Protein Structure & Function Flashcards
What is the primary protein structure?
Sequence of amino acids in the polypeptide chain
What is the secondary protein structure?
Folding/coiling of polypeptide chain (alpha helix/beta pleated sheet)
What is the tertiary protein structure?
Polypeptide chain folds upon itself further
What is the quaternary protein structure?
Folded polypeptide chains join together
List the bonds present in proteins in ascending strength
Van der Waals
Hydrogen
Ionic
Covalent
List the types of hydrogen bond combinations in descending strength
F-H F
O-H N
O-H O
N-H N
N-H O
Why are there partial charges on the nitrogen and oxygen of a peptide bond?
Peptide bond resonance (delocalised electrons)
What is the pitch of an alpha helix?
0.54nm
How many amino acids are there per turn of an alpha helix?
3.6
What type of helix is an alpha helix?
Right handed
Where are the R groups of an alpha helix?
On the outside
Where are the R groups in a beta pleated sheet?
Alternately above and below the plane of sheet
How long is one fold of a beta pleated sheet?
0.7nm
What is the difference between a parallel and antiparallel beta pleated sheet?
Parallel = all chains run in same direction
Antiparallel = adjacent chains run in opposite directions
What percentage of haemoglobin is made up of alpha helices?
60%
What do silk fibres/fibrillar proteins (fibroin) contain a lot of?
Beta pleated sheets
What is the super-secondary structure?
Common domains formed from combinations of alpha helices and beta pleated sheets found in many proteins
What are ionic bonds/salt bridges?
Electrostatic attractions between charged side chains
What is the main driving force for folding of soluble proteins?
Hydrophobic side chains (forming a hydrophobic core)
On proteins spanning the lipid bilayer, where are the hydrophobic side chains?
Outside (hydrophilic core)
What is O-linked glycosylation?
Addition of sugar onto the OH of Thr/Ser
What is N-linked glycosylation? Give an example
Addition of sugar onto NH2 of Asn
SIBLING protein family = Small Integrin-Binding Ligand N-linked Glycoprotein
What processes is phosphorylation of proteins involved in?
Cell signalling (phosphorylation of Tyr with insulin receptor)
Change in enzyme activity (phosphorylation of pyruvate kinase in response to blood glucose)
Explain how acetylation affects DNA gene transcription.
Binds to Lys in histones to “remove” positive charge so negatively charged DNA is attracted less strongly and moves away
Increased transcription
What is the most abundant protein in vertebrates?
Collagen
What is the structure of collagen?
Triple helix - three left hand helices join to form a right hand helix (triangular)
In collagen, how many residues are there per turn?
3
What is the amino acid sequence of collagen?
Gly - X - Y - Gly - X - Y
X = mainly proline
Y = mainly hydroxyproline
Where is type I collagen found? (4)
Skin
Bone
Tendon
Dentin
Where is type II collagen found?
Cartilage
Where is type III collagen found? (2/3)
Extensible tissue (blood vessels and lungs)
Dental pulp
(Minor component in dentin)
What causes scurvy?
Vitamin C deficiency
Explain why scurvy occurs.
Vitamin C = cofactors for proline hydroxylase
No vitamin C means no hydroxylation of proline
Resulting in unstable collagen as less hydrogen bonds can be formed
What are the symptoms of scurvy? (5)
Skin bruises easily
Old wounds reopen
New wounds heal poorly
Gums bleed
GI tract bleeding
