Protein Structure

Question 1

How many types of amino acid ?

Answer 1

20

Question 2

Name some type of amino acid

Answer 2

Serine, valine

Question 3

What are the three main components of Protein structure ?

Answer 3

Amino group, R group and Carboxyl group .

Question 4

1. Alaine
2. Argine
3. Asparagine
4. Aspartic Acid
5. Cysteine
6. Glutamic
7. Histidine
8. Glycine
9. Isoleucine ,
10. Leucine
11. Lysine

Answer 4

1. Ala, A
2. Arg , R
3. Asn, N
4. Asp ,D
5. Cys , C
6. Glu , Q
7. His , H
8. Gly, G
9. ILLE , I
10. Leu , L
11. Lys k

Question 5

What are some of the functions of Protein ?

Answer 5

Catalysing chemical reactions
Synthesising /replacing DNA
Receiving and sending chemical signals
Providing structural support

Question 6

What type of R side chain does Valine have and how does it react ?

Answer 6

Its hydrocarbon

Determines how they react , they don’t have a polarity so therefore its hydrophobic side chain .They define shape and structure .

Question 7

How does the R group on Serine react ?

Answer 7

Alcohol group

Oxygen are electronegative and hydrogen have a low electron negativity causing a polarity .In which becomes hydrophilic.

Question 8

What occurs during a aqueous solution ?

Answer 8

Side chains which are hydrophobic want to be inside and hydrophilic want to be on the outside .

Question 9

What happens during peptide formation ?

Answer 9

Alpha carbon is going to be bonded to a hydrogen /Side chain , forming a water molecules on a different diagram .

Nitrogen forms a bond carbon using lone pair.

Question 10

What is a DI-peptide bond ?

Answer 10

Have two amino acids which they can add more chains forming a polypeptide chains

Question 11

What process occurs during a polypeptide/and peptide linkage ?

Answer 11

Dehydration synthesis and condensation .

Question 12

What are the Primary structure and how do they function ?

Answer 12

Its a sequence of amino acids
ALA-GLY-TY

The DNA is coding for the order of amino acids .This type of structure is how polypeptide bonds are formed /Identity of side chains and the sequence they are found in

Question 13

What about secondary structures ?

Answer 13

They are the interaction within the backbone .
a-helix and B-sheet.

Beta sheets consist of beta strands (also β-strand) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet.

A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation.

Always between the carboncy and nitrogen there is always peptide bonds which occur .

Occurs always between the carbony C and Nitrogen there is always peptide bonds which occur .

The beta sheet is stabilized by hydrogen bonds between the carbonyl oxygen of an amino acid in one strand and the backbone nitrogen of a second amino acid in another strand. Beta sheets can be either parallel or anti-parallel.

Question 14

What are the types of secondary structures ?

Answer 14

Parallel

They are interactions within the backbone .Nitrogen is electronegative .Hydrogen smaller electronegative in which they have a position in which oxygen becomes partial negative

Not circle one

Its repeats forming a beta pleated sheet

Both of the side chains interacting a parallel .Going in the same direction

The “R group” can mainly rotate .

N-C

Question 15

Other type of Secondary Structure

Answer 15

N-C
C-N
Anti-parallel beta pleated sheet
Circle

Nitrogen ,alpha carbon ,carbonyl carbon right side

Left side - carbonyl ,hydrogen bonds ,carbon , alpha carbon ,nitrogen going opposite direction .

However they are going in different directions .

Allowing each residue to interact with other residue .To adopt lowest electron level.

A-helix

Backbone is going helical structure .

Hydrogen bonds .giving it a cyclical structure

Interaction between backbone and secondary structure .

Question 16

What does X-ray Crystallography

Answer 16

Is a technique used to obtain the three dimensional structure of protein .By x-ray diffraction of its crystallised form.

Three dimensional structure is crucial in determining the protein functionality.

Use of X-ray diffraction is used to determine the structure of crystals or molecules such as nuclei acids .

Question 17

What is Protein domain ?

Answer 17

protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain.

Each domain forms a compact three-dimensional structure and often can be independently stable and folded.

each domain characterized by having a sequence that matches the motif of its family.

They can retain their structure outside .

Each domain forms a compact three-dimensional structure and often can be independently stable and folded.

Its related to some function of and protein DNA

Domains are more complex and larger

They are compact structures of multiple secondary structures that are at a distance from each other.

