Lecture 15: Protein structure and function

Question 1

Proteins are..

Answer 1

single, un-branched chains of a.a with numerous diverse functions

Question 2

Proteins divers functions:

Answer 2

• Catalysis
• Energy production
• Host/pathogen interaction: antibodies, mucus
• Structural: keratin, fibroin, collagen
• Motion (cytoskeleton, muscle, flagella)
• Organisation of DNA and regulation of transcription (histones)
• Regulation (e.g. kinases)
• Storage (seeds, eggs etc)
• Toxins and venoms
• Transport: across membranes, haemoglobin.

Question 3

catalysis:

Answer 3

enzymes accelerate biochemical reactions

Question 4

Energy production:

Answer 4

(light harvesting, electron transport, rotary ATPases)

Question 5

Proteins comprise chains of amino acids joined by

Answer 5

peptide bonds

Question 6

peptic bonds formation:

Answer 6

Condensation reaction:

Loss of water.

Question 7

peptide bond:

Answer 7

O
       || 
(+) -C -N-  (-)
       |
      H

Question 8

2 types of terminus

Answer 8

• Amino ‘N’ terminus

- Carboxyl ‘C’ terminus

Question 9

The polypeptide protein backbone has

Answer 9

amino acid side chains (can be polar and non polar)

Question 10

3 types of amino acid

Answer 10

• nonpolar
• polar
• Electrically charged

Question 11

__ protein amino acids have side chains with ____ properties

Answer 11

20

different

Question 12

polypeptide backbone is..

Answer 12

identical in all proteins

Question 13

Side chins determine…

Answer 13

how the polypeptide chains of the protein interact and how the protein is folded

Question 14

Four levels of structural organisation of proteins

Answer 14

Primary
Secondary
Tertiary
Quaternary

Question 15

Primary

Answer 15

Linear sequence of amino acids

Question 16

Secondary:

Answer 16

localized organization of parts of polypeptide chain (e.g.  helix or  sheet) - using hydrogen bond

Question 17

Tertiary:

Answer 17

three‐dimensional arrangement of polypeptide chain. Non‐polar amino acids typically inside and polar side chains on outside. Stabilised by H‐bonds and disulphide bonds.

Question 18

Quaternary:

Answer 18

association of two or more polypeptides into multi‐subunit complex. Rubisco has 16 subunits.

Question 19

Proteins are held together by

Answer 19

different ionic interactions;

• ionic,
• van der Waals
• hydrogen bonds
• electrostatic interactions

Question 20

ionic

Answer 20

Atraction between +ve and -ve charged ions:

O- & N+

Question 21

van der Waals

Answer 21

Short-range weak electrical attraction & repulsion

Question 22

Hydrogen bonds:

