Protein Structure l

Question 1

Whats a building block of protein and what does it look like

Answer 1

Amino acids and look at the lec.

Question 2

Whats the a amino group

Answer 2

The one attached to alpha carbon

Question 3

Whats the alpha carboxyl group

Answer 3

The one attached to a carbon

Question 4

Does R group differ. Whats it in gylcine and what makes glycine not assymetrical or chiral

Answer 4

R groups differ and glycine has H as an R group therefore its not assymetrical or chiral

Question 5

What are peptide bonds

Answer 5

They are the ones that link am8no acids

Question 6

Each polypeptide chain has a __________

Answer 6

Linear sequence

Question 7

What reaction haplpens when polypeptide chains form

Answer 7

Condensation or dehydration

Question 8

When does the water molecule remove itself

Answer 8

When the amino acid comes in contact with another to form a peptide bond causing a condensation or a dehydration reaction

Question 9

What does n terminus and c terminus mean

Answer 9

N terminus means when the chain is formed and one end is amino and second end of it is carboxyl.

Question 10

What are some characteristics of peptide bonds

Answer 10

It has partial double bond
It has trans configuration
It is not charged but polar

Question 11

What is partial double bond and what does it do

Answer 11

It is shorter than a single bond, it rigid and planar.
It causes free rotation between the a carbon and a amino group and prevents free rotation between carbonyl carbon and nitrogen causing stable protein

Question 12

What makes peptide bonds uncharged but polar

Answer 12

The carbonyl group

Question 13

What are the four levels of proteins

Answer 13

Primary, seoncdary, tertiary, quartenary

Question 14

Whats the primary structure

Answer 14

Primary is unique and determines the tertiary as well because of the similar Rgroups. It is inherited genetically.

Question 15

Whats lysozyme

Answer 15

An enxyme that is primary structure that kills bacteria and consists of 129 am8no acids

Question 16

Whats the secondary structure

Answer 16

It is the one that has hydrogen bond8ngs between the primary sequence

Question 17

What are the forms of secondary

Answer 17

A helices
Beta sheets
Turns

Question 18

Whats a helices

Answer 18

This happens due to coiling and whihc includes h bonds forming between the amide hydrogen and carboxyl oxygen. These h bonds are wak but meany making it strong. They are all in the same direction making it dipole causing the ends to be opposiltely charged. These hydrogen bonds extend upwards and are parellel. The side chains also extend outwards and dont interfere in sec. structure. Each turn has 3.6 aa.

Question 19

What are the examples of a helices

Answer 19

Myoglobin whihc js glubular and keratin which is fibrous

Question 20

What are beta sheets

Answer 20

They are extension or folding of the chain that involves two polypeptide to form hydrogen bonds. These strands could be parellel or anti parellel making antiparellel more strong therefore stabalising more. The h bonds are perpendicular. When on 1 chain folds onto itself then the hydrogen bonds formed are inrachain. For example anti bodies

Question 21

What are b turns or bends

Answer 21

They are the ones that reverse the direction causing globular protein to be formed to stabalize more. They may include charged residues and four aa like proline or glycine (smallest R group). These b bends are stabalised by the h bonds between the first and the last residue

Question 22

Whats the tertiary structure

Answer 22

They have interactions between the r group like
Hydrophobic
Ionic
Disulfide
H bonds

Question 23

Whats hydrophobic

Answer 23

Between non polar groups. They are weka but many and repel charged or polar molecules

Question 24

What are h bonds

Answer 24

They are weak but many between H and SNOF. These cause structural change

Question 25

What are ionic bonds

Answer 25

Usually charged and polar that form salt bridges

Question 26

What is disulfide bond

Answer 26

Its between 2 cysteines which is covalent and is more in secreted proteins than in inracellular.

Question 27

Whats the enzyme that reduces the disulfide bonds

Answer 27

Disulfide isomerase

Question 28

What are below 50 aa called and what above

Answer 28

Below are poly peptide and above are proteins

Question 29

Whys the first aa known as n terminal and whys last aa known as c terminal

Answer 29

Because the first has free amino group and the last has free carboxyl group

Question 30

How to find out the composition or sequence of amino acids in a protein

Answer 30

Hydrolyze with a strong acid & then, use cation - exchange the achie manogeaphy, for which elute themselves acc- to charges hydrobhobicily,affinities.Ther,mix with hin hydrin which gives a burble derivative that can be detected in the spectobhorometry. (For composition)

The edman technique which again requires hydrolyzing with an acid first that cleaves the peptide bonds I then treating with PICT (phenylisothioLyanate) which attaches to the first a a and removes it from the peplide chain shorkmine it. Then reple can be used to defect it

Another way could be by clearing by proteales like trypsin (Lys, Arg) & chymotrybsin LPhe, Leu, tyr, trp). An enzyme that acts like proteas es can be used hoo called eyanogen bromide which cleaves at methioning site.

Another undirect broces’ could be knowing the DrAt-seq-but, this will not position the disultide bonds I won’t let us know of the bost translational modifs of
the protein

Question 31

Whats the one that has a and b sheets

Answer 31

Falvadoxin