Domains can contain a motif. Both domains and motifs can be functional or just mere structural.

Separated by protease

Question 18

What is Protein motif ?

Answer 18

Mainly in Secondary structure and is to do with alpha helix and beta sheet.

Random coiled

They are present between protein domains

Cannot retain its structure outside of the motif .

Particular arrangement of amino acids

motifs can be structural or sequence. Sequence motifs share certain sequence of amino acids.

Structural motifs are made of multiple secondary structures that are sequential to each other within the primary structure of a protein (e.g. Helix-loop-helix) and not separated by a random structure.

Domains can contain a motif. Both domains and motifs can be functional or just mere structural.

Question 19

How do proteins exert their function ?

Answer 19

Protein Domains :

1. Adaptor :It binds other protein by structure complementation and can
   lead to changes in 3D conformation (changes in activity/function)
   - complementing 3D structures
   - Chemical interaction between side chain of aa
2. Enzymatic: Induce chemical modification of substrate that they bind

They can work both as an enzyme and adaptor.

Question 20

What can denaturation do ?

Answer 20

They can cause disruption to hydrogen bonds, disulfied bonds , ionic bonds which maintain the shape of proteins .

Question 21

Can denaturation be caused by excessive heat ?

Answer 21

Causes a disruption to the polypeptide chains which can cause a weak interaction cause a disruption to the structure

Question 22

What type of bonding does secondary structures involve ?

Answer 22

It involves hydrogen bonds between atoms of the backbone

Question 23

Where are β-sheet and alpha sheets found ?

Answer 23

They are found in the polypeptide chains.
Haemoglobin is an examples and consists of β-globin and alpha globin .

Alpha helices and beta pleated sheets are two types of secondary structure found in proteins. …

An alpha helix is a right-handed helix that is held together by hydrogen bonding.

In this structure the hydrogen bond is formed between the N-H on one amino acid and the C=O on another amino acid 4 residues away.

Question 24

Name three non-polar molecules are were are they found ?

Answer 24

Valine, leucine and isoleucine .Not in contact with aqueous environment .

Question 25

What can denaturation also affect ?

Answer 25

Other bonds apart from peptide bonds

High Temp 41 degrees will break the interactions in many proteins /denature them .

Question 26

Name some factors which can affect the protein denaturation ?

Answer 26

Mutation :
mutation can change the amino acid sequence of the resulting protein. Sometimes a change in the protein’s amino acid sequence can have dramatic results.

Glucose levels
Oxidation :
Oxidative modifications of proteins can change their physical and chemical properties, including conformation, structure, solubility, susceptibility to proteolysis, and enzyme activities

Changes in physiological pH :
A change in PH simply means a change in the amount of (H+) atoms. As you can see these hydrogen atoms are positively charged, and attract the negative side of the polar amino acids. So a change in the PH changes the stability of a protein structure and can cause its denaturation.

Binding to ions, Levels of concentration

Question 27

What are Storage Protein ?

Answer 27

Ovalbumin is the protein in egg whites

Casein is the protein in milk, source of amino acids for baby mammals

Question 28

How do secondary structure form ?

Answer 28

Hydrogen bonds joined with the backbone
Oxygen has partial negative /partial positive
Forming between these atoms
Hydrogen bonds could be weak but can form between these times to form structures

Question 29

What are the two types of Secondary Structure ?

Answer 29

Beta Sheet and Alpha sheet.

B sheet are another type of secondary structure connected by hydrogen bonds. Made up of many globular proteins , dominate some fibrous proteins including spider webs

Alpha helixes bond through hydrogen bonding in which between every fourth amino acid.

Question 30

Tertiary Structure

Answer 30

3D dimensional shape

mostly determined by the amino acid sequence.

amino acid sequence cannot entirely predict on how the three-dimensional structure is formed.

tertiary structure is stabilized by the sequence of hydrophobic amino acid residues in the backbone of the protein.

The interior consists on hydrophobic side chains while the surface consists of hydrophilic amino acids that interact with the aqueous environment.

is formed by interactions between side chains of various amino acids - in particular disulphide bonds formed between two cysteine groups.

At this stage, some proteins are complete, while other proteins incorporate multiple polypeptides subunits which creates the quaternary structure.

Tertiary structure refers to the spatial arrangement of amino acid residues that are far apart in the sequence and to the pattern of disulfide bonds. Tertiary structure is also the most important protein structure that is used in determining the enzymatic activity of proteins.