Chapter 1 Amino Acids

Question 1

there are less that 300 different amino acids described in nature, how may are found in as constituents of mamalian proteins ?

Answer 1

20

Question 2

Non standard amino acids are produced by modification of ?

Answer 2

standard amino acids

Question 3

the only amino acids encoded by DNA

Answer 3

standard amino acids

Question 4

has a secondary amino group

Answer 4

proline

Question 5

at what pH is when the carboxyl group is dissociated, forming the negatively charged carboxylate ion, and then the amino group is protonated

Answer 5

7.4

Question 6

in protein terms

1. what groups are combined through peptide linkages ?
2. proteins are not available for chem rxn except for ?

Answer 6

carboxyl and amino groups are combined through peptide linkages and not available for chemical reaction; except for hydrogen bond formation

1. carboxyl and amino groups
2. hydrogen bond formation

Question 7

Amino Acids with NON-polar side chains

1. name reactions that they do not participate in

Answer 7

• do not gain or lose protons
• do not participate in hydrogen or ionic bonds
• has an oily and lipid like property

Question 8

1. the side chains of NON-POLAR** amino acids tend to **CLUSTER in the interior of the protein

Answer 8

1. proteins found in a polar environment (aqueous solution)

Question 9

name all the uncharged POLAR SIDE CHIANS

Nemonic

Sorry, The , Time, And Game Ceased

Answer 9

• Serine
• Threonine
• Tyrosine
• Aspargine
• Glutamine
• Cysteine

Question 10

Acidic side chains

Answer 10

Aspartic acid

Glutamic acid

Question 11

name the “Basic” Side chains

BASE dominant

Answer 11

Histidine

Lysine

Arginine

Question 12

• side chain and alpha amino nitrogen form rigid five membered ring
• has a secondary rather than primary amino group
• referred to as an IMINO acid
• contributes to the structure of collagen
• interupts alpha-helices in globular proteins

Answer 12

Proline

Question 13

Amino Acids with uncharged polar side chains

Serine, Threonine, Tyrosine, Aspargine, Glutamine Cysteine

Answer 13

• have zero at physiologic pH
• Serine Threonine and Tyrosine contain a polar hyhdroxyl group that can play a role in hydrogen bond formation
• Aspargine and Glutamine contain both carboxyl and amide groups that can participate in hydrogen bonds.

Question 14

Disulfide bond:

1. the side chain of CYSTEINE contains what ?
2. i_mportant component of the active site_ of _enzymes_?
3. -SH group of two cysteine can be oxidized to form a covalent cross-link is called what ?
4. Two disulfide-linked cysteins are referred to as ?

Answer 14

1. sulfhydryl
2. thiol group (-SH)
3. disulfide bond
4. CystINE

Question 15

^{page 4.}

Side chains as attachment sites for other compounds

1. what A.A. can serve as a site of attachment for structures like phosphate groups?
2. the amide group of Aspargine, as well as Hydroxyl group of Serine and Threonine can serve as a site of attachment to what ?

Answer 15

1. the polar hydroxyl grp of serine, threonine and rarely tyrosine
2. Oligosaccharide chains in glycoproteins

Question 16

^{<strong><u>page 5. </u></strong>}

Amino Acids with Acidic Side Chains

1. name the two acidic A.A.
2. are they proton donors or proton acceptors ?
3. describe these AA’s a physiologic pH
4. what are the fully IONIZED forms called

Answer 16

1. Aspartic and Glutamic acid
2. proton donors
3. side chains are fully ionized containing a negatively charged carboxylate group (-COO^- )
4. Aspartate and Glutamate

Question 17

1. Amino acids with a chiral alpha carbon exist in two isomeric forms, what are these two forms ?
2. All amino acids in mammals are in what form ?
3. what form is found in antibiotics

page 5.

Answer 17

1. D and L
2. L form
3. D form (cell bacterial walls)

Question 18

^{<strong><u>page 6.</u></strong>}

B. Buffers

1. what is a buffer ?
2. buffers can be created by ?
3. when HCL is added into a buffer
4. when does maximum buffer capacity happen ?
5. If the amounts of HA and A^- is equal; then the pH is equal to the?
6. at pH values less than pKa, the protonated acid in the (CH3-COOH) is the
7. what is the predominant specie at pH values greater than pKa?
8. overall, what can serve as buffers ?

Answer 18

1. a solution that resist pH following an addition of an acid or base.
2. mixing weak acid (HA) with its conjugate base A^{<u><span>-</span></u>}
3. converted to HA in the process by A^- neutralized
4. at a pH equal to pKa
5. pKa = maximum buffer
6. predominant specie in the solution
7. (CH3-COO-)
8. free amino acids, plus charged amino acids in peptide chains.

