PROTEIN STRUCUTRE AND FUNCTION

Question 1

What are the forces stabilising secondary structures such as alpha helices?

Answer 1

• ionic interactions b/w side chains
• H bonding between side chains
• Hydorphobic interactions between side chains
• Van der waals forces
• dipole-dipole

Question 2

Which two amino acids are often found in beta turns?

Answer 2

glycine and proline due to proline having a high cyclic structure and glycine having a small side chain.

Question 3

What is protein structure determined by?

Answer 3

amino acid sequence

Question 4

What are some non polar side chian amino acids?

Answer 4

Glycine, alanine, valine,leucine, proline

Question 5

What are some polar amino acid side chians?

Answer 5

Serine, cystine, glutamine

Question 6

What are acidic side chains?

Answer 6

Aspartic acid and glutaminc acid

Question 7

What are some basic side chains?

Answer 7

Lysine and histidine

Question 8

What are non covalent interactions?

Answer 8

Ionic interactions (salt bridges) , Hydrogen bonds, van der waals interactions and HYDROPHOBIC INTERACTIONS (water wants to maximise H bonds)

Question 9

What is secondary structure defined through?

Answer 9

Hydrogen bonding patterns between peptide bonds but also stabilised by other weak forces.

Question 10

What is characteristic of the alpha helix?

Answer 10

Positions residues to form max number of hydrogen bonds .

NH2 forms bond with oxygen of 4 amino acids previously (3.6 residues when it turns)

Question 11

What does a helix destabiliser do?

Answer 11

Destabilises the chain to form kinks

Question 12

What is an alpha helix destabiliser?

Answer 12

Proline; side chain of proline cannot form H bond cannot form bond with carbonyl group. If proline is in the chain you get a kink

Question 13

What are helix stabilisers?

Answer 13

Amino group with + and carboxyl with -ve

Question 14

What are beta strands?

Answer 14

Planar group that links chiral centres together

- side chains point up and down

Question 15

What is a beta sheet?

Answer 15

the interacting beta strands

Question 16

What is the direction of the sheets?

Answer 16

NH2 direction to carbonyl terminus

Question 17

Which is better antiparallel sheets or parallel?

Answer 17

Antiparallel because more stable bonds

Question 18

What is a beta turn and which two amino acids are usually found in beta turns?

Answer 18

Form of secondary structure that helps in forming antiparallel sheets-reverses direction of peptide strucutre and compacts the seondary strucutre; glycine and proline

Question 19

What is the tertiary structure?

Answer 19

Spacial conformation of all atoms in a SINGLE polypeptide chain (3D structure of protein)

Question 20

What is the native conformation and what is it driven by?

Answer 20

Mst energeticlaly favourable state. Driven by maximisation of H-bonds and burying of hydrophobic residues

Question 21

Can proteins fold in and out of native states?

Answer 21

YES, this is like when urea unfolds a protein but when removed it folds back to native catalytically active state. (disulfide links are reformed)

Question 22

What is myoglobin?

Answer 22

Tightly folded protein mostly consisting of 8 alpha helices, has iron heme group, found in muscle, stores O2 -globular protein

Question 23

What are quaternery strucutres?

Answer 23

Structure of proteins made up of MORE THAN ONE SUBUNIT (2 subunits= dimer, 3 subunits=trimer, many subunits= oligomer

Question 24

What type of strucutre is haemoglobin?

Answer 24

Tetromer

Question 25

What happens with the iron atom and protein surrounding it?

Answer 25

It makes contact with the amino acids in the protein such as histidine residue.

Question 26

What happens when oxygen binds to the haemoglobin?

Answer 26

The porphyrin ring moves from the T state (low affinity for oxygen) (fe2+) to R state Fe3+.

Question 27

What is the coorperative effect?

Answer 27

When one oxygen binds to one subunit heme ring,this triggers the binding of all other units. - when o2 binds it changes the surrounding amino acids.T–>R state.

Question 28

What are symptoms of sicke cell anaemia?

Answer 28

Low blood pressure, fatigue and difficultybreathing, yellowing of skin and paleness, muscular weakness, heart palpitations.

Question 29

What occurs in sickle cell anaemia?

Answer 29

Change from a glutamate (polar-charged)to a valine (non polar). It is the valine that then forms a ‘sticky’ patch on surface of beta subunits. At position 6. - on alpha helix.

Question 30

In sickle cell anaemia why are the cells elongated?

Answer 30

Because there are fewer cells and the cwlla that exist have abnormalities.- this alters the gas carrying capactiy of RBCs. BEta subunits join to form strands.

Question 31

What is the sickle cell protein?

Answer 31

Haemoglobin S

Question 32

What are fibrous proteins?

Answer 32

Elongated, filamentous chains usually joined by cross linkages. Composed of single secondary structure element. E.g. keratin,- alpha helix, silk- b sheet, collagen-alpha helix. Usually insouble in water

Question 33

What does collagen consist of?

Answer 33

3 left handed (weird) alha helices coiled around one another in right handed superhelix. Important strucural functrion in extrscellular matrix. Most abundent protein in vertebrates.

Question 34

What stabilises collagen?

Answer 34

H bonds between the chains. Made up of Gly-X-Pro or Gly-X-HyPro. The chains are cross linked via lysine residues.

Question 35

What happens when there is more cross linking of collagen chains with increasing age?

Answer 35

Makes bones brittle and skin less elastic.

Question 36

Which substance is vital to human tissue maintainance?

Answer 36

Hydroxyproline.

Question 37

What are amphitropic proteins

Answer 37

Found associated with membranes or free in solution.(biological regulation)

Question 38

What is glycophorin?

Answer 38

Integral transmembrane protein found in RBCs. N terminus is highly glycosylated. and hydrophillic.

Question 39

What does the membrane spanning protein type III bacteriohodopsin do?

Answer 39

Acts as receptor, contains pignment retinal and responds to light.

Question 40

What are residues in zones at boundary between lipid tails and phosphate head groups?

Answer 40

Tyr and Trp residues.

Question 41

What type of transmembrane protein is GLUT1 and where is it found?

Answer 41

type III and found in all cell membranes (ubiquitous) , moves from outside cell to inside

Question 42

What is an amphipathic helix?

Answer 42

One face of GLUT1 has hydrophillic R groups pointing outwards whilst the other face has hydrophobic amino acids pointing outwards- hydrophobic faces contact the membrane and hydrophillic faces form channel for glucose.