Intro to Protein Structure Flashcards
1
Q
What is the name of the bond that links two amino acids and how is it formed
A
- Amino acids are linked by peptide bonds to form polypeptide chains
- Peptide bonds are amide bonds formed by reacting the COOH group of one amino acid with the NH2 group of the next one
- Lose H2O
2
Q
What is a single amino acid unit called
A
- Each amino acid unit in the chain is called a residue
3
Q
Describe the direction of a polypeptide chain
A
- A polypeptide chain has an alpha-amino group at one end and an alpha-carboxyl group at the other
- By convention the amino end is the beginning of the chain so the sequence is written starting with the amino-terminal residue
4
Q
Are peptides with reverse sequence the same
A
- Peptides that have reverse sequences are different
- Peptide Tyr-Gly-Gly-Phe-Leu is different from the peptide Leu-Phe-Gly-Gly-Tyr, although they both have the same amino acids
5
Q
What are the components of a polypeptide chain
A
- Consists of regular repeating part called the main chain or backbone
- And a variable part comprising the distinctive side chains
- 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.
6
Q
What are different size polypeptide chains called
A
- Polypeptides chains that contain at least 50 amino acids are called proteins
- If there are only a small number of amino acids, the chain is referred to as an oligopeptide or a peptide
7
Q
What is the largest known protein
A
- The largest known protein is the muscle protein titin with around 30000 amino acids
8
Q
How is the size of a protein commonly described
A
- The size of a protein is commonly described in terms of its relative molecular mass, Mr
- Molecular mass units are daltons where a Dalton is a unit nearly equal to the mass of a hydrogen atom.
- Average amino acid is around 110 Da (110 gmol-1)
- It is convenient to speak in terms of kilodaltons for proteins (thousands of Daltons)
9
Q
What are cross-links
A
- In some proteins, the linear polypeptide chain is covalently cross-linked
- The most common cross-links are disulphide bonds
10
Q
How are disulphide bonds formed
A
- Formed by oxidation of two cysteine residues that are nearby in the 3D structure
- The unit of two linked cysteines is called cystine
- 2 Cysteine cystine + 2 H+ + 2e-
11
Q
What is the importance of amino acid sequences
A
- Amino acid sequences can determine the 3D structures of proteins- Structure can be predicted from its sequence
- Changes in sequence can disrupt function and produce disease- Some inherited disorders result from a single amino acid change in a protein
- The sequence of a protein can provide insight into its evolutionary history
- Knowledge of the sequence of a protein is usually essential to elucidating its function
12
Q
What is the conformation of a peptide bond
A
- Essentially planar
- For a pair of amino acids linked by a peptide bond, 6 atoms lie in the same plane
- This is because the peptide bond C-N has considerable double bond character preventing rotation around it
13
Q
What two configuration are possible for a planar peptide bond
A
- In the trans configuration, the two alpha carbons are on opposite sides of the bond
- In the cis configuration the groups are on the same side
- Almost all peptide bonds are trans to avoid steric clashes between side chains
14
Q
Describe the flexibility of polypeptide chains
A
- There is no free rotation around peptide bonds CO-N
- Rotations can occur around the other two bonds in the chain – N-Calpha and Calpha-CO
- The angles of rotation around these bonds are called phi and psi respectively
15
Q
What is a Ramachandran plot
A
- Only certain combinations of phi and psi are allowed in proteins because of steric clashes between atoms
- This can be visualised in a Ramachandran plot which shows most favourable, borderline and disfavoured angles
16
Q
Describe how secondary structures are formed
A
- The N-H and C=o groups in a peptide bonds are polar and can form hydrogen bonds
- The N-H group acts as a hydrogen bond donor, and the O in the carbonyl is a hydrogen bond acceptor
- When a protein chain folds into its 3D structure, it tends to maximise the number of hydrogen bonds theses groups make
- 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
- The main types of structures are Alpha helix and Beta pleated sheets- 2 or more aligned beta strands
17
Q
Describe an alpha helix
A
- Backbone C=O groups hydrogen bond to N-H groups that are four residues further along
- 5.4 A between helix (3.6 residues)
18
Q
Which amino acids are not easily accommodated in an alpha helix
A
- Pro is a helix breaker
2. Val, Thr and lle destabilise
19
Q
Describe how beta sheets are formed
A
- Formed from two or more beta strands
- Each strand has an extended zig-zag structure
- In a beta sheet, beta strands line up and form backbone hydrogen bonds with a neighbouring strand
- As in the alpha-helix, H-bonds are between N-H groups of one amino acid and the carbonyl O of another
- But here the interacting residues are on different segments
- Can contain anywhere from 2 to more than 10
20
Q
What are the types of beta sheets
A
- Parallel, antiparallel, or mixed
- Beta strands can be nearby in the sequence or far away
- Strands can be arranged in parallel or antiparallel depending on whether they are travelling in the same direction of opposite direction
21
Q
How do polypeptide chains change direction
A
- Most proteins have compact globular structures requiring reversals in the direction of their polypeptide chains
- These are accomplished by reverse turns and loops, which lie on the surface of proteins and serve to connect segments of regular secondary structure
22
Q
Describe secondary structure of these examples:
