E2 Introduction to proteins

Question 1

what is binding of proteins characterised by?

Answer 1

• affinity: how strong the interaction is
• specificity: does it have the right association between amino acids for its binding

Question 2

what are proteins made of?

Answer 2

amino acids

Question 3

name some molecules that are proteins

Answer 3

• enzymes: highly efficient and specific catalysts
• receptors: sense and transmit signals via cascades of signal transduction pathways
• antibodies: part of our immune defence

Question 4

what does chirality allow for in amino acids?

Answer 4

• 2 non-superimposable mirror images
• distinguished by optical rotation of plane of polarised light
• dextrorotatory (D, right) or laevorotatory (L, left)
• L amino acids are predominant in proteins
• D amino acids are rare in nature but are seen in bacterial cell walls and some antibiotics

Question 5

what is the only amino acid that does not have a chiral carbon?

Answer 5

• glycine
• its R group is a hydrogen

Question 6

how are hydrophilic amino acids sub-classified?

Answer 6

• according to charge at neutral pH
• basic (positive, amino groups)
• acidic (negative, carboxyl groups)
• polar (uncharged at neutral pH, negative and positive charges balance)

Question 7

what happens to zwitterions as pH changes?

Answer 7

• higher pH / alkaline: lose proton (COO-)
• lower pH / acidic: gain proton (NH3+)

Question 8

are aromatic side chains of amino acids hydrophilic or hydrophobic?

Answer 8

hydrophobic

Question 9

describe cis and trans peptide chains

Answer 9

• cis means the R groups are on alternating sides of the chains
• trans means all the R groups are on the same side of the chain

Question 10

describe the primary structure of proteins

Answer 10

• the linear sequence of amino acids in a polypeptide
• also includes the location of where other covalent bonds are possible eg. cysteine residues have potential for disulphide bonds

Question 11

what are super-secondary structures?

Answer 11

• specific combination of several secondary structure elements
• bridge between secondary and tertiary structures

Question 12

what are secondary structures?

Answer 12

• the localised organisation of a parts of a polypeptide
• involves hydrogen bonding

Question 13

what are motifs in proteins?

Answer 13

• simple arrangement of structures that occur in more than one protein
• help ascertain function eg. a binding site

Question 14

name 3 major secondary structures

Answer 14

• alpha helices
• beta-pleated sheets
• connecting loops (coils)

Question 15

describe alpha helices

Answer 15

• repetitive local hydrogen bonding between carboxyl and amino groups with distinct spacing
• cylindrical, rod-like structures with R groups all positioned on the outside of the helix facing outwards
• right had twisting, 3.6 amino acids per turn
• hydrogen bonding occurs between carbonyl group of first amino acid and amino group of fifth (then second and sixth etc.)

Question 16

which amino acid is a ‘helix-breaker’ and what does this mean?

Answer 16

• proline
• has a distinct hydrogen bond pattern and can’t participate in an alpha helix
• proline is often found at the end of an alpha helix forcing a directional change in the polypeptide
• proline can be found in other types of helix eg. collagen

Question 17

describe beta-pleated sheets

Answer 17

• repetitive hydrogen bonding between alternating residues on adjacent sections of beta strands
• R groups protrude above and below the plane of the sheet

Question 18

what is the difference between parallel and anti-parallel beta-sheets?

Answer 18

• parallel: polypeptide sections running in the same direction
• anti-parallel: polypeptide sections running in opposite directions

Question 19

describe connecting loops (coils)

Answer 19

• not repetitive
• contain fewer backbone hydrogens
• sections that connect the regular structures of helices and sheets

Question 20

what is the tertiary structure of a protein?

Answer 20

• the overall 3D arrangement of the polypeptide
• includes details of binding of any prosthetic groups eg. haem
• creates geometric relationships between distinct and often distant segments

Question 21

what is the tertiary structure of a protein stabilised by?

Answer 21

non-covalent bonds:
- hydrogen bonds
- hydrophobic interactions
- ionic interactions

covalent bonds:
- disulphide bridges (can be intramolecular or intermolecular)

Question 22

what are domains in proteins?