Question 19

Understanding the Henderson-Hasselbalch

1. A drug passes through more readily if ?
2. explain these simple drug penetration

• weak acid (aspirin)
• weak base (morphine)

3. what equation is useful in determining how much drug is found on either side of the membrane ?(separates two components that differ in pH ?

Answer 19

1. the drug is uncharged
2. aspirin ( uncharged HA CAN A- cannot) ———–morphine (uncharged B CAN BH+ cannot)
3. Henderson -Hasselbalch equation

Question 20

page 8. and pag 9.

Net Charge at Neutral pH

1. Negatively charged COO- and positively charged NH3+ happens at ?
2. what are they called if they can either act as an acid or a base ?
3. what is another term for amphoteric ?

Answer 20

1. at physiologic pH (7.4)
2. Amphoteric
3. Ampholytes ( amphoteric electrolytes)

Question 21

Essential Amino Acid

I Love Lisa For Trying To Make Vicky Happy

Answer 21

Isoleucine

Leucine

Lysine

Phenylalanine

Threonine

Tryptophan

Methionine

Valine

Histidine

Question 22

All molecules with a chiral center is optically ACTIVE or INACTIVE ?

Answer 22

Optically Active

Question 23

Name the three nonpolar (hydrophobic) A.A.

-they can all participate in hydrophobic interactions

Answer 23

1. Phenylalanine
2. Tyrosine
3. Tryptophan

Question 24

1. Weak bases: what can it release ?

BH+ ——-→ B + H+

2. however the protonated form of basic drugs is usually ? charged or uncharged ?
3. the loss of a proton produces what ?

Answer 24

1. hydrogen
2. charged
3. uncharged base

Question 25

The effective concentration of the permeable form of a drug at its absorption site is determined by ?

Answer 25

the relative concentrations of the charged and uncharged forms

Question 26

**_Permeable or Impermeable_** charged forms cause uncharged forms cause

Answer 26

impermeability permeability

Question 27

Proteins located in a hydrophobic environment such as the membrane protein- where would the non polar R groups found ?

Answer 27

on the outside surface of the protein --interacting with the lipid environment

Question 28

1. The concentration of protons [H⁺] in a solution is expressed as ? 2. The quantitive **_relationship between the pH**_ of the solution _**and concentration of a weak acid (HA) and it's conjugate base (A_^-_)_** is described by ?

Answer 28

1. pH 2. The Henderson-Hasselbalch equation

Question 29

Acidic drugs release ?

Answer 29

H+ to cause a charged molecule

Question 30

at physiologic pH amino acids have a negatively charged group (COO-) and a … ?

Answer 30

positively charged (NH3+) group

Question 31

Amino Acids that can either act as an acid or a base are defined as what?

Answer 31

amphoteric

Question 32

**_Henderson Hasselbalch application:_** **Bicarbonate as a BUFFER** - what causes the pH to rise in the blood ? - what causes the increase in CO2 - when CO2 increases it causes a rise or fall in pH ? - the falling levels of pH results in what condition

Answer 32

_-an increase in HCO_₃ ^_ causes the pH to rise - Pulmonary obstruction - fall in pH - respiratory acidosis

Question 33

**_Amphoteric properties._** Amino acids are amphoteric molecule 1. what does amphoteric mean ? 2. **_Monoamino-monocaboxylic_** amino acids exist in aequeous solution as dipolar molecules, which means? they have both positive and negative charges and the overall molecules is electrically neutral. 1. At low pH, the carboxyl group ? 2. At high pH, the amino group loses its proton and becomes uncharged (neutral) , thus the overall charge on the molecule is negative. pH at which an amino acid is electrically neutral is known as the isoelectric point for the molecule and the symbol is pI.

Answer 33

1. (dipolar ions), that is they have both basic and acidic groups. 2. they have both positive and negative charges and the overall molecules is electrically neutral 3. 1. **_accepts a proton**_ and _**become uncharged,_** so that the overall charge on the molecule is positive. 4. **_loses its proton**_ and _**becomes uncharged_** (neutral) , thus the overall charge on the molecule is negative. 5. isoelectric point for the molecule and the symbol is pI.

Question 34

1. describe protein denaturation ? 2. structures of proteins are dependent on weak secondary forces; give examples

Answer 34

1. unfolding and loss of natural function 2. pH, radiation, temperature, detergents, heavy metals etc..