Proteins

Question 1

Name 2 structural proteins

Answer 1

keratin

Collagen

Question 2

What is the function of transcription factors?

Answer 2

Regulate cell activities by switching genes on and off

Question 3

What is the role of enzymes in metabolic reactions?

Answer 3

Speed up the rate of reaction

Question 4

Explain the structure and role of K-channels

Answer 4

K-channels have 4 multipass subunits, cental selectivity pore

Determine what molecules enter and leave the cell

Question 5

Explain the role and structure of ferritin and hemoglobin

Answer 5

Ferritin:

24 subunits, up to 4500 iron atoms

Haemoglobin:

4 subunits, 4 haem groups, 4 iron atoms

Both store essential molecules and transport them across the body

Question 6

Explain the structure and role of insulin

Answer 6

Insulin is a signaling molecule and receptor

It has 6 subunits, coordinated by a central Zn 2+ cation

Communication between and within cells

Binding and regulation of other proteins

Question 7

Explain the structure and role of antibodies - Immunoglobulin G

Answer 7

Immunoglobulin G has 4 peptide chains, 2 heavy chains, and 2 light chains

Immune response to invasion by viruses, bacteria, allergens and other toxins (antigens)

Question 8

Explain the 2 motor proteins - Kinesin and Myosin

Answer 8

Kinesin moving along a microtubule

Myosin sliding on an actin filament

Common structure: catalytic core (head) + neck + coiled-coil

Transport of molecules and organelles across the cell

Membrane fusion/fission, exocytosis/endocytosis

Cell contraction/motility

Question 9

Name some of the functions of proteins

Answer 9

Defense

Signaling

Transport

Catalysis

Movement

Structure

Regulation

Question 10

Explain why side chains of amino acids are either polar or non-polar

Answer 10

polar or hydrophobic

Polar side chains - hydrophilic, wtaer-loving

Non-polar side chains - hydrophobic, water-fearing

Question 11

Name the 2 ways amino acids are distributed and what it depend on

Answer 11

Amino acid distribution depends on the protein environment

Cytosolic proteins - Mostly polar on the outside and mostly hydrophobic on the inside

Membrane proteins - Most hydrophobic on the outside and mostly polar on the inside

Question 12

Name the 2 main hydrophobic amino acids and explain their structure/bonding

Answer 12

Glycine - Local flexibility

Cysteine - disulfide bonds

Proline - helix breaker

Question 13

Name the 5 polar charge amino acids

Answer 13

Lysine

Arginine

Histidine

Aspartic acid

Glutamic acid

Question 14

Name the 5 polar uncharged amino acids

Answer 14

Serine

Threonine

Tyrosine

Asparagine

Glutamine

Question 15

Name the amino acid the following are modified into and how they modified into these amino acids

Answer 15

Lysine into hydroxylysine

Serine into phosphoserine

Formed by post-translational modification

Question 16

Deptide are linked with what bond (give both names) what molecule is removed

Answer 16

Peptide bond or amine bond

Water molecule is removed when the 2 amino acids join together to form a dipeptide

Question 17

What formation are peptide bonds and give the exception

Answer 17

Almost all peptide bonds are in trans configurations

Only for proline, the two configurations have similar energies - trans form and cis form

Question 18

Explain the resonance structure of proteins

Answer 18

Peptide bond has a partial double bond character and exist as two resonance structures

There is no rotation around the peptide bond, only around the alpha-carbon

Question 19

Explain the structure of amino acids

Answer 19

All amino acids have the following groups linked to the carbon alpha atom: amino group, carboxyl group, hydrogen atom, and side chain (R group)

Question 20

Side chains of amino acids can be:

Answer 20

Hydrophobic

Polar charged

Polar uncharged

Question 21

Explain the primary structure of amino acids

Answer 21

Read from the amino terminus to the carboxyl terminus

Encoded by the nucleotide sequence of DNA

unique characteristic of the protein

Alteration of even a single amino acid can cause disease

Stabilization by peptide bonds

Question 22

Explain the secondary structure of amino acids

Answer 22

Results of local folding of the polypeptide chain and formation of hydrogen bonds between C=o and N-H groups in the backbone (chain without groups)

