Amino Acids and Proteins

Question 1

What is the Central Dogma of DNA?

Answer 1

DNA –> RNA –> Amino Acids –> Protein
(DNA is transcribes into mRNA which is then translated into a string of Amino Acids which forms a chain that makes a specific Protein)

Question 2

What is an Amino Acid?

Answer 2

The monomers of proteins- molecules that combine to form protein
(building blocks of life)

Question 3

What is the general structure of alpha-amino acids?

Answer 3

A central carbon with 4 groups:
1. Amino Group (NH3+ or NH2/ OH (dependent on type)) - R1 Group
2. Carboxyle Group (COOH/ COO-)
3. Hydrogen (H)
4. R2 group

Question 4

What are the characteristics of Amino Acids

Answer 4

• Amphoteric- acts as both an acid and a base
• Ampholyte (Amphoteric electrolyte)- they contain acidic and basic groups
• pKa= -log (acid dissociation constant)

Question 5

How do you tell the difference between D and L Isomerism of Amino Acids?

Answer 5

L- look at the chiral carbon and if the NH3+ or OH group is on the left OR if the priority of groups run in a counterclockwise direction then it is said to be a L- isomer

D- look at the chiral carbon and if the NH3+ or Oh group is on the right OR if the priority of groups run in a clockwise direction then it is said to be a D- isomer

*L sterioisomers are more common!

Question 6

What is an Aliphatic Amino Acid?

Answer 6

An amino acid containing an aliphatic side chain functional group:
- cyclic structures with no alternating double bonds
- non-polar and hydrophobic
- hydrophobicity increases as the number of carbon atoms on the hydrocarbon chain increases

Question 7

What is an Aromatic Amino Acid?

Answer 7

An amino acid containing an aromatic side chain functional group:
- cyclic structures with alternating double bonds
- non-polar and hydrophobic

Question 8

Can Amino Acids act as both an Acid and a Base? Why?

Answer 8

Yes! They have both an acid group, COOH, that has a small pK value and and a basic group, either OH- or NH3+, which has a large pK value.

Question 9

What is the Hydropathy Index of Amino Acids?

Answer 9

A measure of polarity of an amino acid residue

(the lower the value, the more polar the amino acid)
- the free energy of transfer of the residue from a medium of low dielectric constant to water.

Question 10

What are the 5 main classes of Amino Acids?

Answer 10

The 20 commonly occurring amino acids can be grouped based on properties of their R groups.

1. Nonpolar, aliphatic R groups
2. Aromatic R groups
3. Polar, uncharged R groups
4. Positively charged R groups
5. Negatively charged R groups

Question 11

Nonpolar, Aliphatic R group characteristics

Answer 11

• hydrophobic
• tend to cluster together within proteins
• stabilize proteins through hydrophobic interactions

eg. Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine

Question 12

Aromatic R group characteristics

Answer 12

• hydrophobic
• nonpolar

eg. Tyrosine, Tryptophan, Phenylalanine

NB: Tyr and Trp are much more polar than Phe as seen from their Hydropathy indices.

Question 13

At what wavelength do amino acids absorb UV Light?

Answer 13

@ 280 nm

Contrary to Nucleic Acids- absorb @ 260nm

Question 14

Polar, Uncharged R group characteristics

Answer 14

• polar because of the O (oxygen) atom (except for cysteine which contains S (Sulphur) instead)
• Uncharged because all electrons are accounted for

eg. Serine, Threonine, Cysteine, Asparagine, Glutamine

Question 15

What type of bonds do Cysteine form?

Answer 15

Disulphide bonds
2H+ + 2e-
Cysteine + Cysteine ————-> Cystine (w/ a disulphide bond)

Question 16

Positively charged R group characteristics

Answer 16

• positive due to the R group having a positive species (mostly on the N in the amine of R group; Histidine is an exception due to the positive charge being on the H attached to the N of the pentose ring)

eg. Lysine, Arginine Histidine

Question 17

Negatively charged R group characteristics

Answer 17

• negative due to two carboxylic groups with O bearing a negative charge (each)

eg. Aspartate, Glutamate

Question 18

What is a Zwitterion?

Answer 18

It is an ion possessing both positive and negative charged groups (COO- and NH3+). Therefore, zwitterions are mostly electrically neutral (the net formal charge is usually zero).

NB: the Nonionic form (without any charge) does not exist

Question 19

Why does the Nonionic form of the amino acid not exist?

Answer 19

The stronger (or strongest) acid will always dissociate (give up a proton) first. When considering amino acids, the alpha-carboxylic group (COO-) is always the strongest acid. For this reason, the nonionic form of the amino acid can never exist .

Question 20

What is the Post Translational Modification of Amino Acids?

Answer 20

• The covalent process of changing proteins following protein biosynthesis (after the protein is made)
• Covalent processing events that change the properties of a protein by proteolytic cleavage and adding a modifying group, such as acetyl, phosphoryl, glycosyl and methyl, to one or more amino acids

Question 21

What is collagen? What is the important component of collagen?

