Mcat biochem

Question 1

A- all chiral amino acids used in eukaryotes are what type of amino acids?
B- and where are they drawn in a fischer projection?
C-also what absolute configuration does this translate to in the cahn-ingold-prelog system?
D- what is the exception and why?

Answer 1

A-all chiral amino acids used in eukaryotes are L-amino acids
B-this translates to being drawn on the left in a fischer projection
C- this translates to an S absolute configuration for almost all chiral amino acids
D- the exception is cysteine; even though its still an L-amino acid it has an R absolute configuration cuz the CH2SH group has priority over the COOH group

Question 2

what are the seven amino acids that have nonpolar, nonaromatic side chains?

Answer 2

they are alanine, valine, leucine, isoleucine, methionine, proline, and glycine

Question 3

what special atom does methionine have in its side chain? why is methionine considered relatively nonpolar?

Answer 3

methionine has a sulfur atom in its side chain. bcuz the sulfur has a methyl group attached it is considered relatively nonpolar.

Question 4

A- how is proline unique?
B- why is its amino group different from in the other amino acids?
C- what does the amino nitrogen become a part of, and what does it form?
D- what places constraints on the flexibility of proline and what does this limit?

Answer 4

A- proline is unique becuz it forms a cyclic amino acid
B- in all the other amino acids, the amino group is attached only to the alpha-carbon
C- in proline, though, the amino nitrogen becomes a part of the side chain, forming a five-membered ring
D- the five membered ring places constraints on the flexibility of proline which limits where it can appear in a protein and can have significant effects on proline’s secondary structure.

Question 5

draw and know the 7 amino acids with nonpolar, nonaromatic side chains.

Answer 5

confirm their structures here

Question 6

describe the structure of tryptophan

Answer 6

a double ring system that contains a nitrogen atom

Question 7

describe the structure of phenylalanine

Answer 7

a benzyl side chain( a benzene ring plus a -CH2 group)

Question 8

describe the structure of tyrosine

Answer 8

a benzyl side chain(a benzene ring plus a -CH2 group with an OH group attached to the ring

Question 9

draw and know the three amino acids with aromatic side chains

Answer 9

confirm their structures after drawing

Question 10

what are the five amino acids with polar side chains?

Answer 10

they are serine, threonine, asparagine, glutamine, and cysteine.

Question 11

what makes serine and threonine polar and able to participate in a certain type of bonding?

Answer 11

they both have OH groups in their side chains which makes them highly polar and able to participate in hydrogen bonding

Question 12

what type of side chain do asparagine and threonine have?

Answer 12

they have amide side chains

Question 13

A- whats the difference between the amino group in all amino acids and the amide nitrogens in asparagine and glutamine?
B- do the amide nitrogens become charged?

Answer 13

A- unlike the amino group in all amino acids, the amide nitrogens DO NOT gain or lose protons with changes in PH
B- amide nitrogens DO NOT become charged

Question 14

what sort of group does cysteine have in its side chain?

Answer 14

it has a thiol -SH group in its side chain

Question 15

what are two characteristics of the sulfur and what fact does this contribute to and what does this leave the thiol group prone to?

Answer 15

the sulfur is larger and less electronegative than oxygen, the s-h bond is weaker than the o-h bond. this leaves the thiol group in cysteine prone to oxidation

Question 16

draw and know the structures of the five amino acids with polar side chains

Answer 16

confirm them

Question 17

what are the two amino acids with negative charges on their side chains at physiological pH?

Answer 17

they are aspartic acid(aspartate) and glutamic acid(glutamate) at 7.4(physiological pH).

Question 18

how are glutamic acid and aspartic acid different from asparagine and glutamine?

Answer 18

glutamic acid and aspartic acid are different from asparagine and glutamine because glutamate and aspartate have carboxylate COO- groups in their side chains, rather than amides.

Question 19

A- what is the deprotonated form of aspartic acid?

B- what is the deprotonated form of glutamic acid?

Answer 19

A- aspartate

B- glutamate

Question 20

on the mcat, why are you likely to see anion names instead of acid names?

Answer 20

this is because most acids in cells exist in the deprotonated form

Question 21

draw and know the amino acids with negatively charged side chains(also draw the deprotonated forms)

Answer 21

confirm them

Question 22

what are the three amino acids with basic side chains?