Answer 22

involve a H shared between O and N atoms

Question 23

alpha helix resembles a

Answer 23

spring with h-bonds joining loop to loop

Question 24

Beta sheet resembles a

Answer 24

folded piece of paper (fan) H-bonds lie length ways

Question 25

polypeptide chains can be linked by

Answer 25

``` covalent bonds (tertiary structure) -forms inter and intrachain disulphide bonds ```

Question 26

intrachain disulfide bonds -

Answer 26

between the same chain

Question 27

interchain disulphide bonds -

Answer 27

between 2 separate chains

Question 28

Where do | Proteins undergo ________ to enhance their _____ before secretion

Answer 28

In the ER. Proteins undergo processes such as glycosylation and disulphide bond formation to enhance their stability before secretion.

Question 29

Glycosylation:

Answer 29

he controlled enzymatic modification of an organic molecule, especially a protein, by addition of a sugar molecule

Question 30

The ER lumen has a

Answer 30

Distinct environment

Question 31

Eg. of protein passage through ER

Answer 31

1) polypeptide enters rough ER, brought by ribosome. 2) Sugar chains attached = glycoprotein 3) Transport vesicle buds off 4) Secretory (glyco) protein inside transport vesicle

Question 32

Glutathione is a

Answer 32

tripeptide of Gly, Cys and Glu. | Exists i reduced (GSH) and oxidised (GSSG) forms

Question 33

The OXIDISING redox environment of secretory pathway supports

Answer 33

disulphide bond formation (~ equal concentrations of GSH and GSSG)

Question 34

In the cytosol (GSH AND GSSG)

Answer 34

[GSH] >> [GSSG] so glutathione reduction potential is also reducing.

Question 35

Secretory pathway involves

Answer 35

ER + Golgi

Question 36

Mucin is a

Answer 36

Glycosylated protein/ proteoglycan

Question 37

Man produces ____ of mucus

Answer 37

~ 1 litre/day

Question 38

Mucin has

Answer 38

Large, extracellular glycoproteins with hundreds of oligosaccharide chains linked to a protein backbone. Either anchored (transmembrane) or secreted

Question 39

High glycosylation of mucins makes them

Answer 39

resistant to acids (stomach acid), proteolysis, and adds gel-like properties found in mucosal barriers

Question 40

Examples of animals with mucin

Answer 40

Fish (hagfish), amphibians, corals

Question 41

Keratin: The formation of disulphide bridges between two cysteines on separate polypeptide chains allows for

Answer 41

the cross-linkage of the chains.

Question 42

% of amino acids in keratin are cysteine

Answer 42

25

Question 43

in keratin S-S bonds give

Answer 43

Great stability

Question 44

Beta keratins:

Answer 44

feathers, beaks & claws composed of beta-pleated sheets, twisted and cross-linked by disulphide bridges

Question 45

Alpha-helical keratins

Answer 45

mammalian hair, horns and hoof

Question 46

Beta keratins vs alpha-helical keratins

Answer 46

BETA STRONGER

Question 47

Sulphurous smell of

Answer 47

burning keratin

Question 48

Perming hair:

Answer 48

example of how secondary & tertiary structure of a protein can be modified. 1) natural hair 2) distorted in roller 3) heat/ reducing agent, ammonium thioglycolate added 4) S-S linkages broken (by reduction) 5) add H2O2 6) New S-S linkages form (by oxidation)

Question 49

Collagen is the

Answer 49

major extracellular insoluble fibrous protein and most abundant protein in animals. Help tissues withstand stretching.

Question 50

Helices cannot form in the absence of

Answer 50

scorbic acid (no hydroxyproline formed), hence blood vessels, tendons and skin become fragile, leading to scurvy

Question 51

Fibroin

Answer 51

Silk

Question 52

Glycine and alanine in silk

Answer 52

High glycine and less alanine, have small non-polar side chains

Question 53

In silk what do the small non-polar side chains allow

Answer 53

tight packing of the antiparallel β sheets, which contributes to silk's rigid structure and tensile strength, comparable to that of high‐grade alloy steel, although density is ~6 times less

Question 54

Spinning a silk web: | Where is it stored?

Answer 54

Silk protein stored as an emulsion. C‐ terminus ensures solubility, core is hydrophobic

Question 55

Spinning a silk web: What leads to silk emulsion unfolding

Answer 55

change in the environment

Question 56

Spinning a silk web: The thread leaves the ____ through the ____ which...

Answer 56

SPINNERET SPIGOT ...strips off residual water. The molecules are stretched out and linked together to form long strands

Question 57

Spinning a silk web: | Molecule movement

Answer 57

Water and Na+ leave lumen; K+, surfactants and lubricants enter, pH falls from 7.6 to 5.7

Question 58

Spinning a silk web: Folded conformation in aqueous environment

Answer 58

- hydrophobic core region contains non polar side chains | - Polar side chains on the outside of the molecule can form hydrogen bonds to water

Question 59

Spinning a silk web: | unfolded polypeptide

Answer 59

long unfolded polypeptide with polar and non-polar side chains distributed along it

Question 60

Making bread:

Answer 60

Protein (gluten) is key constituent of wheat flour (~12% protein). Gluten forms a matrix trapping CO2 bubbles. Gluten proteins linked by hydrogen bonds and disulphide bridges (broken by adding ascorbate).

Question 61

Making bread: mechanical work:

Answer 61

As mechanical work stretches the dough, more hydrogen bonds can form between chains of gluten subunits

Question 62

Sickle cell anaemia - is a ____ mutation. what happens?

Answer 62

Single muta on (GAG → GTG) replaces Glu6 (polar, hydrophilic) with Val6 (nonpolar, strongly hydrophobic) in the β‐ globin chain of haemoglobin (a single‐nucleotide polymorphism).

Question 63

HbS =

Answer 63

The sickle cell genes make the body produce abnormal haemoglobin called HbS

Question 64

Sickle cell anaemia: What happens during deoxygenation (loos of O2)

Answer 64

hydrophobic residues rapidly associate. Generates rigid fibres of HbS

Question 65

Is polymerisation of HbS reversible?

Answer 65

YES fibres ‘melt’ as O2 is taken up and the normal discoid shape returns. Sickling/unsickling cycles lead to damage to the cytoskeleton and erythrocyte membrane, resulting in sickle‐shaped cells and anaemia.

Question 66

% of birth in sub-Saharan Africa with sickle cell anaemia

Answer 66

0.74