Answer 21

Collagen is a type of structural protein. Mainly composed of the amino acids; glycine and proline and substituted amino acid; hydroxyproline.
These AA form a three stranded structure (triple helix) which is extremely strong and flexible (due to fibrils).

Found in: Skin, hair, connective tissue…

Question 22

What are substituted Amino acids? What are some examples and where can they be found?

Answer 22

The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another (functional equivalent)

eg. Hydroxyproline and 5-Hydroxylysine found in collagen
6-N-Methyllysine found in myosin (a protein that converts chemical energy in the form of ATP to mechanical energy, thus generating force and movement- found in muscles)

Question 23

Why does gamma-carboxyglutamate (substituted AA) found in some proteins that bind Ca2+?

Answer 23

An uncommon amino acid introduced into proteins by a post-translational carboxylation of glutamic acid residues. This modification is found, for example, in clotting factors and other proteins of the coagulation cascade.

γ-Carboxyglutamic acid/ -glutamate is a calcium-binding amino acid and is required for the function of vitamin K-dependent proteins. The blood clotting and regulatory proteins require γ-carboxyglutamic acid/- glutamate for Ca2+-induced interaction with membrane surfaces

Question 24

How is γ-Carboxyglutamate used in/ with prothrombin?

Answer 24

The vitamin K-dependent carboxylation of glutamic acid to form y-carboxyglutamic acid (2-6) in prothrombin is essential for forming the calcium-binding sites and for binding pro- thrombin to phospholipid surfaces (7-12).

Question 25

Where is desmosine found?

Answer 25

Desmosine is found in elastin (gives elasticity to tissues) and its detection in urine, plasma, or sputum samples can be used as a marker for excessive elastin degradation - an aromatic amino acid- common isomer is isodesmosine.

Question 26

What is a buffer?

Answer 26

A buffer is an aqueous solution of either a weak acid and its conjugate base or a weak base and its conjugate acid that can resist pH change upon the addition of acidic or basic components.

Question 27

When do buffers perform its best?

Answer 27

Buffers function best when the pKa of the conjugate weak acid / weak base used is close to the desired working range of the buffer.

Question 28

What is the Henderson- Hasselbalch Equation? What does it tell us?

Answer 28

pH= pKa + log [A-]/[HA] pH= pKa + log [conjugate base]/[weak acid]

Question 29

What is the pI value? How is it calculated (2 dissociable groups)?

Answer 29

The pH at which a particular molecule carries no net electrical charge. ie, the pH of the zwitterion. When there is 2 dissociable groups (buffer ranges) the mean of the two pKa values is the pI: pI= (pK1 + pK2)/2

Question 30

How is the pI calculated for 3 dissociable groups?

Answer 30

1. Identify the zwitterion, by assessing the net charge of each ionic species 2. The pI value lies between the pKa values on either side of the zwitterion 3. Work out pI: pI= (pK1 + pK2)/2

Question 31

What are essential Amino Acids? Consequences?

Answer 31

Amino acids that an organism (humans/ vertebrates) cannot metabolically synthesize on their own. It has to be supplied via a specified diet as the organism cannot synthesize them on their own. Proteins our diet provides the amino acids for the body to synthesize its own proteins via the break down of the food proteins to component amino acids by hydrolytic enzymes (in the stomach and small intestine). On absorption they join the body's amino acid pool which includes amino acids from the constant turnover of cells (continuous shedding dead skin cells, replacing with younger cells). AA are also used to provide raw material for the synthesis of purine pyrimidines, porphyrins...

Question 32

What is the fate of excess amino acids?

Answer 32

Amino acids can be converted into fat and stored in fat depots, or if required, made into glucose for energy by gluconeogenesis.

Question 33

What are the consequences of shortage of an essential amino acid?

Question 34

What are the pros and cons of proteins from Plant Sources and Animal Sources?

Answer 34

Animal products contain saturated fat and higher levels of cholesterol than sources of plant protein. A person may wish to avoid animal products for these reasons. Fiber is another important factor. Only plant-based foods contain fiber, which helps to keep the digestive system balanced. But plant source are not readily absorbed by the human body and it lacks Vitamin B12 which is supplied via meat and diary products.

Question 35

What are the Essential Amino Acids?

Answer 35

There are 9: - Histidine - Isoleucine - Leucine - Lysine - Methionine - Phenylalanine - Threonine - Tryptophan - Valine

Question 36

What are: Marasmus, Kwashiorkor and Cachexia?

Question 37

What is a Protein?

Answer 37

Proteins are complex molecules that are maid up of long chains of amino acids

Question 38

Proteins Diversity... what are the different ways protein can be used?

Answer 38

- Structural Protein - Catalysts - Transport Proteins - Signaling Proteins - Antibodies - Motor proteins - Receptor proteins

Question 39

Different Structures of Protein...

