Chapter 3-theory

Question 1

what are amino acids

Answer 1

the building blocks of proteins

Question 2

what are proteins

Answer 2

linear polymers of amino acids

Question 3

what are all proteins produced from

Answer 3

20 standard amino acids

Question 4

what do all living organisms make there proteins from

Answer 4

the same pool of amino acids

Question 5

how does 20 building blocks enable sequence diversity

Answer 5

for example a peptide of three residues could be produces 8000 ways

a protein on 100 residues has 1.3x10130 possible sequences

Question 6

what is the advantages of making biomolecules as polymers of smaller, simpler building blocks

Answer 6

1) simplicity of chemistry
(one type of reaction for polymerization, a second type of reaction for degration)

2) recycling
(biomolecs can be digested back to component building blocks which are reusable for production of other biomolecs)

3) diversity
(the vast number of varying lengths and sequences)

Question 7

what are the common features of amino acids

Answer 7

a hydrogen
central alpha C
Amino group
carboxyl group
side R chain

Question 8

how do amino acids differ

Answer 8

the side chain group

Question 9

how are amino acids constructed except glycine

Answer 9

the alph carbon is bonded to four different groups, this creates chiral caneter

Question 10

how do amino acids have stereoisomers

Answer 10

the four different groups occupy unique spatial arrangements giving stereoisomers labelled as the L and D isomers

Question 11

what stereoisomer are proteins made from

Answer 11

biologically proteins are made almost exclusively from L amino acids

Question 12

what are the groups that amino acids are grouped into based off there properties

Answer 12

non-polar aliphatic
aromatic
polar, uncharges
polar, positively charges
polar, negatively charged

Question 13

what are some characteristics of the non-polar, aliphatic amino acids

Answer 13

-mainly hydrocarbon side chains
-residues with non-polar chains are often buried in the core of the protein

Question 14

what are the amino acids that fit into non-polar, aliphatic amino acids (7)

Answer 14

glycine
alanine
valine
leucine
isoleucine
proline
methionine

Question 15

what are some unusual amino acid characteristics of nonpolar, aliphatic amino acids

Answer 15

glycine-only one thats not a cyro C and smallest acid
proline-has a ring
methionine-has a S group present

Question 16

what amino acids are in the aromatics

Answer 16

tyrosine
phenylalanine
tryptophan

Question 17

what is the largest amino acid

Answer 17

tryptophan

Question 18

what is a phosphoralation

Answer 18

it is a type of post-translational modification
-phosphoryl groups are added by kinases to specific, hydroxyl-group containing amino acids (tyr, ser, thr)

Question 19

what is post translation modification phosphorylation

Answer 19

phosphorylation is when certain amino acids can be covalently modified after their incorporation into a protein (post-translation)

Question 20

in post translational modification what removes the phosphatases

Answer 20

phosphoryl

Question 21

in post translational modification what adds the phosphatases

Answer 21

kinase

Question 22

are post translational modifications reservable

Answer 22

yes

Question 23

what amino acids are in the polar, uncharged group

Answer 23

cysteine
asparagine
glutamin
serine
threonine

Question 24

what can two cystines do

Answer 24

they can form covalent linkages called disulphide bond

Question 25

disulfide bonds important...

Answer 25

for stabilization of some protein structures

Question 26

why can cystine form a disulphide bond

Answer 26

because the S is at the end of the amino acid

Question 27

what polar, uncharged amino acids can be modified through phosphoralation

Answer 27

serine threonine

Question 28

how do disulphide bonds form

Answer 28

through the oxidation of the sulfhydryl groups of two cysteine residues to for, a covalent linkage

Question 29

what do disulphides do

Answer 29

they stabilize protein structures

Question 30

cystine residue forming a disulphide bond must...

Answer 30

be within close proximity in space within the protein structure

Question 31

are disulphide bonds intra or inter-molecular

Answer 31

they can be both

Question 32

what is the effects of cooking an egg

Answer 32

heat+protein=protein starting to unfold and get tangled and ppt out of solution

Question 33

what amino acids are in the positively charged group

Answer 33

lysine arginine histidine

Question 34

what is the most polar group

Answer 34

the positively charged group

Question 35

what amino acids in the polar group carry a + charge at physiological pH

Answer 35

lysine arginine

Question 36

if histidine isnt + charges at biological pH why is in the + group

Answer 36

-because it has the potential to carry a + charge -its imidazole has a pKa of 6 (near physiological pH) (that fraction will be +1 and the rest will carry a net 0 charge) -cell pH=7 -10:1=90% unprotinated

Question 37

what does histidine do in enzymatic reactions

Answer 37

it serves as a proton accepter/donor

Question 38

what amino acids are in the negatively charged group

Answer 38

aspartate glutamate

Question 39

what is is glutamate responsible for

Answer 39

-for one of the five basic tastes (umami) -it is used for a flavor enhancer (monosodium glutamate (MSG))

Question 40

what can aspartate and glutamate also be called

Answer 40

glutamic acid aspartimic acid

Question 41

what does it mean that every amino acid has diprotic

Answer 41

every amino acid has at least two groups that accept and donate protons

Question 42

what do triprotic amino acids have

Answer 42

ionizable groups in their side chains (lys, arg, his, asp, glu, cys and tyr)

Question 43

what do diprotics have

Answer 43

two buffering groups

Question 44

what do triprotics have

Answer 44

three buffering regions

Question 45

what are the ionizable groups in the amino acids

Answer 45

carboxyl group amino group side chains off the triprotic amino acids

Question 46

what does each ionizable group have

Answer 46

a specific pKa

Question 47

what is the pKa

Answer 47

the pH at which that group changes its protonation state

Question 48

when pH is below the pKa...

Answer 48

the protonated form predominates (HA)

Question 49

when pH is above pKa...

Answer 49

the unprotonated form predominates (A-)

Question 50

what groups do all amino acids have and what are there pKa

Answer 50

carboxyl (pKa=2.0) amino (pKa=10.0)

Question 51

at a pH of 7.4 what form will carboxyl and amine group be in

Answer 51

COO- and NH3+ forms

Question 52

what is the acids and conj base forms of carboxyl

Answer 52

COOH (acid) COO- + H+ (conj base)

Question 53

what is zwitterion

Answer 53

dipolar ion of and amino acid

Question 54

what is the isoelectric point (pI) of an amino acid

Answer 54

it is the average of the pKas on either side of where the net charge is equal to zero it is the pH at which the net charge on the molecule is equal to 0

Question 55

how do you calculate the pI

Answer 55

it is the average of the pKas on either side of where the net charge is equal to zero pI=(pKa 1 + pKa 2) /2