Answer 22

lysine, histidine and arginine

Question 23

these three amino acids have side chains with positively charged “what” atoms?

Answer 23

they have side chains with positively charged nitrogen atoms.

Question 24

describe the structure of lysine

Answer 24

lysine has a terminal primary amino group

Question 25

describe the structure of arginine; and wat charge is delocalized and how?

Answer 25

arginine has three nitrogen atoms in its side chain; the positive charge is delocalized over all three nitrogen atoms

Question 26

describe the structure of histidine` | NOW KNOW HOW TO DRAW ALL THREE AMINO ACIDS WITH BASIC SIDE CHAINS

Answer 26

histidine has an aromatic ring with 2 nitrogen atoms(this ring is called an imidazole) CONFIRM THEM ON PAGE 9

Question 27

how can histidine acquire a positive charge

Answer 27

histidine can acquire a positive charge becuz the pKA of the side chain is close to 7.4(its about 6) so at physiologic pH, one nitrogen atom is protonated and the other isnt. Under more acidic conditions, the second nitrogen atom can become protonated, giving the side chain a positive charge.

Question 28

where are amino acids with long alkyl side chains more likely to be found?

Answer 28

inside the protein

Question 29

where are amino acids with polar and charged side chains more likely to be found?

Answer 29

surface of the protein

Question 30

study the one letter and tree letter abbrev's of the amino acids

Answer 30

``` Alanine Ala A Arginine Arg R Asparagine Asn N Aspartic acid Asp D Cysteine Cys C Glutamic acid Glu E Glutamine Gln Q Glycine Gly G Histidine His H Isoleucine Ile I Leucine Leu L Lysine Lys K Methionine Met M Phenylalanine Phe F Serine Ser S Threonine Thr T Tryptophan Trp W Tyrosine Tyr Y Valine Val V ```

Question 31

when do ionizable groups gain or lose protons

Answer 31

they gain them in acidic conditions and lose them in basic conditions

Question 32

what happens when the pH is less than the pKa? greater than the pKa?

Answer 32

when the pH is less than the pKa the majority of the species will be protonated when the pH is greater than the pKa the majority of the species will be deprotonated

Question 33

at a pH of 1 what happens to the amino acid in regards to whats protonated/deprotonated?

Answer 33

they exist as pos charged under acidic conditions at a pH of 1, there are lots of protons in solution we are far below the pKa of the amino group will be fully protonated NH3 and thus positively charged we are also below the pKa of the carboxylic acid group, it will be fully protonated COOH and neutral At very acidic pH values, amino acids tend to be positively charged

Question 34

at physiologic pH how do amino acids exist?

Answer 34

they exist as zwitterions at intermediate pH at a pH of 7.4 we have moved above the pKa of the carboxyl group the carboxyl group will be in its conjugate base form and be depronated, becoming COO- we are also well below the pKa of the basic amino group so it will be fully protonated and its conjugate acid form NH3 so we will have a molecule that has a pos and negative charge but overall the molecule is elec neutral these moles are called zwitterions the charges neutralize each other and zwitterions exist in water as internal salts

Question 35

know how to draw when carboxylic acids become deprotonated at neutral PH?

Answer 35

know how to draw it and check it with the drawing on page `13

Question 36

at basic conditions how do amino acids exist?

Answer 36

amino acids are neg charged under basic conditions

Question 37

know how to draw when amino groups become deprotonated at basic pH forming an anion

Answer 37

know how to draw it and compare with the drawing on page 14

Question 38

if a side chain is charged, how many titration curves does it have? how does glycine exist at low pH values? protonated/deprotonated? with what charge? when the soln is titrated with NaOH, what group is deprotonated first and why?

Answer 38

3 curves fully protonated positively charged the carboxyl group is deprotonated first becuz it is more acidic than than the amino group

Question 39

what happens when 0.5 equivalents of base have been added(what concs are equal?) at this point, what does the PH equal? what happens when the pH is close to the pKa(and what happens to the curve?)

Answer 39

when 0.5 equivalents have been added, the concs of the fully protonated glycine and its zwitterion are equal - at this point the pH=pKa 1 - when the pH is close to the pKa the soln is acting as a buffer, and the titration curve is flat

Question 40

what happens to the concs, what 2 things happen just to the pH, and every molecule when you add 1.0 equivalents of base? how does the molecule exist? what is the pI? how to calc pI for a neutral amino acid?

Answer 40

