Intro to Protein Structure

Question 1

What is the name of the bond that links two amino acids and how is it formed

Answer 1

1. Amino acids are linked by peptide bonds to form polypeptide chains
2. Peptide bonds are amide bonds formed by reacting the COOH group of one amino acid with the NH2 group of the next one
3. Lose H2O

Question 2

What is a single amino acid unit called

Answer 2

1. Each amino acid unit in the chain is called a residue

Question 3

Describe the direction of a polypeptide chain

Answer 3

1. A polypeptide chain has an alpha-amino group at one end and an alpha-carboxyl group at the other
2. By convention the amino end is the beginning of the chain so the sequence is written starting with the amino-terminal residue

Question 4

Are peptides with reverse sequence the same

Answer 4

1. Peptides that have reverse sequences are different
2. Peptide Tyr-Gly-Gly-Phe-Leu is different from the peptide Leu-Phe-Gly-Gly-Tyr, although they both have the same amino acids

Question 5

What are the components of a polypeptide chain

Answer 5

1. Consists of regular repeating part called the main chain or backbone
2. And a variable part comprising the distinctive side chains
3. The backbone contains N-C-C repeats where the N has a hydrogen attached, the first C has an H and a side chain, and the second C is in a carbonyl group.

Question 6

What are different size polypeptide chains called

Answer 6

1. Polypeptides chains that contain at least 50 amino acids are called proteins
2. If there are only a small number of amino acids, the chain is referred to as an oligopeptide or a peptide

Question 7

What is the largest known protein

Answer 7

1. The largest known protein is the muscle protein titin with around 30000 amino acids

Question 8

How is the size of a protein commonly described

Answer 8

1. The size of a protein is commonly described in terms of its relative molecular mass, Mr
2. Molecular mass units are daltons where a Dalton is a unit nearly equal to the mass of a hydrogen atom.
3. Average amino acid is around 110 Da (110 gmol-1)
4. It is convenient to speak in terms of kilodaltons for proteins (thousands of Daltons)

Question 9

What are cross-links

Answer 9

1. In some proteins, the linear polypeptide chain is covalently cross-linked
2. The most common cross-links are disulphide bonds

Question 10

How are disulphide bonds formed

Answer 10

1. Formed by oxidation of two cysteine residues that are nearby in the 3D structure
2. The unit of two linked cysteines is called cystine
3. 2 Cysteine cystine + 2 H+ + 2e-

Question 11

What is the importance of amino acid sequences

Answer 11

1. Amino acid sequences can determine the 3D structures of proteins- Structure can be predicted from its sequence
2. Changes in sequence can disrupt function and produce disease- Some inherited disorders result from a single amino acid change in a protein
3. The sequence of a protein can provide insight into its evolutionary history
4. Knowledge of the sequence of a protein is usually essential to elucidating its function

Question 12

What is the conformation of a peptide bond

Answer 12

1. Essentially planar
2. For a pair of amino acids linked by a peptide bond, 6 atoms lie in the same plane
3. This is because the peptide bond C-N has considerable double bond character preventing rotation around it

Question 13

What two configuration are possible for a planar peptide bond

Answer 13

1. In the trans configuration, the two alpha carbons are on opposite sides of the bond
2. In the cis configuration the groups are on the same side
3. Almost all peptide bonds are trans to avoid steric clashes between side chains

Question 14

Describe the flexibility of polypeptide chains

Answer 14

1. There is no free rotation around peptide bonds CO-N
2. Rotations can occur around the other two bonds in the chain – N-Calpha and Calpha-CO
3. The angles of rotation around these bonds are called phi and psi respectively

Question 15

What is a Ramachandran plot

Answer 15

1. Only certain combinations of phi and psi are allowed in proteins because of steric clashes between atoms
2. This can be visualised in a Ramachandran plot which shows most favourable, borderline and disfavoured angles

Question 16

Describe how secondary structures are formed

Answer 16

1. The N-H and C=o groups in a peptide bonds are polar and can form hydrogen bonds
2. The N-H group acts as a hydrogen bond donor, and the O in the carbonyl is a hydrogen bond acceptor
3. When a protein chain folds into its 3D structure, it tends to maximise the number of hydrogen bonds theses groups make
4. It does this by forming regular secondary structures, short segments (4-5 residues) whose residues all have the same backbone conformation phi and psi angles
5. The main types of structures are Alpha helix and Beta pleated sheets- 2 or more aligned beta strands

Question 17

Describe an alpha helix

Answer 17

1. Backbone C=O groups hydrogen bond to N-H groups that are four residues further along
2. 5.4 A between helix (3.6 residues)

Question 18

Which amino acids are not easily accommodated in an alpha helix

Answer 18

1. Pro is a helix breaker

2. Val, Thr and lle destabilise

Question 19

Describe how beta sheets are formed

Answer 19

1. Formed from two or more beta strands
2. Each strand has an extended zig-zag structure
3. In a beta sheet, beta strands line up and form backbone hydrogen bonds with a neighbouring strand
4. As in the alpha-helix, H-bonds are between N-H groups of one amino acid and the carbonyl O of another
5. But here the interacting residues are on different segments
6. Can contain anywhere from 2 to more than 10

Question 20

What are the types of beta sheets

Answer 20

1. Parallel, antiparallel, or mixed
2. Beta strands can be nearby in the sequence or far away
3. Strands can be arranged in parallel or antiparallel depending on whether they are travelling in the same direction of opposite direction

Question 21

How do polypeptide chains change direction

Answer 21

1. Most proteins have compact globular structures requiring reversals in the direction of their polypeptide chains
2. These are accomplished by reverse turns and loops, which lie on the surface of proteins and serve to connect segments of regular secondary structure

