E2: Intro to proteins

Question 1

binding is characterised by what two properties?

Answer 1

affinity and specificity

Question 2

how do receptors work?

Answer 2

sense and transmit singals via a cascade signal transduction pathways

Question 3

what do antibodies do?

Answer 3

part of our immune defenses and recognize and help destroy foreign bodies that enter
our bodies

Question 4

what is a glycoprotein

Answer 4

Protein + carbohydrate

Question 5

what is a lipoprotein

Answer 5

Protein + lipid

Question 6

how many standard amino acids are there which are common to all species?

Answer 6

20

Question 7

Describe the structure of an amino acid

Answer 7

central carbon atom (C) with 4 groups attached;
* Primary amino group (- NH2 )
* Carboxyl group ( - COOH)
* Hydrogen atom
* Variable ‘R’ group or side chain (one exception to this structure is proline; R group bonds with Ca & amino
group)

Question 8

what is chirality?

Answer 8

2 non-superimposable mirror images; enantiomers or stereoisomers. Distinguished by optical rotation of plane polarized light

Question 8

all amino acids except which are enantiomers?

Answer 8

glycine (R group is hydrogen so it is symmetrical)

Question 9

Describe D-amino acids, Dextrorotatory (D; right)

Answer 9

rare in nature, but seen in bacterial cell wall and some antibiotics

Question 10

Describe L-amino acids, laevorotatory (L; left)

Answer 10

predominant form found in proteins

Question 11

what contributes the the properties and functions of proteins

Answer 11

R side chains vary in size, shape, charge, H-bonding capacity, hydrophobicity and chemical reactivity

Question 12

In terms of pH, what is the usual form amino acids exist in solution?

Answer 12

(neutral) zwitterion, depending on the pH, there are two other forms, an anion and a cation: anion at high pH and cation at low pH (look at one note for diagram)
As the pH decreases a H+ ion will be added to the carboxylate; as the pH increases the H+ will be removed from the NH3+ and this also applies to the R groups

Question 12

which amino acids have hydrophobic interactions

Answer 12

non-polar, aliphatic amino acids. The aromatic side chains are hydrophobic

Question 13

which amino acids undergo hydrophilic interactions

Answer 13

-polar, uncharged amino acids
-positive or negative side chains tend to be hydrophilic

Question 14

what is the primary sequence?

Answer 14

linear sequence of amino acids to form a polypeptide

Question 15

Describe a peptide bond

Answer 15

covalent; amino group of one amino acid and carboxyl of another

Question 16

peptide bond is planar meaning…

Answer 16

restricting movement of the backbone of proteins

Question 17

Describe torsion angle in proteins

Answer 17

Torsion angle is the angle between groups on either side of a rotatable chemical bond; in proteins;
* The C-N (phi) bond is called phi
* The C-C (psi) bond is called psi
These rotations drive protein folding and how amino acids interact with each other

Question 18

Describe secondary structure of proteins

Answer 18

the localized organization of parts of a polypeptide chain (e.g.,  helix or  sheet) Super-secondary structure; specific combination of several secondary structure elements
Simple arrangement of structures that occur in more than one protein are called motifs or folds and can help ascertain function e.g., a binding site

Question 19

Describe tertiary structure

Answer 19

the overall, three-dimensional (3-D) arrangement of the polypeptide chain Also includes details of binding of any prosthetic groups

Question 20

Describe the quaternary structure

Answer 20

the organisation of two or more polypeptides chains into a multi-subunit complex

Question 21

Describe alpha helix secondary structure

Answer 21

-formed/stabilized by H-bonding between carbonyl of first and amino group of fifth amino acid in helix, then second with sixth etc
-R side chains face outwards
-Cylindrical structure with R groups all positioned on outside of helix
-Proline has distinct hydrogen bond pattern and cannot contribute to a-helix structure; often found at end
of a-helix ‘forcing’ directional change in polypeptide

Question 22

Describe beta ‘pleated’ sheet

Answer 22

-H-bonds between alternating residues on beta strands: occurs between the amino and carbonyl groups of alternating residues
-R groups face up and down out of the plane of the sheet
-Can run in anti-parallel and parallel arrangements
-multiple beta sheets provide strength and rigidity

Question 23

Describe connecting loops (coils) secondary structure

Answer 23

Not repetitive, containing fewer backbone hydrogen bonds. Sections that connect the regular structures of helices and sheets

Question 24

Describe the tertiary structure

Answer 24

-determined by amino acid sequence and R- group properties
-Stabilised by non-covalent: hydrogen bonds, hydrophobic interactions, ionic interactions and covalent disulfide bridges between cysteine residues (if present)
-Tertiary structure is also driven by hydrogen bonding interactions of the hydrophilic side chains and the backbone with water

Question 25

what are domains

Answer 25

distinct regions with specific geometry/structure performing specific function e.g., enzyme binding a substrate

Question 26

Describe quaternary structure

Answer 26

• The association of two or more polypeptide chains into a multi- subunit structure
• Homomeric (identical polypeptide chains) heteromeric (different chains)
• Stabilized by hydrogen bonds and van der Waals forces`
• May also include prosthetic groups

Question 27

What is protein folding determined by?