myoglobin, interleukin 1, ribonuclease A, fibroblast growth factor
A
- Myoglobin- alpha helix only
- Interleukin 1- beta sheet only
- Ribonuclease A- mix
- Fibroblast growth factor- mix
23
Q
Describe a collagen helix
A
- Most abundant in mammals
- Contains specialised helix different from alpha helix
- Contain 3 helical polypeptide chains of around 1000 amino acids that wind around each other to form a superhelical cable
- The inside of the triple-helical cable is very crowded-
- only residue that can fit is Gly with only H as side chain
- every third residue must be Gly
- side chains on either side lie on outside of helix
- Also contains many prolines which stabilise the helical structure
24
Q
How is a collagen helix stabilised
A
- 3 helical polypeptide chains in collagen are held together by hydrogen bonds between glycine NH groups and CO groups on residues on other chains
- H bonds of hydroxyproline residues in collagen are also essential for stabilising the triple helix
- Hydroxyproline is a modified form of proline made enzymatically in a reaction that requires vitamin C
- Why vitamin c deficiency results in less-stable collagen
25
Q
Describe what tertiary structure is
A
- 3d structure
- Largest force contributing to protein structure is the hydrophobic effect, which cause hydrophobic residues to aggregate to minimise contact with water
- These residues form the hydrophobic core of the protein
- Polar and charged residues tend to be on surface of protein where they can interact with water
26
Q
What interactions are involved in tertiary structure
A
- Involved H-bonds and cross-links
- Ionic bonds
- Covalent disulphide bridges
27
Q
What are the classes of tertiary structure
A
- Either globular (compact and roughly spherical) or fibrous (elongated)
- The majority of proteins including enzymes are globular
- Fibrous proteins- Commonly have structural roles and are not soluble in water
- Fibrous proteins only single type of secondary structure generally
28
Q
State if myoglobin and collagen are globular or fibrous
A
- Myoglobin-Globular proteins, Stores oxygen in muscle
2. Collagen- Fibrous, Main structural component of connective tissue
29
Q
What are Multidomain proteins
A
- Some polypeptide chains fold into two or more compact regions that may be connected by a flexible segment
- These compact globular units are called domains
- The various domains can be either similar or quite distinct in shape
30
Q
What is quaternary structure
A
- Arrangement of 2 or more polypeptide chains (subunits) into a common 3d structure
- Only multi-subunit proteins have quaternary structure
- Forces holding subunits together are similar to ones that determine tertiary structure
31
Q
What are different names of proteins with subunits
A
- Proteins with subunits
- Identical- homodimers
- Different- heterodimers
- Tetramers- if 4
32
Q
Describe experiment which shows amino acid sequence determines 3D structure
A
- Afinsen in 1950s USED RNase A which cleaves RNA
- Single chain whose 3D structure is stabilised by 4 disulphide bonds
- 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
- When denatured RNase A is freed of urea and mercaptoethanol by dialysis it slowly regains enzymatic activity
- Analysis shows that RNase A has renatured into its native 3D structure with the same Disulphide bond
- Shows information needed to specify the 3D structure of RNase A is contained in its amino acid sequence
33
Q
Describe protein folding in cells
A
- Many proteins like RNase A can be denatured and will refold spontaneously in the lab
- In cells, the spontaneous process is too slow and newly formed proteins can aggregate instead of folding properly
- Other proteins called molecular chaperones can prevent aggregation
- After folding in the cell, some proteins undergo proteolysis or post-translational modification of specific amino acids
- Some of these types of processing would prevent the protein from being able to renature after it is denatured
34
Q
Describe how proteins fold in short time
A
- Would take too long if done by trying out all possible conformations
- Instead when a Partially correct conformation (intermediate) is reached, it is retained because it is somewhat more stable
- This vastly reduces the amount of time
35
Q
Which diseases are associated with misfolding of proteins
A
- Alzheimers
- Huntington’s
- Transmissible spongiform enxephalopathies
36
Q
What do all the diseases associated with misfolding of proteins result in
A
- All of theses diseases result in deposition of protein aggregates called amyloid fibrils or plaques
37
Q
What are prions
A
- One class of diseases associated in misfolding of proteins can be transmitted by agents similar in size to viruses but consisting only of protein
- These agents are called prions and they cause bovine spongiform enxephalopathies, scapie and Creutzfeld-Jacob disease
38
Q
Describe structure of prions
A
- Prions are composed of a cellular protein called PrP which is normally present in solution in the brain
- Prions are aggregated forms of this protein termed PrPSC where the protein has an abnormal conformation
- A PrPSC nucleus (obtained by ingestion of infected neural tissue or formed spontaneously) grows by addition of proteins from the normal PrP pool
- This leads to the formation of aggregates that cause neurological damage and typically death
39
Q
What are IUPs
A
- Some proteins don’t have unique structure
- 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
- IUPs are especially important in signalling and regulatory pathways
- Metamorphic proteins have two or more quite different conformations
- Each conformation of a metamorphic protein interacts with different proteins and has a different function
