Lecture 1: Amino acids- The building blocks of proteins

Question 1

What is the general structure of the amino acid?

Answer 1

NH3 (amino) group and COOH (carboxyl) group bonded to an alpha carbon

Question 2

What is the reaction which results in the formation of a dipeptide called?

Answer 2

dehydration reaction

removal of H2O

Question 3

true or false; peptide bonds are a form of covalent bonding?

Answer 3

true

- a covalent bond forms between the (-H)N terminal of one amino acids and the (-OH) C- terminal of another amino acids

Question 4

What is an R group?

Answer 4

• bonded to an alpha carbon

- determines the identity of the particular amino acid

Question 5

What is a stereoisomer?

Answer 5

• same molecular formula

Question 6

What kind of stereoisomer are amino acids?

Answer 6

• chiral : due to 4 different groups being bonded to the alpha carbon
• optical isomers
• non superimposable mirror images

Question 7

How are amino acids classified?

Answer 7

• L/D classification ( the position of theAMINO group on the left or right side of alpha carbon determines the L or D designation)
• L: left
• D: right

Question 8

What are the functions of proteins?

basic examples:

• enzymes
• antibodies
• receptors
• carriers
• hormones
• materials

Answer 8

1. ) Enzymatic catalysis: eg. hexokinase: ATP -dependent phosphorilation of glucose
2. ) Transport and Storage : hemoglobin (red blood cells; binds oxygen)
3. ) Hormones: Insulin (regulates plasma glucose)
4. ) Immune protection: Immunoglobulins, bind infectious organisms
5. ) Gene regulation: transciption factors
6. ) structural: collagen (provides tensile strength to skin and bones
7. ) Contraction (actin and myosin)
8. ) Receptors: neurotransmitters

Question 9

What are proteins involved in? What are their generalized functions?

Answer 9

• cell structure
• movement
• storage
• transport
• nerve cell signalling
• blood clotting
• immune defence

Question 10

What is a proteins distiguishing feature?

Answer 10

abbility to fold into specific patterns to form unique 3D structures

Question 11

How much dry weight do proteins comprise of?

Answer 11

50%

Question 12

Why is the protein structure important?

Answer 12

defines the important property of proteins, an abbility to recognize other molecules

Question 13

What is a protein?

Answer 13

• have highly specific 3- dimensional structure
• consists of one or more polypeptide chains
• each polypeptide chain consists of a long chain of amino acids joined end to end in a linear sequence known as the PRIMARY STRUCTURE

Question 14

What does it mean by primary structure?

Answer 14

• LINEAR chain of amino acids , as linked by peptide bonds
• sequence of amino acids is in accordance to the gene translated by ribosomes during protein synthesis
• determine the other levels of structure
• its sequence is critical to proper proteins functioning

Question 15

What does it mean by secondary structure?

- characterized by the repetative organisation of the peptide bond

Answer 15

• the arrangement in space of the atoms in the peptide backbone
• have repetative interactions resulting from hydrogen bonding between amide N-H and the carbonyl groups of the peptide backbone
• the conformations of the side chains of amino acids ARE NOT PART OF THE SECONDARY STRUCTURE
• alpha helix, and beta pleated sheet (examples)

Question 16

What does it mean by tertiary structure?

Answer 16

• includes the 3D arrangement of all the atoms in the protein
• including those in the side chain
• and in any other prostheic groups (other groups of atoms other than amino acids)
• refers to the complete 3D structure of a protein

Question 17

What does it mean by Quaternary structure?

- association of two or more polypeptides to make up a protein

Answer 17

• the arrangement of the subunits with respect to each other
• interactions between subunits is mediated by non covalent interactions such as :
  hydrogen bonds
  electrostatic attraction
  hydrophobic interactions

Question 18

What factors affect the properties of amino acids?

- nature of the side chain

Answer 18

1. ) polar and non polar nature of side chain
2. ) presence of acidic or basic group
   etc. .

Question 19

How are amino acids classfied?

