intro to protein structure

Question 1

what are proteins made of

Answer 1

amino acids

Question 2

what are conformational changes

Answer 2

structural arrangement changes associated with function

Question 3

what are enzymes

Answer 3

proteins that are highly efficient and specific catalysts, substrate binds to its active site

Question 4

general structure of amino acids

Answer 4

primary amino group (NH2)
carboxyl group
hydrogen atom
variable R group

-all are enantiomers except glycine

Question 5

how are enantiomers of amino acids distinguished

Answer 5

optical rotations of plane polarised light
right-D
left-L
L mostly found in proteins, D mostly found in bacteria cell wall

Question 6

how are amino acids distinguished

Answer 6

by their R chain

Question 7

2 main classes of amino

Answer 7

hydrophobic and hydrophillic

Question 8

describe a zwitterion, cation and anion

Answer 8

zwitterion=normal amino acid form, NH3+ and COO-
cation= at low pH, NH3+ and COOH
anion= high pH, NH2 and COO-

as pH decreases, a H+ will be added to carboxylate, as pH increases, H+ is removed to the NH3+

Question 9

what joins amino acids together

Answer 9

peptide bonds
-amino group and carboxyl group joins, covalent, partial double bond character, planar, restricts movement of the backbone

Question 10

why are rotations about the peptide bond restricted

Answer 10

due to the resonance of the double covalent bond that helps define how proteins are folded

Question 11

describe the different structures of proteins

Answer 11

primary- linear structure of amino acids (polypeptide)

secondary- localised organisation of parts of the polypeptide chain, alpha helix and beta sheets, folding due to H bonds

tertiary- 3D arrangement of polypeptide chain maintained by VDW, H bonds, disulphide bonds

quaternary- two or more polypeptide chains into a multi subunit complex

Question 12

describe the primary structure of proteins

Answer 12

linear structure of amino acids (polypeptide)

Question 13

describe the secondary structure of proteins

Answer 13

localised organisation of parts of the polypeptide chain, alpha helix and beta sheets, folding due to H bonds

Question 14

describe the tertiary structure of proteins

Answer 14

3D arrangement of polypeptide chain maintained by VDW, H bonds, disulphide bonds

Question 15

describe the quaternary structure of proteins

Answer 15

two or more polypeptide chains into a multi subunit complex, can also contain prosthetic groups

Question 16

describe alpha helix structure

Answer 16

-repetitive local hydrogen bonding between carboxyl and amino group
-cylindrical rod shape with R groups outside of helix

Question 17

describe beta pleated sheet structure

Answer 17

-repetitive hydrogen bonding between adjacent sections of the polypeptide
-parallel sheets=sections running in same direction
-antiparallel sheets= sections running in opposite directions
-R groups appear above and below plane of sheet

Question 18

describe the structure of connecting loops/coils

Answer 18

-not repetitive hydrogen bonding
-less hydrogen bonds
-connects alpha helices and beta sheet

Question 19

what is a domain

Answer 19

distinct region with specific structure performing specific functions

Question 20

what does homomeric and heteromeric mean when describing quaternary structure

Answer 20

homomeric- identical chains
heteromeric- different chains

Question 21

how can protein contribute to diseases

Answer 21

errors in protein folding can contribute to diseases like alzheimers

Question 22

location of hydrophobic and charged residues on proteins

Answer 22

-hydrophobic residues are usually buried in the core of the protein
-charged residue on the water exposed surface

Question 23

what are the two main classes of domains

Answer 23

functional- mediate a particular activity of the protein

structural- region of 40+ amino acids that form a stable secondary and tertiary structure

Question 24

describe globular proteins

Answer 24

high water solubility, compactly folded, includes most enzymes/transporters like haemoglobin and regulators

Question 25

describe fibrous proteins

Answer 25

elongated, low water solubility, large amounts of regular secondary structure, often forms stiff multimeric fibres like collagen/elastin/keratin

Question 26

describe integral membrane proteins

Answer 26

associated with membranes, usually alpha helices, contains hydrophobic amino acids that span the lipid region of membrane, includes receptors/transporters

Question 27

examples of integral membrane proteins

Answer 27

receptors, transporters, cell matrix proteins

Question 28

example of globular proteins

Answer 28

enzymes, transporters like haemoglobin and regulators of gene expression

Question 29

example of fibrous proteins

Answer 29

collagen, elastin, keratin

Question 30

name the 3 structural classes of protein

Answer 30

globular, fibrous, membrane

Question 31

biological functions of proteins

Answer 31

enzyme catalyst, transport, structural, signalling

Question 32

where are non polar side chains found

Answer 32

in hydrophobic regions of the protein

Question 33

where are uncharged polar/acidic/basic side chains found

Answer 33

found on the outside, hydrophilic regions, in aqueous environments