at 1.0 equivs of base, the amounts of glycine soln and base are now equal the pH starts to go up fast(soln stops acting like a buffer); the pH equals the pI of glycine every molecule is electrically neutral the molecule exists exclusively as a zwitterion the pI is the point at which the molecule is electrically neutral the pI for a neutral amino acid is calculated by adding the pKas for the amino and carboxyl group and divided by 2

Question 41

what happens to the pH(2 things) and concs when we add more base(1.5 equivs)? what phase does it go thru?

Answer 41

the pH is constant the pH equals the pKa2 the concs of the fully deprotonated and zwitterion are equal it goes thru a second buffering phase

Question 42

what happens to the amino acid when you add more base (2.0 equivs)? what happens to the pH?

Answer 42

at 2.0 equivs, the amino acid is fully deprotonated | any more base will only increase the PH

Question 43

what charge does the amino acid have at very acidic pH values? what charge does the amino acid have at very basic pH values?

Answer 43

at very acidic pH values, the amino acid tends to be positively charged at very acidic pH values, the amino acid tends to be negatively charged

Question 44

how many amino and carboxyl groups does glutamic acid have? what is glutamic acid's charge in it fully protonated state? describe the process of titration for glutamic acid.

Answer 44

glutamic acid has 2 carboxyl groups and one amino group the charge in its fully protonated state is +1 during titration, it undergoes the first deprotonation, losing the proton from its main carboxyl group, just like glycine does; then it becomes electrically neutral when it loses it second proton its overall charge will be -1(the second proton that is removed in this case comes from the side chain carboxyl group, NOT THE AMINO GROUP !!!!

Question 45

what is the pI for amino acids with non ionizable side chains

Answer 45

the pI for amino acids with non ionizable side chains, the pI is usually around 6

Question 46

how many amino and carboxyl groups does lysine have what is its charge in its fully protonated state? describe the titration of lysine

Answer 46

2 amino groups and 1 carboxyl group the charge in its fully protonated state is +2 losing the carboxyl proton happens around a pH of 2, brings the charge down to +1 lysine doesnt become electrically neutral until it loses the proton from its main amino group, which happens around 9 it gets a negative charge when it loses the proton from the amino group in its side chain which happens at pH 10.5

Question 47

what pI do amino acids with acidic side chains have? | what pI do amino acids with basic side chains have?

Answer 47

amino acids with acidic side chains have pI values well below 6 amino acids with basic side chains have pI values well above 6

Question 48

how are residues in peptide chains made(what is the bond and how does it form?) what func group does it form?

Answer 48

residues in peptide chains are made from peptide bonds, which is a specialized amide bond that forms between the COO- group of one amino acid and the NH3 group of another amino acid the func group formed is C(O)NH-

Question 49

what type of reaction is a peptide bond formation

Answer 49

this is an example of a condensation or dehydration reaction, becuz it results in the loss of a water mole

Question 50

how does a peptide bond form specifically(what attacks what?)

Answer 50

in the peptide bond, the electrophilic carbonyl carbon on the first amino acid is attacked by the nucleophilic amino group on the second amino acid after the attack, the hydroxyl group of the carboxylic acid is kicked off

Question 51

know how to draw peptide bond formation and cleavage

Answer 51

confirm it on page 18

Question 52

where do amino groups have delocalizable pi electrons AND what do these electrons help the amino acid exhibit? what character does the C-N bond have? as a result of all this what happens to rotation of the protein backbone around C-N amide bonds, which makes the protein more what? describe rotation around the remaining bonds in the backbone?

Answer 52

amino groups have delocalizable pi electrons in the carbonyl and in the lone pair on the amino nitrogen, so they can exhibit resonance the C-N bond has partial double bond character rotation of the protein backbone around its C-N amide bonds is restricted which makes the protein more rigid rotation around the remaining bonds in the backbone is not restricted, as they remain single bonds

Question 53

how are proteins broken down?in living organisms?

Answer 53

proteins are broken down by acid or base catalysis | in living orgs, hydrolysis is catalyzed by hydrolytic enzymes like chymotrypsin and trypsin

Question 54

how does hydrolysis really work