- according to two major criteria

Answer 19

1. ) the polarity of the side chain

2. ) the presence of acidic or basic group on the side chain

Question 20

What are the 4 groups of amino acids?

Answer 20

1. ) non polar side chains
2. ) electronically neutral/ polar side chain
3. ) carboxyl groups in their side chain
4. ) basic side chains

Question 21

Describe the properties of glycine

Answer 21

• the smallest amino acid
• side chain -H
• the small side chain allows glycine to fit into small spaces thus providing CONFORMATIONAL FLEXIBILITY to proteins

Question 22

True or false; Glycine is the only achiral amino acid?

Answer 22

true

Question 23

What are the properties of proline

Answer 23

• has a side chain that is bonded to a nitrogen atom of its amino group
• this results into greater RIGIDITY to proteins
• and this can cause KINKS in the protein structure

Question 24

Cysteine

Answer 24

• contains sulphydryl group (-SH)

- this is used to STABILIZE proteins by disulfide bonds

Question 25

What does tyrosine, tryptophan and phenylalanine have in common?

Answer 25

they all absorb UV light which can be used to detect the proteins in the solution

Question 26

What are the properties of amino acids?

Answer 26

- variable side chain - zwitterion - chiral - acid base chemistry

Question 27

What does the biological activity of a protein depend on?

Answer 27

- their chemistry | - their structure

Question 28

Why does the charge of some amino acids alter with pH?

Answer 28

the presence of ionizable groups

Question 29

What is an ionizable group?

Answer 29

- these groups convey positive and negative charged groups to proteins - each ionizable group HAS PH VALUE AT WHICH EQUAL AMOUNTS OF CHARGED AND UNCHARGED FORMS EXIST - this is known as pKa

Question 30

what is the significance of the amino acid side chain?

Answer 30

- gives chemical and structural diversity: - size - charge - shape - chemistry

Question 31

Amino acid side chains groups?

Answer 31

- acidic - basic - neutral polar - neutral non polar

Question 32

Why is cysteine so special? Describe its properties

Answer 32

- polar side chains consist of a thiol group (-SH-) - which can react with OTHER Cysteine groups to form DISULFIDE BRIDGES in proteins during an OXIDATION REACTION - thiol group can also lose a proton - can form cross links

Question 33

What is the effect of a carboxyl group in an amino acid side chain?

Answer 33

- negatively charged at neutral pH - can lose a proton that's why ( glutamate and aspartate)

Question 34

What do the pKa values of amino acids depend on?

Answer 34

the environment, and can change significantly in the confines of the protein

Question 35

What does pKa mean?

Answer 35

- the pH at which have equal amounts of protonated (charged) and non protonated forms (uncharged)

Question 36

If an amino acid has a hydrophobic side chain, where does this amino acid tend to be found?

Answer 36

are usually located in the interior of the protein away from contact with water

Question 37

hydrophilic side chain and polar side chain? where does amino acid orientate?

Answer 37

found usually on the exterior of the protein, in contact with water, where they can be hydrated by the surrounding aqueous environment

Question 38

acid and basic side chain? where found on protein?

Answer 38

also on the exterior of the protein

Question 39

give 3 examples of basic side chains? | positively charged; can gain a proton

Answer 39

Hist, Arg, Lys

Question 40

give 3 examples of acidic side chains? | negatively charged side chains; because they can lose a proton H+

Answer 40

``` Asparitc ACID (Asp) Glutamic acid (Glu) ```

Question 41

give 3 examples of neutral (uncharged side chain)l, polar side chains?

Answer 41

Ser (serine), Thr (threonine), Gln (glutamine)

Question 42

give examples of neutral (uncharged side chain), non polar side chains?

Answer 42

aliphatic: Val (valine), ala (alanine), Ile (Isoleucine) aromatic: Phe (phenylalanine)

Question 43

What are neutral, polar side chains good for?

Answer 43

GOOD FOR H-BONDING Ser, Thr through -OH group Asn, Gln through C=O or NH2 groups

Question 44

define isoelectric PI

Answer 44

The pH at which negative an positive charges on the protein are equal