the r group will be protonated
R group —> +ve —-> basic
What is the relationship between the pH of a solution and the pKa of an ACIDIC amino acid?
If the pH of a solution>greater than the pKa value then the R group will be deprotonated
Therefore -ve charged —-> acidic
What is the primary structure of a protein?
The linear amino acid sequence of the polypeptide chain
What is the secondary structure of an amino acid? Give 2 examples of ways a protein can arrange itself in its secondary structure.
The local spatial arrangement of the polypeptide backbone
Into a-helical, b-sheets
What does the tertiary structure of the protein refer to?
The overall 3d shape of a protein
What does the quaternary structure of a protein refer to?
Association between different polypeptide chains to form a multi subunit protein
What is the bond connecting two amino acids together called? What molecule is produced when this bond is created?
Peptide bond
Water molecule
Peptide bonds are planar, what does this mean?
C-alpha, C, O, N, H and C-alpha are all in the same plane
As well as being planar, peptide bonds are rigid and demonstrate partial double bond characteristics - what is meant by this?
They are unable to rotate
What sort of conformation do peptide bonds show?
Trans conformation
What is meant by the trans conformation of peptide bonds?
The c-alpha’s on each side of the peptide bond are on opposite sides of the peptide bond
Why can’t peptide bonds show a cis conformation?
Would result in steric clashes
Are bonds on each side of the peptide bond able to rotate?
Yes - free to rotate
What are Psi and Phi bonds?
Psi = bond between c-alpha and carbon Phi = bond between c-alpha and N
What is the isoelectric point (pI) of a protein?
The pH at which there is no net overall charge on a protein
Basic proteins have a pI…
pI greater than 7
Acidic proteins have a pI…
pI smaller than 7
If pH>pI then the protein will be…
Deprotonated
If pH
Protonated
What are conjugated proteins?
Proteins containing covalently linked chemical components in addition to amino acids
What determines the initial conformation of a protein?
The angles of the Phi and Psi bonds
What type of helix is an alpha-helix?
Right handed helix
How many amino acids are seen per turn in an alpha helix?
3.6 aa per turn
What is meant by the pitch of an alpha helix?
Distance to go up 1 complete turn of the alpha helix
What is the pitch in an alpha helix?
0.54nm
What stabilises the structure of an alpha helix?
Hydrogen bonds between the N-H and C=O
The C=O group of one residue makes hydrogen bonds with the N-H group 4 amino acid’s away
Which sorts of amino acid residues tend to form alpha helices? Give two examples
Small hydrophobic residues
Alanine
Leucine
Give two amino acid residues that act as helix breakers
Proline
Glycine
What is the distance between adjacent amino acids in a B-strand? What is the position of the R groups at these strands?
0.35nm
R groups alternate between opposite sides of the strand
What results in the formation of a beta-sheet?
Side by side arrangement of beta strands
What two different forms of beta sheet exist? What stabilises their structure?
Anti-parallel
Parallel
Hydrogen bonds
Give an example of a protein that is largely alpha-helical.
Ferritin - iron storage molecule
Give an example of a protein that is mainly b-sheets
Fatty acid binding protein
What is the difference in secondary structures between globular and fibrous proteins?
Fibrous = single type of repeating secondary structure Globular = several types of secondary structure
What is the general 3D shape of membrane proteins?
They have an ‘inside-out’ configuration, with hydrophobic groups on the outside rather than buried on the inside
What bonds are found in the primary structure of a protein?
Peptide (covalent)
What bonds are found in the secondary structure of a protein?
Hydrogen bonds
Which bonds are found in the tertiary and quaternary structures of proteins?
Ionic, hydrogen bonds, hydrophobic interactions, and disulphides bonds
Disulphides bonds are formed between which amino acid residues? What can be used to break them?
Cysteine residues
Reducing agents
Ionic bonds are formed between…
Charged groups
A normal, functional protein is said to be in its ______ conformation
Native
What 3 things can denature a protein?
Heat
pH
Detergents/organic solvents
How can heat denature a protein?
Increased vibrational energy —> breaks bonds
How can pH denature a protein?
Affects ionic/hydrogen bonds
Alters ionisation states of amino acids
How can detergents denature a protein?
Disrupt hydrophobic interactions
Where is information for folding of a protein found? What is this ordered folding process driven by?
In the primary sequence
The need to find the most stable conformation
What are amyloid fibres?
Misfolded, insoluble forms of normally soluble proteins
