Amino acids + proteins

Question 1

what makes up most of cell’s dry mass

Answer 1

amino acids

Question 2

how many amino acids are in plants, animals + microbial + how many are encoded by genetic code

Answer 2

300

20

Question 3

what does a alpha carbon mean

Answer 3

central Carbon - hydrogen + amine + carboxyl group + variable side chain attached to

Question 4

what do optical isomers mean

Answer 4

same structural formula but different spatial arrangement of atoms
2 enantiomers - mirror images

Question 5

which amino acid doesn’t have a optical isomer and why

Answer 5

glycine

doesn’t have asymmetric carbon - doesn’t have 4 diff gaps attached

Question 6

what way can most amino acids rotate the polarised light

Answer 6

L - rotates light to the left

Question 7

what does it mean if optical isomers are optically active

Answer 7

can rotate the plane of polarised light
L - light to the left
D - light to the right

Question 8

what are the charges on amino acids

Answer 8

dipolar ions = positive + negative charged

but are zwitterions - net charge = 0

Question 9

what is pK values for carboxylic acid groups

Answer 9

2.2 - strong acid

readily donate protons

Question 10

what is pK value for alpha amino group

Answer 10

9.4

readily ionise

Question 11

what happens to amino groups + carboxylic acid groups on AA at pH 7.4

Answer 11

amino acid group protonated - POSITIVE (NH3+)

carboxylic acid grp –> carboxylate (conjugate base)(COO-)

Question 12

what happens to the amino acid in very acidic conditions

Answer 12

net charge is positive

excess number of free protons present from acid

Question 13

what happens to the amino acid at neutral pH

Answer 13

net charge is neutral

it is a zwitterion

Question 14

what happens if the amino acid net charge is negative

Answer 14

it is in Anionic form

its in basic condition

Question 15

why are amino acids amtopheric

Answer 15

they have basic + acidic groups

Question 16

what happens to the groups on the amino acid at a high pH

Answer 16

carboxylic group will lose proton first –> bound more loosely than amino group
COO- + NH2

Question 17

what happens to the groups on amino acid as the pH decreases

Answer 17

NH3+ AND COOH

amino group is protonated

Question 18

describe the beginning of graph of titration of amino acid

Answer 18

1. • curve is steep up to pH 2 –> there’s no buffer - so can’t resist pH change
2. pH 2.34 carboxyl group acts as buffer + loses proton (COO-) –> Ph doesn’t change much = BUFFERING REGION

Question 19

what is the isoelectric pH of amino acid

Answer 19

pH 6.1

net charge of molecule = 0

Question 20

what is the pKa of carboxylate ion

Answer 20

pKa 2.34

Question 21

what happens to the amino group of the AA at around pH 10 and what is the pKb of the amino group

Answer 21

amino group acts as a buffer now

pKb = 9.87

Question 22

what does it mean if the AA is negatively charged

Answer 22

all groups have been ionised

Question 23

what is the overall trend of the AA graph

Answer 23

as the pH increases, AA net charge goes from positive –> negative

Question 24

how many inflection point are there on the AA titration graph + what do they mean

Answer 24

4 inflection points

1. half zwitterions + half cations (NH3+ , COOH)
2. all AA are zwitterions
3. half zwitterions + half anions (NH2 , COO-)
4. all AA are anions

Question 25

what does anion mean

Answer 25

negative charged NH2 and COO-)