Question 23

Name the 4 main types of secondary structures

Answer 23

Alpha helix

Beta pleated sheet

Beta turns

Loops

Question 24

Explain alpha helix

Answer 24

Most common type of helix

3.6 residues per turn

Hydrogen bonds between the carbonyl group ( C=O) of reside X and the N-H group of the residue X+4

Right-handed (clockwise)

Has a dipole moment corresponding to a partial positive charge at the N-terminus and a partial negative charge at the C-terminus

Question 25

Explain what a 3 10 - helix is

Answer 25

Occurs mostly at the ends of alpha helices 3 residues per turn H-bonds between residue X and the X+3 Called 3 10 helix because the H bond closes a loop of 10 atoms containing 3 residues

Question 26

Explain what a pi-helix is

Answer 26

Very rare Occurs mainly at the ends of alpha-helices 4.4 residues per turn H-bonds between residue X and X+5

Question 27

Explain what a beta-pleated sheet is

Answer 27

Peptide chains fully extended - pleated shape Stabilized by H-bonds between C=O and N-H groups of the backbone (flanking regions) Side chains project above and below the sheet

Question 28

Name and explain the 2 types of beta-pleated sheets

Answer 28

Parallel B-sheets: Two polypeptide strands running in the same direction Non-linear hydrogen bonds, less stable, parallel B-sheets with less than five parallel strands are rare Antiparallel B-sheets: Two polypeptide strands running in opposite directions Well oriented hydrogen on bonds Strong and stable

Question 29

Explain what beta-turns are

Answer 29

B-turns (or reverse turns) reverse the direction of the polypeptide chain In standard turns the C=O group of residue X is bonded to the N-H group of residue X+3 Most turns contain at least one residue of glycine or proline

Question 30

Explain what loops are

Answer 30

Various lengths, irregular shapes, very flexible Connect other elements of the secondary structure

Question 31

Explain what super secondary structure is

Answer 31

A simple combination of a few secondary structure elements with a specific geometric arrangement Often perform a particular function

Question 32

Explain tertiary structure

Answer 32

Over\ll three-dimensional structure of a protein molecule Spatial relationship of the secondary structure elements to one another Stabilized by bonds and interactions between side chains

Question 33

Give an example of a protein with a tertiary structure and explain the structure

Answer 33

Lysozyme Alpha+beta fold Five helices (three alpha, of which one is closer to the pi-helix, two intermediate alpha/310) Three standard antiparallel beta sheets

Question 34

Explain the quaternary structure and give 2 examples

Answer 34

Spatial arrangements of subunits in a protein composed of more than one polypeptide chain Stabilized by interactions between side chains (same types as in tertiary structure) Subunits can be identical or different Examples: Neurotrophin-4: two identical subunits Haemoglobin - two alpha and 2 beta subunits

Question 35

Explain simply the following: Primary structure Secondary structure Supersecondary structure Tertiary structure Quaternary stcruture

Answer 35

Primary structure - Amino acid sequence of the protein stabilized by peptide bonds Secondary structure - local rearrangement of residues in helices, sheets, turns, and loop stabilized by H-bonds between C=o and N-H groups of the backbone Spersecondary structure - Combination of a few secondary structure elements usually performing a particular function Tertiary structure - Overall 3D structure of the protein stabilized by interactions between side chains Quaternary stcrture - Arrange,elements of subunits in a protein made of ore that one chain and stabilized by interactions between side chains

Question 36

Explain what protein domains are explain how they are organised

Answer 36

Proteins domains are spatially distinct fragments of a polypeptide chain Protein domains are organised in functional and/or structural units that all called domains