Answer 54

hydrolysis- they break apart the amide bond by adding a hydrogen atom to the amide nitrogen and an OH group to the carbonyl carbon

Question 55

how is a proteins secondary structure made(also what bonds are involved)

Answer 55

its made of the local structure of neighboring amino acids(it is the result of hydrogen bonding btween nearby amino acids)

Question 56

describe the structure of the alpha helix(what does it look like and what else?) how is the helix stabilized where do the side chains point what protein is associated with alpha helix

Answer 56

it looks like a rod and the peptide chain coils clockwise around a central axis the helix is stabilized by intramolecular hydrogen bonds btween a carbonyl oxygen atom and an amide hydrogen atom four residues down the chain the side chains of the amino acids point away from the helix core keratin

Question 57

describe the structure of the b-pleated sheet how do the sheets lie and what do they form what bonds are involved specifically

Answer 57

they can be parallel or anti parallel the sheets lie alongside one another, forming rows or strands held together by intramolecular hydrogen bonds btween carbonyl oxygen atoms on one chain and amide hydrogen atoms on the chain next to it

Question 58

how do the r groups point?

Answer 58

the r groups of amino residues point above and below the plane of the b-pleated sheet

Question 59

what feature of proline causes a kink and where?

Answer 59

becuz of its rigid cyclic structure proline will introduce a kink in the peptide chain when its found in the middle of an alpha helix

Question 60

where is proline found

Answer 60

proline is found between the chains of a beta pleated sheet and it is often found at the start of an alpha helix

Question 61

what are the two categories of proteins and how do they look?

Answer 61

fibrous like collagen which looks like long strands | and globular like myoglobin which looks like a globe

Question 62

what is a protein's tertiary structure? and how are tertiary structures determined?

Answer 62

this is its 3d shape | they are det'd by hydrophilic and hydophobic interactions btween r groups

Question 63

are c=o and n-h bonds philic or phobic

Answer 63

they are philic

Question 64

what bonds are 3d prot struc also helped by? | what interactions btween amino acids with "what" are also a factor, creating what?

Answer 64

3d prot strucs are also helped by hydrogen bonds, acid base interactions btween amino acids with charged r groups creating salt bridge

Question 65

what other bonds are apart of tertiary structure? and how do they form? what do they create in the protein chain

Answer 65

disulfide bonds, they form when two cysteine molecules become oxidized to form cystine they create loops in the protein chain

Question 66

know how to draw disulfide bond formation

Answer 66

confirm it by page 23

Question 67

hydrocarbons are more stable in what than what?

Answer 67

more stable in aqueous solns than in organic ones(H<0)

Question 68

what happens when hydrophobic side chains are placed in aqueous soln,

Answer 68

the water moles in the solvation layer cant form H bonds with the side chain

Question 69

quaternary structures exist for proteins that contain more than one what

Answer 69

more than one polypeptide chain

Question 70

what kind of specific effects can quaternary structures induce what are quats made of and what is 2 of their possible functions

Answer 70

they can induce allosteric effects or cooperativity | they are made of subunits and they pretty much reduce either DNA needed to encode the prot or reducing surface area

Question 71

where do conjugated proteins derive part of their function from "what" give examples of "what"

Answer 71

they derive part of their function from covalently attached molecules called prosthetic groups prosthetic groups could be organic molecules like vitamins or metal ions like iron

Question 72

give a popular example of a prosthetic group, what does it contain, bind and carry?

Answer 72

heme group. contains an iron atom in its core and binds to and caries oxygen

Question 73

how does heat denature a protein?

Answer 73

heat denatures a protein by overcoming hydrophobic interactions that hold a protein together causing the protein to unfold

Question 74

how do solutes denature a protein?

Answer 74

solutes denature a protein by disrupting tertiary and quaternary structures, by breaking disulfide bridges, by turning cystine back to two cysteine moles, they can overcome hydrogen bonds, even by breaking apart forces that hold alpha helices and beta pleated sheets together

Question 75

how do detergents denature proteins, and what does this disrupt?

Answer 75

detergents solubilize protein which disrupts noncovalent bonds