Answer 39

- Primary structure (linear sequence of AAs in a polypeptide chain) - Secondary Structure - Tertiary Structure - Quaternary Structure

Question 40

Primary Structure- Peptide Bonds

Answer 40

The linear sequence of AAs in a polypeptide chain is called the *primary structure* The linkage formed between AAs is a secondary amide bond called a peptide bond Groups involved in peptide bonds carry no charges (are are NOT ionizable) Relates to both the AA sequence as well as the AA composition of a protein

Question 41

Is it expected for pH to affect the solubility of a protein?

Answer 41

Yes, protein solubility is effected by the pH of environment. Protein solubility is lower in more acidic pH than in alkaline pH. (but also dependent on optimal pH) More acidic = less soluble (vice versa) *Alters the charge on the protein hence affecting solubility Due to the electrostatic forces being less and therefore the less water interacts with the protein molecules (causes an increase in protein-protein interaction)

Question 42

Is it expected for pH to affect the shape of a protein?

Answer 42

Yes, the pH of the environment affects the shape of the protein. If the pH alters from optimal range drastically the protein's hydrogen bonds can break causing the protein to lose its shape (denature). *Alters the charge on the protein hence affecting solubility (due to ionization of amino acid atoms and molecules)

Question 43

Is it expected the pH to have any effect on the activity of an enzyme?

Answer 43

Yes, the pH can have an affect on the activity of the enzymes. Since as the pH of the environment is being altered which causes the solubility as well as the shape of the protein to change, the optimal conditions for the enzyme to strive gets disrupted which can damage the function of the enzyme and can possible cause denaturation. This is because if the pH alters from optimal pH range, either increase or decrease in pH, the enzyme activity would decrease until there is no activity due to denaturation of the enzyme.

Question 44

There are two specific instances of the importance of amino acids to the exact shape of a protein. They are...

Answer 44

1. Insulin 2. Haemoglobin

Question 45

Insulin and shape change of Protein due to Amino Acids

Answer 45

Although AA sequence is important to the shape and function of the protein, changing one or even a few AAs may have no effect on the overall function of the protein. There are many different types of insulin sources throughout medical history starting from deriving it from the pancreases of cows (bovine insulin) and pigs (porcine insulin) - no longer available- and due to religious practices insulin is now derived from bacteria (insulin Lispro, insulin Aspart and insulin Glargine). All these insulin contribute a small variation of about 1 or 2 AA in the AA sequence of insulin although they all function the same and hence has no effect on the overall function of the protein.

Question 46

Haemoglobin and shape change of Protein due to Amino Acids

Answer 46

Normal adult haemoglobin has 2 alpha chains and 2 beta chains. A change at only a single AA residue (Glu --> Val) in the beta chain (146 AAs) is sever enough to cause a high death rate in the homozygous state--- Sickle Cell Anaemia The change in amino acid sequence causes haemoglobin molecules to crystalize when oxygen levels in the blood are low. As a result, red blood cells sickle and get stuck in small blood vessels.

Question 47

What are Conjugated Proteins? Examples?

Answer 47

Conjugated proteins are proteins that have another chemical group (eg. lipids) attached to them via covalent bonding or other interactions. *Classes, prosthetic groups and examples in slides or book

Question 48

Secondary Structure- local conformation of polypeptide

Answer 48

Secondary structure refers to the local conformation of some part of a polypeptide. Two types of secondary structures: 1. Alpha Helix 2. Beta Pleated Sheets

Question 49

The Alpha Helix

Answer 49

- An alpha helix may be right or left handed - Those found in proteins are almost always right handed - - Those found in nature typically have 3.5 - 3.7 AA residues per turn - Has hydrogen bonding between each turn - The R groups point outwards from the helix S -Some AAs occur in alpha ociciesn

Question 50

Why is the Alpha Helix structure so common?

Answer 50

1. It makes optimal use of internal H bonds H-bonds form between the hydrogen attached to the N of a peptide bond and the carbonyl O of the 4th AA on the N terminal side of that peptide bond 2. Almost every* peptide bond participates in such H bonding 3. Each turn is held to the adjacent turn by 3-4 H bonds

Question 51

What is the least common residue in alpha helix and why?

Answer 51

Pro (proline) is the least common residue in an alpha- helix H-bonds form between the hydrogen attached to the N of a peptide bond and the carbonyl O of the 4th AA on the N- terminal side of the peptide bonds; 3 reasons: 1- Its rigid cyclic chain disrupts the r-handed helical conformation by occupying space. So what? 2- Pro lacks a hydrogen atom on its amide N. (recall that when alpha-helix forms the h-bonds form between the H attached to the N of the peptide bond and the carbonyl O o =f the 4th AA of the N-terminal side of the peptide bond but there is no H -bond present) Hence... 3- Proline forms peptide bonds which can readily adopt a cis conformation (amino acids prefer to adapt the trans conformation, 1000:1, rather than cis-, 4:1) Note that the cis isomer has greater steric repulsion/ hinderance -less stability- while the trans isomer has less steric repulsion/ hinderance-more stability.

Question 52

The Beta Pleated Sheet/ Strand