Answer 22

• distinct regions with a specific structure that performs a specific function
• often function and fold independently

Question 23

what are the 2 main classes of domains in proteins?

Answer 23

functional:
- mediate a particular activity of the protein
- eg. ability to bind to DNA of an enzymatic activity

structural:
- a region of around 40 or more amino acids that form a stable secondary and tertiary structure
- often the domain can fold into this structure independently of the rest of the protein

Question 24

what is quaternary structure of a protein?

Answer 24

• the association of 2 or more polypeptides into a multi-subunit complex
• stabilised by hydrogen bonds and van Der Waals forces
• may include prosthetic groups

Question 25

what is meant by homomeric and heteromeric quaternary structure in proteins?

Answer 25

homomeric: identical polypeptide chains

heteromeric: different polypeptide chains

Question 26

how are 3D structure and stability maintained?

Answer 26

• by a combination of non-covalent and covalent interactions

covalent:
- disulphide bonds

non-covalent:
- electrostatic forces
- van der Waals forces
- hydrogen bonds
- hydrophobic forces

Question 27

what is required to assist the process of polypeptide folding?

Answer 27

accessory proteins (chaperones)

Question 28

where is a hydrophobic R group most likely to be in a protein?

Answer 28

• buried inside the protein
• away from the hydrophilic environment

Question 29

what is a disulphide bond?

Answer 29

• a covalent bond that forms between 2 cysteine residues closely located with each other in the final protein conformation
• however, they may be separated by many amino acids in the primary sequence

Question 30

what is the function of a disulfide bond?

Answer 30

• facilitates intra and intermolecular bonding
• stabilises the overall 3D structure

Question 31

how are disulfide bonds formed and where are they? normally found?

Answer 31

• under oxidising conditions in the ER
• mainly found in secreted proteins and proteins of the extracellular matrix

Question 32

what sector do structural motifs / folds fall into and what significance do they have?

Answer 32

• they are super-secondary structures
• they often mediate a similar function in different proteins eg. binding a particular ion or molecule

Question 33

what do domains represent in proteins?

Answer 33

larger recognisable regions of proteins

Question 34

what features usually make up larger proteins?

Answer 34

• structural motifs and domains
• these also occur in other proteins but with small variations and different combinations

Question 35

describe the structural class of globular proteins

Answer 35

• high water solubility
• compactly folded
• includes most enzymes and transporters eg. haemoglobin

Question 36

describe the structural class of fibrous proteins (scleroproteins)

Answer 36

• elongated proteins
• low water solubility
• large amounts of regular secondary structure
• often form stiff multimeric fibres

Question 37

give 3 examples of fibrous proteins and describe one in detail

Answer 37

• collagen, elastin, keratin
• collagen is a triple, left-handed helix structure with each polypeptide having a regular repeating amino acid sequence of ‘Gly-Pro-X’
• many of these triple helix molecules pack together to form fibres

Question 38

describe the structural class of integral membrane proteins and state examples of what kinds of proteins are included

Answer 38

• associated with membranes
• usually have alpha helices containing hydrophobic amino acids that span the hydrophobic, lipid region of the membrane
• includes receptors, transporters, cell-cell and cell-matrix proteins

Question 39

what knowledge facilitated the discovery of new painkillers such as ibuprofen?

Answer 39

aspirin covalently binds and inactivates cyclooxygenases which produce prostaglandins and contribute to the sensation of pain associated with tissue inflammation

Question 40

what is the name of the enzyme that degrades a protein?

Answer 40

protease

Question 41

what kinds of proteins are difficult to access for proteases?

Answer 41

proteins with well-structures domains

Question 42

how are most proteins degraded?

Answer 42

• by the ubiquitin-proteasome pathway
• multiple copies of the small protein ubiquitin are coupled to a lysine residue in the protein to be degraded by specific ligases (this is called polyubiquitination)
• a large protein complex called the proteasome recognises the polyubiquitin chain
• it unwinds the secondary structure of the ubiquitinated protein and hydrolyses it into small peptides

Question 43

which amino acid is NOT found in alpha helical secondary structures?

Answer 43

proline