Question 26

what does cation mean

Answer 26

positive charged NH3+ AND COOH

Question 27

what amino acids are non-polar, neutral + aliphatic inside + outside protein

Answer 27

``` glycine alanine valine leucine isoleucine ```

Question 28

what amino acid are non - polar, neutral + imino acid (bent chain)

Answer 28

proline

Question 29

what amino acids are non polar, neutral + aromatic

Answer 29

phenylalanine | tryptophan

Question 30

what amino acids are non- polar, neutral + contain sulphur

Answer 30

cysteine | methionine

Question 31

what amino acids are polar, neutral + aromatic --> what is it used for

Answer 31

tyrosine | aromatic = site for phosphorylation

Question 32

what amino acids are polar, neutral + contain OH group --> what is used for

Answer 32

threonine serine OH group --> site for glycosylation

Question 33

what amino acids are polar, neutral + contain NH2 groups + what reason

Answer 33

asparagine glutamine site for glycosylation

Question 34

what amino acids are polar, acidic + carry negative OH carboxyl group

Answer 34

aspartic acid | glutamic acid

Question 35

what amino acids are polar, basic + carry positive NH3 amino group

Answer 35

arginine lysine histidine

Question 36

what is the isoelectric point

Answer 36

point at which AA doesn't carry net charge

Question 37

what is the formula to work out pI (isoelectric point) + when can you use this formula

Answer 37

pI = (pKa + pKb) / 2 | when there are more than 2 ionisable groups

Question 38

what to do if you want to find pI but have 3 or more ionisable groups on AA

Answer 38

take pK values closest to neutral + use those vlues

Question 39

how to find pI of glutamic acid

Answer 39

acidic, take lowest pK charges

Question 40

how to find pI of arginine

Answer 40

basic | take pK charges of 2 highest values

Question 41

which AA are precursors of nucleotides

Answer 41

aspartate, glycine, glutamine

Question 42

what is serotonin and which AA is its precursor

Answer 42

it is a neurotransmitter | tryptophan is precursor

Question 43

In a polypeptide, what is the N terminal and the C terminal

Answer 43

N terminal = free amino group at the first AA in polypeptide | C terminal = free carboxyl group in polypeptide

Question 44

which terminal is always synthesised first in protein synthesis

Answer 44

N terminal | left to right

Question 45

what is post translational modification

Answer 45

AA contained in proteins are altered after translation in protein synthesis

Question 46

what can post translational modifications include

Answer 46

phosphorylation | glycosylation are essential for protein function

Question 47

what are most common function + uses of protein

Answer 47

growth + repair | enzymes, hormones, DNA, RNA

Question 48

what is protein folding

Answer 48

protein has more than 1 stable folded conformation, each has its own conformation + function but only 1 is active its reversible

Question 49

what is a prosthetic group

Answer 49

proteins tightly associated with other chemical/non-protein species helps to perform function

Question 50

what is the primary structure of a protein

Answer 50

AA sequence peptide bonds between each AA determined by our DNA

Question 51

what is secondary structure of protein

Answer 51

folding/ coiling of polypeptide chain into alpha helix or beta pleated sheet weak H bonds between H atom + electronegative atoms (N or O)

Question 52

how many turns in secondary structure for polypeptide chain in alpha helix + how do the bonds form

Answer 52

3.6 amino acids | H atom in peptide bond is shared with 4th AA instead

Question 53

what is the tertiary structure of protein

Answer 53

3D shape of polypeptide chain | fibrous or globular

Question 54

what type of bonds are there in terry structure of protein

Answer 54

electrostatic attraction/ salt bridge van der Waals forces disulphide bon hydrophobic interaction

Question 55

how does electrostatic attraction / salt bridge occur in tertiary structure

Answer 55

between oppositely charged ions or groups

Question 56

how do van Der Waals forces occur in tertiary structure

Answer 56

weak but needed in close packed interior of proteins + specific shape of enzyme active site

Question 57

how do disulphide bonds occur in tertiary structure

Answer 57

strong bond between specific cysteine AA | locks protein in configuration

Question 58

how does hydrophobic interaction occur in tertiary structure

Answer 58

between non-polar hydrophobic AA

Question 59

what is quaternary structure of protein

Answer 59

combo of more than 1 proteins + involves non-covalent bonds between proteins

Question 60

give example if 1 protein with 4 polypeptide chains + 1 protein with 3

Answer 60

haemoglobin - 4 polypeptide chains + 4 haem groups | collagen - 3 helical polypeptide chain supercoiled with each other

Question 61

what are the 3 protein classes

Answer 61

globular fibrous membrane associated

Question 62

what are the characteristics of globular proteins

Answer 62

soluble enzymes/ antibodies Tertiary structure when non - polar hydrophobic AA move in + polar hydrophilic AA bound outwards

Question 63

give 2 examples of globular proteins + give their uses

Answer 63

carbonic anhydrase - large beta pleated sheet in centre + active site has Zn ion ---> catalyses hydration of CO2 --> HCO3- + H+ Hb - 4 globular proteins bound together - electrostatic attraction + H bonds + hydrophobic interaction each protein associated with haem grp contains iron that binds to O2

Question 64

what are the characteristics of fibrous proteins

Answer 64

``` wire like structural/storage function used to construct connective tissues + bones repeated AA sequences contains cross links between chains ```

Question 65

what is use + nature of keratin

Answer 65

keratin - tough + insoluble high proportion of small AA (glycine + alanine) lots of cysteine --> lots disulphide bridge -- thermal stable + permanent --> rigid can assemble into intermediate filaments for cell cytoskeleton

Question 66

what are 2 examples of fibrous proteins

Answer 66

keratin | collagen

Question 67

what is use + nature of collagen

Answer 67

secreted by connective tissue cells | most abundant protein in mammals (25%)

Question 68

what do membrane associated proteins include (where found)

Answer 68

transmembrane proteins integrated in phospholipid bilayer lipid associated proteins -- inner + outer of membrane + proteins transporters, linkers, receptors, enzymes on cell membrane