Answer 27

• Folding is determined by their amino acid composition, which involves their physico-chemistry and thermodynamics
• Secondary structures often form spontaneously, but the full 3D tertiary structure does not, and accessory proteins are required to assist the process of folding

Question 28

Describe the disulphide bond

Answer 28

-covalent bond between cysteine amino acids
* Facilitates intra and inter-molecule bonding
* Function to stabilize the overall 3D structure
* Formed under oxidizing conditions in the ER and are mainly found in secreted proteins and proteins of the extra-cellular matrix

Question 29

what are super-secondary structures (sometimes called structural motifs)?

Answer 29

combinations of 2 or more secondary structure elements

Question 30

what are the two main classes of domain?

Answer 30

functional and structural
-domains represent larger recognisable regions of proteins

Question 31

Describe functional domains

Answer 31

mediate a particular activity of the protein, for instance the ability to bind to DNA or an enzymatic activity

Question 32

Describe structural domains

Answer 32

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 33

what are globular proteins

Answer 33

high water solubility, compactly folded. Includes most enzymes and transporters like haemoglobin

Question 34

What are fibrous proteins?

Answer 34

elongated proteins, with low water solubility, large amounts of regular secondary structure, that often form stiff multimeric fibres e.g., Collagen, elastin, keratin

Question 35

What is collagen

Answer 35

triple, left-hand helix structure with each polypeptide having a regular repeating amino acid sequence; Many of these triple helix molecules pack together to form fibres

Question 36

why is protein structure important for drug development?

Answer 36

we can model, predict and demonstrate specific binding/interactions of many drug molecules and is a key aspect of understanding how they work (and new ones
discovered/developed)

Question 37

how are most proteins degraded?

Answer 37

Proteins with well-structured domains are difficult to access for proteases therefore they are degraded by the ubiquitin-proteasome pathway

Question 38

what occurs in the ubiquitin-proteasome pathway

Answer 38

-Multiple copies of the small protein ubiquitin are coupled to a lysine residue in the protein to be degraded by specific ligases: a process called polyubiquitination
* A large protein complex called the proteasome recognises the polyubiquitin chain, unwinds the secondary structure of the ubiquitinated protein and hydrolyzes it into small peptides

Question 39

Describe biomarkers to detect tissue damage/disease

Answer 39

• Myocardial infarction (heart attack) damages the myocardium
• Can result in release of cardiac muscle proteins into circulation, which can be detected and gauge severity of damage
  e.g Creatinine kinase (involved in ATP synthesis) and Troponin (sarcomere protein, interacting with actin)

Question 40

Describe proline amino acid

Answer 40

R-group bonds back onto the amino group

Question 41

Describe cysteine amino acid group

Answer 41

can form disulfide bonds between the side chains

Question 42

The protein backbone can only rotate on what two bonds with the alpha carbon?

Answer 42

the φ (psi) angle rotation around the bond with the nitrogen and the ψ (phi) angle rotation around the bond with the carbonyl carbon. Steric hindrance prevents some combinations of these angles also from occurring

Question 43

proteins can be divided in what classes?

Answer 43

-Structural proteins
-Scaffold proteins
-Enzymes
-Membrane transport proteins
-Regulatory and signalling proteins
-Motor proteins

Question 44

Where is the form and function of a protein derived from?

Answer 44

protein function is derived from the three-dimensional structure and this structure is determined primarily by the non-covalent interactions between the amino acids in the linear amino acid chain. It is therefore specified by the amino acid sequence.

Question 45

What is the N terminus and C terminus

Answer 45

The free amino terminal end of the peptide chain is called the N terminus and the free carboxyl end the C terminus. amino acid sequences are numbered from N to C terminus

Question 46

what is the secondary structure of a protein

Answer 46

regular arrangements of the backbone of the polypeptide chain, which are stabilized by the formation of hydrogen bonds between the amino and carbonyl groups in the backbone of the protein

Question 47

what is protein stability and the 3D conformation maintained by?

Answer 47

a range of non covalent interactions (electrostatic forces, hydrogen bonds and hydrophobic forces) and covalent interactions (peptide and di-sulphide bonds). Some proteins need prosthetic group that binds tightly to protein and participates in its function.

Question 48

what are the three main structural classes of proteins

Answer 48

1) Globular
2) Fibrous
3) Membrane- transmembrane proteins (integral) and lipid-anchored proteins (peripheral)

Question 49

what structural motifs or folds?

Answer 49

some short combinations of secondary structures. They often mediate a similar function, for instance binding

Question 50

Describe the structure of myoglobin?

Answer 50

single polypeptide chain that folds to give a tertiary structure that comprises 8 alpha helices, which are labeled A-H in 3D models. Also contains haem group.

Question 51

Describe the haem group?

Answer 51

protoporphyrin IX ring structure with a single iron atom (Fe2+). Iron atom bonds with 4 nitrogen atoms and forms two additional bonds- one with a histidine amino acid along the F helix; the other bond it makes is with oxygen