Proteins 1+2 Flashcards
What is organization like in primary secondary tertiary and quaternary proteins
Primary- disulfide bonds
Secondary- Local arrangements
Tertiary- 3D packing
Quaternary- Number and position of polypeptide subunits
How many amino acids do humans synthesise
11
What side chain do proteins always start with
Methionine
What side chain is relatively unreactive
Methionine
Which side chain can form complexes with various metal ions
Cysteine
What does a disulfide bond form between
Cysteine molecules. 2 form CYSTINE
When do disulfide bonds not form
In cytosol
What is the peptide bond like
Has double bond character. There is delocalization of pie electrons over the entire peptide bond rather than just over the c=o bond. The partial double character of N-C bond means restricted rotation and the bond is planar.
Is a cis or trans formation favored in a peptide bond?
Trans, because of steric clashes
Where do hydrogen bonds form in secondary structures?
Carboxyl group of one amino acid and an amino group of another
What is the secondary structure?
Doesn’t include side chains
What is the alpha helix like compared to the beta pleated Sheet?
Alpha helix side chains-
Beta side chains- up and down
In beta side chains, parallel goes from N to C terminal, antiparallel goes from C to N
Whats a tertiary structure?
Refers to the exact 3D structure, and the packing of the secondary structural elements within it
What do polypeptides greater than 200 amino acids display?
Domains (which often serve as independent units of function)
What are structural motifs? And what are made of structural motifs?
Secondary structures linked by loops in specific 3D arrangements
Domains
When are structural motifs and domains achieved?
After biosynthesis
What does the conformation attained in a structural motif dependent on? And what is folding caused by?
Amino acids present
Caused by position and extent of secondary structure
what are the major stabilizing forces of conformation?
Hydrophobic interactions
Electrostatic attraction
Covalent linkages
What’s a hydrophobic interaction caused by?
Nonpolar residues are buried on the inside of a polypeptide’s interior
How are IM forces different in thermophiles and psychrophiles?
Thermophiles- increased IM interactions
Psychrophiles- decreased IM interactions
How many common amino acids are there?
20
What’s an oligomer
A multi-subunit complex
- identical polypeptides (homo-oligomer)
- non-identical polypeptides (hetero-oligomer)
What’s a protomer?
The identical subunits of a complex
HOW do chains associate with each other permanently
Disulfide bonds
How do chains associate with each other transiently (non permanently)
electrostatic interaction (e.g. hydrophobic interactions)
What is a quaternary structure
Arrangement in 3D space
How do subunits usually interact
Non- covalently
can have disulfide bonds
What do transcient oligomers show?
Decreases hydrophobicity at the interface
Advantages of subunits
Allow for;
-expansion
-easier repair (can remove and repair each subunit instead of repairing the whole thing)
alternate site of assembly
-reduced genetic coding so less chance of mutation
-Small subunits made so can easily move protein
Why might oligomers make better enzymes
- Size increase supports the 3D structure better
- IN a homo-oligomer, each subunit will have an active site
- Subunits permit regulation
Characteristics of fibrous proteins
Display one type of secondary structure
-only have structural jobs
Example of fibrous protein
alpha keratin
Characteristic of globular protein
Secondary structures interspersed by flexible loops with hydrophilic residues that interact with water
example of globular protein
Haemoglobin
What is the structure of haemoglobin
Perforin ran with Fe2+ coordinated to it in the middle
Names of states of hemoglobin when oxygen is bound to it, and not bound to it
Taut- not bound
Relaxed- bound
What state of haemoglobin means a higher affinity for oxygen?
Relaxed
Advantage of having more than one subunit in haemoglobin
Means that you can take up and release oxygen easily because of cooperativity
When can modifications of proteins take place?
Co translational or post translational
Examples of post translational modifications
introduced by enzyme
- phosphorylation/methylation/acetylation
- can be reversible or not
- Proteolysis (irreversible) is used to activate enzymes
What’s glycosylation?
Attachment of carbs to extracellular and cell-surface proteins- (stabilizes and protects against digestion, or for recognition)
Whats the difference between glycoprotein and proteoglycan
glycoprotein- carb is the major component
proteoglycan- protein is the major component
What’s N-linked glycosylation
attachment of sugar to asparagine
What’s O-linked glycosylation
Attachment of sugar to hydroxyl group of sereine or thymine