Question 37

Explain the domains number of domains in eukaryotic proteins

Answer 37

Most proteins have multiple domains 80% of eukaryotic proteins are multidomain proteins Only 20% or eukaryotic proteins are single domain proteins

Question 38

Explain domains and subunits

Answer 38

A single polypeptide chain can form several domains but only ONE subunit

Question 39

Explain what domain shuffling is - domain shuffling theory

Answer 39

Some domains appear in more than one protein It is though that many multidomain proteins have arisen during evolution bu the fusion of genes that encoded separate proteins in an ancestor

Question 40

Explain Domain movement

Answer 40

Flexible connections between domains allows their movement in relation to each other

Question 41

Name the 3 different types of cofactors in enzymes and give examples

Answer 41

Prosthetic groups (covalently bound to the protein, e.g. haem in haemoglobin) Metal ions ( Zn2+, Fe3+, etc.) Coenzymes (often vitamins)

Question 42

Explain what the active site of an enzyme is

Answer 42

A cleft or groove in the protein containing residues that bond the substarte and residues that perform the catalytic reaction Active site is complementary to the substrate in terms of size, shape, charge and hydrophobicity

Question 43

Explain the lock and key model

Answer 43

According to this model the active site is rigid and the substarte fits the active site like a key fits a lock The model cannot explain why some enzymes act on a large range of substrates

Question 44

Explain the induced fit model

Answer 44

According to this model, the substrate induces a change in the enzyme structure that allows fitting Enzymes are not rigid but flexible and mould to fit the substarte molecule This model explains why sone enzymes can act on a very large range of substrates

Question 45

Explain the role of Hexokinase in the induced fit model

Answer 45

Hexokinases phosphorylates glucose to glucose 6- phosphate Conformational changes in hexokinase are associated with glucose biding to the active site

Question 46

Explain the function of Phosphofructokinase 2 (PFK2) Give the equation

Answer 46

PFK2 is a bifunctional enzymes wit 2 domains: a. Kinase domain b. Phosphate domain Fructose 6-phopshate makes fructose 2,6-bisphospahate using kinase Reversible reaction going from fructose 2,6-bisphopstae to fructose 6-phophaste using phosphate

Question 47

Explain the 3-point attachment model

Answer 47

Two chemically identical groups in the substarte, a1 and a2 can be distinguished by an enzyme because the substrate binds in the active site at three or more points

Question 48

Explain what sickle cell anaemia is and the difference with RBC'S

Answer 48

Normal red blood cells live ~ 120 days in the bloodstream, but sickle cells die after 10-20 days Sickled cells cause blockage that deprive organs and tissues of oxygen Not enough red blood cells in the bloodstream to carry oxygen resulting in anaemia

Question 49

Explain the molecular mechanism of sickle cell anaemia and what happens during glutamate to valine mutation in haemoglobin

Answer 49

Glu is hydrophilic whereases Val is hydrophobic In deoxygenated HbS a hydrophobic picket with Phe and Leu is exposed on the surface Val is attracted to Phe and Leu on another HbS molecule by hydrophobic interactions Many HbS molecules aggregate into HbS fibres These fibres cause red blood cells to become stiff and assume a distorted shape that can block blood vessel Frequent episodes of sever pain, organ damage (oxygen deprivation), serious infections or ven stroke

Question 50

Explain what Goucher disease is

Answer 50

Most common lipid storage disease Caused by mutations in acid-beta-glucosidase that break down glucosylceramide: Glucosylceramide makes glucose + ceramide Intracellular accumulation of glucosylceramide, particularly in the spleen, liver and bone marrow

Question 51

Explain the structure of acid-beta-glucosidase

Answer 51

Some of the known mutations are in a surface loop that forms part of the active site of the enzyme They appear to stabilize the conformation that limits access to the active site These mutations reduce enzyme catalytic activity

Question 52

Explain the molecular mechanism of acid-beta-glucosidase

Answer 52

Open conformation with access to the active site Closed conformation with restricted access to the active site