Question 22

Describe secondary structure of these examples:

myoglobin, interleukin 1, ribonuclease A, fibroblast growth factor

Answer 22

1. Myoglobin- alpha helix only
2. Interleukin 1- beta sheet only
3. Ribonuclease A- mix
4. Fibroblast growth factor- mix

Question 23

Describe a collagen helix

Answer 23

1. Most abundant in mammals
2. Contains specialised helix different from alpha helix
3. Contain 3 helical polypeptide chains of around 1000 amino acids that wind around each other to form a superhelical cable
4. The inside of the triple-helical cable is very crowded-
5. only residue that can fit is Gly with only H as side chain
6. every third residue must be Gly
7. side chains on either side lie on outside of helix
8. Also contains many prolines which stabilise the helical structure

Question 24

How is a collagen helix stabilised

Answer 24

1. 3 helical polypeptide chains in collagen are held together by hydrogen bonds between glycine NH groups and CO groups on residues on other chains
2. H bonds of hydroxyproline residues in collagen are also essential for stabilising the triple helix
3. Hydroxyproline is a modified form of proline made enzymatically in a reaction that requires vitamin C
4. Why vitamin c deficiency results in less-stable collagen

Question 25

Describe what tertiary structure is

Answer 25

1. 3d structure
2. Largest force contributing to protein structure is the hydrophobic effect, which cause hydrophobic residues to aggregate to minimise contact with water
3. These residues form the hydrophobic core of the protein
4. Polar and charged residues tend to be on surface of protein where they can interact with water

Question 26

What interactions are involved in tertiary structure

Answer 26

1. Involved H-bonds and cross-links
2. Ionic bonds
3. Covalent disulphide bridges

Question 27

What are the classes of tertiary structure

Answer 27

1. Either globular (compact and roughly spherical) or fibrous (elongated)
2. The majority of proteins including enzymes are globular
3. Fibrous proteins- Commonly have structural roles and are not soluble in water
4. Fibrous proteins only single type of secondary structure generally

Question 28

State if myoglobin and collagen are globular or fibrous

Answer 28

1. Myoglobin-Globular proteins, Stores oxygen in muscle

2. Collagen- Fibrous, Main structural component of connective tissue

Question 29

What are Multidomain proteins

Answer 29

1. Some polypeptide chains fold into two or more compact regions that may be connected by a flexible segment
2. These compact globular units are called domains
3. The various domains can be either similar or quite distinct in shape

Question 30

What is quaternary structure

Answer 30

1. Arrangement of 2 or more polypeptide chains (subunits) into a common 3d structure
2. Only multi-subunit proteins have quaternary structure
3. Forces holding subunits together are similar to ones that determine tertiary structure

Question 31

What are different names of proteins with subunits

Answer 31

1. Proteins with subunits
2. Identical- homodimers
3. Different- heterodimers
4. Tetramers- if 4

Question 32

Describe experiment which shows amino acid sequence determines 3D structure

Answer 32

1. Afinsen in 1950s USED RNase A which cleaves RNA
2. Single chain whose 3D structure is stabilised by 4 disulphide bonds
3. When heated in the presence of mercaptoethanol (breaks disulphide bonds) and urea (disrupts H bonds and weakens the hydrophobic effect) it loses its native 3D structure (denatured) and loses enzymatic activity
4. When denatured RNase A is freed of urea and mercaptoethanol by dialysis it slowly regains enzymatic activity
5. Analysis shows that RNase A has renatured into its native 3D structure with the same Disulphide bond
6. Shows information needed to specify the 3D structure of RNase A is contained in its amino acid sequence

Question 33

Describe protein folding in cells

Answer 33

1. Many proteins like RNase A can be denatured and will refold spontaneously in the lab
2. In cells, the spontaneous process is too slow and newly formed proteins can aggregate instead of folding properly
3. Other proteins called molecular chaperones can prevent aggregation
4. After folding in the cell, some proteins undergo proteolysis or post-translational modification of specific amino acids
5. Some of these types of processing would prevent the protein from being able to renature after it is denatured

Question 34

Describe how proteins fold in short time

Answer 34

1. Would take too long if done by trying out all possible conformations
2. Instead when a Partially correct conformation (intermediate) is reached, it is retained because it is somewhat more stable
3. This vastly reduces the amount of time

Question 35

Which diseases are associated with misfolding of proteins

Answer 35

1. Alzheimers
2. Huntington’s
3. Transmissible spongiform enxephalopathies

Question 36

What do all the diseases associated with misfolding of proteins result in

Answer 36

1. All of theses diseases result in deposition of protein aggregates called amyloid fibrils or plaques

Question 37

What are prions

Answer 37

1. One class of diseases associated in misfolding of proteins can be transmitted by agents similar in size to viruses but consisting only of protein
2. These agents are called prions and they cause bovine spongiform enxephalopathies, scapie and Creutzfeld-Jacob disease

Question 38

Describe structure of prions

Answer 38

1. Prions are composed of a cellular protein called PrP which is normally present in solution in the brain
2. Prions are aggregated forms of this protein termed PrPSC where the protein has an abnormal conformation
3. A PrPSC nucleus (obtained by ingestion of infected neural tissue or formed spontaneously) grows by addition of proteins from the normal PrP pool
4. This leads to the formation of aggregates that cause neurological damage and typically death

Question 39

What are IUPs

Answer 39

1. Some proteins don’t have unique structure
2. Intrinsically-unstructured proteins (IUPs also called intrinsically-disorded proteins, IDPs) don’t have a fixed 3D structure but only acquire a defined structure when they interact with other proteins
3. IUPs are especially important in signalling and regulatory pathways
4. Metamorphic proteins have two or more quite different conformations
5. Each conformation of a metamorphic protein interacts with different proteins and has a different function