Introduction to protein structure

Question 1

what are the two properties binding is characterized into?

Answer 1

affinity
specificity

Question 2

what does protein + carbohydrate give?

Answer 2

glycoprotein

Question 3

what does protein + lipid?

Answer 3

lipoprotein

Question 4

what is the structure of an amino acid?

Question 5

what are the two main classes amino acids are put into?

Answer 5

hydrophilic and hydrophobic

Question 6

what are hydrophilic amino acids classified as?

Answer 6

basic
acidic
polar

Question 7

how do the two forms, anion and cation, of amino acids occur?

Answer 7

as pH decreases a H+ ion added to carboxylate
as pH increases a H+ removed form NH3+

Question 8

what interactions do non-polar, aliphatic amino acids undergo?

Answer 8

hydrophobic

Question 9

what interactions do polar, uncharged amino acids udnergo?

Answer 9

hydrophilic

Question 10

why is the movement of the backbone of proteins prevented?

Answer 10

peptide bond is planar

Question 11

what is the primary structure of the protiens?

Answer 11

‘linear sequence of amino acids’

Question 12

secondary structure of proteins?

Answer 12

‘the localized organization of parts of a polypeptide chain’
e.g. alpha helix and beta pleated sheets dn connecting loops

Question 13

tertiary structure of proteins?

Answer 13

3D structure of polypeptide chain

Question 14

quaternary structure of protiens?

Answer 14

two or more polypeptide chains joined together

Question 15

what is the structure of alpha helix?

Answer 15

cylindrical
H-bonding between carbonyl of first amino acid and fifth amino acid
proline doesn’t have an alpha helix

Question 16

structure of beta sheets?

Answer 16

‘H-bonds between beta strands
run in parallel or anti-parallel
R-groups face up/down’

Question 17

structure of teritiary strucutre?

Answer 17

covalent and non-covalent bonds
determined by amino acid sequence

Question 18

different types of quaternary structures?

Answer 18

Homomeric and heteromeric

Question 19

structure of quaternary structures?

Answer 19

hydrogen bonding and van der Waals

Question 20

what do proteins fold into?

Answer 20

native conformation

Question 21

where are hydrophobic and polar, charged residues buried?

Answer 21

hydrophobic in core of protein
polar/charged on water exposed surface

Question 22

how are disulphide bridges formed?

Answer 22

covalent bonds formed between cysteine residue
intra and inter molecular bonding
formed under oxidizing conditions

Question 23

what are domains?

Answer 23

‘distinct regions of proteins that function and fold independently and are functionally and structurally conserved’

Question 24

what do functional domains do?

Answer 24

control certain activity of protein

Question 25

what are structural domains for?

Answer 25

region of amino acids that form secondary and tertiary structures

Question 26

what are structural motifs?

Answer 26

‘super-secondary structures that control similar function in different proteins’

Question 27

what are the structural classes of protiens?

Answer 27

globular, fibrous, integral membrane

Question 28

what are globular proteins?

Answer 28

high wate solubility
compactly folded
included enzymes, transporters

Question 29

what are fibrous proteins?

Answer 29

‘elongated proteins
low water solubility
large amounts of regular secondary structures’

Question 30

what are integral membrane proteins?

Answer 30

associated with membranes
include hydrophobic amino acids

Question 31

how are proteins related?

Answer 31

‘protein families are evolutionary related’

Question 32

why is protein structure important for drug development?

Answer 32

aspirin covalently bonds to cyclooxygenase

Question 33

how are proteins degraded?

Answer 33

difficult to access with protease for so ubiquitin-proteasome pathway used
then polyubiquitination
polyubiquitination recognised and unwinds secondary structure of ubiquitinated protein and hydrolyzes it

Question 34

what are biomarkers used for?

Answer 34

to detect tissue damage