Proteins 1+2

Question 1

What is organization like in primary secondary tertiary and quaternary proteins

Answer 1

Primary- disulfide bonds
Secondary- Local arrangements
Tertiary- 3D packing
Quaternary- Number and position of polypeptide subunits

Question 2

How many amino acids do humans synthesise

Answer 2

11

Question 3

What side chain do proteins always start with

Answer 3

Methionine

Question 4

What side chain is relatively unreactive

Answer 4

Methionine

Question 5

Which side chain can form complexes with various metal ions

Answer 5

Cysteine

Question 6

What does a disulfide bond form between

Answer 6

Cysteine molecules. 2 form CYSTINE

Question 7

When do disulfide bonds not form

Answer 7

In cytosol

Question 8

What is the peptide bond like

Answer 8

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.

Question 9

Is a cis or trans formation favored in a peptide bond?

Answer 9

Trans, because of steric clashes

Question 10

Where do hydrogen bonds form in secondary structures?

Answer 10

Carboxyl group of one amino acid and an amino group of another

Question 11

What is the secondary structure?

Answer 11

Doesn’t include side chains

Question 12

What is the alpha helix like compared to the beta pleated Sheet?

Answer 12

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

Question 13

Whats a tertiary structure?

Answer 13

Refers to the exact 3D structure, and the packing of the secondary structural elements within it

Question 14

What do polypeptides greater than 200 amino acids display?

Answer 14

Domains (which often serve as independent units of function)

Question 15

What are structural motifs? And what are made of structural motifs?

Answer 15

Secondary structures linked by loops in specific 3D arrangements

Domains

Question 16

When are structural motifs and domains achieved?

Answer 16

After biosynthesis

Question 17

What does the conformation attained in a structural motif dependent on? And what is folding caused by?

Answer 17

Amino acids present

Caused by position and extent of secondary structure

Question 18

what are the major stabilizing forces of conformation?

Answer 18

Hydrophobic interactions
Electrostatic attraction
Covalent linkages

Question 19

What’s a hydrophobic interaction caused by?

Answer 19

Nonpolar residues are buried on the inside of a polypeptide’s interior

Question 20

How are IM forces different in thermophiles and psychrophiles?

Answer 20

Thermophiles- increased IM interactions

Psychrophiles- decreased IM interactions

Question 21

How many common amino acids are there?

Answer 21

20

Question 22

What’s an oligomer

Answer 22

A multi-subunit complex

• identical polypeptides (homo-oligomer)
• non-identical polypeptides (hetero-oligomer)

Question 23

What’s a protomer?

Answer 23

The identical subunits of a complex

Question 24

HOW do chains associate with each other permanently

Answer 24

Disulfide bonds

Question 25

How do chains associate with each other transiently (non permanently)

Answer 25

electrostatic interaction (e.g. hydrophobic interactions)

Question 26

What is a quaternary structure

Answer 26

Arrangement in 3D space

Question 27

How do subunits usually interact

Answer 27

Non- covalently | can have disulfide bonds

Question 28

What do transcient oligomers show?

Answer 28

Decreases hydrophobicity at the interface

Question 29

Advantages of subunits

Answer 29

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

Question 30

Why might oligomers make better enzymes

Answer 30

- Size increase supports the 3D structure better - IN a homo-oligomer, each subunit will have an active site - Subunits permit regulation

Question 31

Characteristics of fibrous proteins

Answer 31

Display one type of secondary structure | -only have structural jobs

Question 32

Example of fibrous protein

Answer 32

alpha keratin

Question 33

Characteristic of globular protein

Answer 33

Secondary structures interspersed by flexible loops with hydrophilic residues that interact with water

Question 34

example of globular protein

Answer 34

Haemoglobin

Question 35

What is the structure of haemoglobin

Answer 35

Perforin ran with Fe2+ coordinated to it in the middle

Question 36

Names of states of hemoglobin when oxygen is bound to it, and not bound to it

Answer 36

Taut- not bound | Relaxed- bound

Question 37

What state of haemoglobin means a higher affinity for oxygen?

Answer 37

Relaxed

Question 38

Advantage of having more than one subunit in haemoglobin

Answer 38

Means that you can take up and release oxygen easily because of cooperativity

Question 39

When can modifications of proteins take place?

Answer 39

Co translational or post translational

Question 40

Examples of post translational modifications

Answer 40

introduced by enzyme - phosphorylation/methylation/acetylation - can be reversible or not - Proteolysis (irreversible) is used to activate enzymes

Question 41

What's glycosylation?

Answer 41

Attachment of carbs to extracellular and cell-surface proteins- (stabilizes and protects against digestion, or for recognition)

Question 42

Whats the difference between glycoprotein and proteoglycan

Answer 42

glycoprotein- carb is the major component | proteoglycan- protein is the major component

Question 43

What's N-linked glycosylation

Answer 43

attachment of sugar to asparagine

Question 44

What's O-linked glycosylation

Answer 44

Attachment of sugar to hydroxyl group of sereine or thymine