4 levels of Protein structures, sickle cell anemia, chaperones

Question 1

Condensation reaction

Peptide bond

Answer 1

An alpha amino group of amino acid A reacts with an alpha carbonyl C=O group of amino acid B

Peptide bond (-CO-NH) is formed, releasing 1 molecule of water, OH comes from COOH and H comes from NH2. Peptide bond joins the alpha COOH of 1 amino acid with the alpha NH2 of another amino acid.

All proteins have a free amino group NH3+ at the N terminus and a free carboxylate group COO- at the C terminus.

Question 2

Draw polypeptide structures

Answer 2

N terminus on the left with NH3+ and C terminus on the right COO-
Draw the R groups below the alpha C of each amino acids

Question 3

The 4 levels of protein structures

Answer 3

Primary(1°), Secondary(2°), Tertiary(3°), Quaternary(4°)

Question 4

Primary structure

Answer 4

It is the sequence and number of amino acids held by peptide bonds in a polypeptide chain

• the precise primary structure is determined by the DNA of the individual
• include the N terminus on the left side and C terminus on the right side

Question 5

Secondary structure

Answer 5

They are regular, repeating configurations of a protein. Long chains of amino acids will commonly fold or curl into a regular repeating structure.

They are the result of hydrogen bonding between amino acids within the peptide, particularly from the main chain

There are 3 types of common secondary structures, namely alpha-helix, beta-pleaded sheet and loops and turns

Question 6

Alpha helix

Answer 6

• mainly forms globular(softer) and water soluble proteins
• composed of right handed spiral amino acid chain
• stabilized by H bonds between 1 peptide bond and the 4th peptide bond parallel to the helix axis

-(Hydrogen bonds form between the polypeptide chain and R groups are oriented outside of the helix)
Mainly part of enzymes and antibodies that functions in a water-soluble environment

Question 7

Beta pleaded sheet

Answer 7

• mainly forms rigid(fibrous), insoluble proteins
• composed of polypeptide chains running parallel and anti-parallel to one another
• stabilized by H bonds between the carbonyl atom of 1 amino acid in 1 strand and backbone nitrogen of a second amino acid in a adjacent strand

-(Hydrogen bonds are formed in between neighboring N-H and C=O groups of adjacent polypeptide chains and R groups are oriented inside and outside of the sheet)
Adds strength, flexibility and stability to the protein. Mainly found in structural proteins like keratin
Beta sheets is the term for a collective group of beta strands* a beta sheets can contain 2 beta strands

Question 8

What are the 3 types of beta sheet?

Answer 8

Anti-parallel where 2 adjacent strands run in opposite direction with each other
H bonds forms between NH2 of 1 amino acid and C=O of another amino acid in the same level

Parallel where 2 adjacent strands run in the same direction with each other
H bonds forms between NH2 of 1 amino acid and C=O of another amino acid in 1 level different below and above

They are also mixed beta sheets

Question 9

What are loops and turns

Answer 9

They cause directional change in the polypeptide backbone
Within 5 a.a residues are turns

Example: beta turn, a small polypeptide that connects 2 anti-parallel beta sheets together

Question 10

What are the amino acids that are favored in alpha helix and

Answer 10

Helix formers include alanine, cysteine, leucine, methionine, glutamic acid, glutamine, histidine, and lysine.

Serine, glycine, aspartic acid, asparagine, and proline are most often found in turns.

Valine and isoleucine side chains are branched at beta carbon which destabilizes alpha helix as the side chains disrupt the geometry of main branch. Serine, asparagine and aspartate contains H bond donor and acceptor in C=O, O or NH2 groups which destabilize alpha helix. Amino acids with large aromatic rings are disfavored in alpha helix as bulky side chains can disrupt the hydrogen bonding in the alpha helixes.

Question 11

Motifs/Super secondary structures

Answer 11

a cluster of mixtures of beta sheets and alpha helixes

• Motif are small specific combinations of secondary structural elements ,
• No specific function
• All alpha, all beta, segregated alpha + beta, mixed alpha and beta

Question 12

Why proline is uncommon in alpha helix

Answer 12

Imino group does have H atom to donate to form H bonds with main chain
Ring structure does not allow 100 degree rotation and thus too rigid to be in the middle of the alpha helix.

Question 13

Why glycine is uncommon in alpha helix

Answer 13

The high variability of its conformation makes it energetically expensive for glycine to adopt a alpha helix structure

Question 14

What amino acids are favored in beta sheets

Answer 14

Beta formers include valine, isoleucine, phenylalanine, tyrosine, tryptophan, and threonine which are beta-carbon branched and aromatic amino acids.

Question 15

Why antiparallel is more stable than parallel?

Answer 15

Parallel beta sheets are less stable than antiparallel beta sheets due to the offset of H-bonding groups between neighboring strands, which slightly distorts and weakens the hydrogen bonds

Question 16

Tertiary structure

Answer 16

Tertiary structure is determined by a variety of interactions (bond formation)

• Among R groups
• Between R groups and the polypeptide backbone.

Weak interaction such as
H bonds between polar side chains
Ionic bonds between charged R groups (basic and acidic side chains)
Hydrophobic interaction between non-polar side chains
Strong covalent bonds such as disulfide bridges that form between sulfhydryl groups (SH) of cysteine monomers and stabilize the structure.

Makes the protein stronger and more stable due to more interactions.
Many proteins at this level are functional.

Question 17

What are the bonds involved in the 4 level of protein structure

Answer 17

Primary - peptide bond
Secondary - peptide bond and hydrogen bond
Tertiary - peptide bond, hydrogen bond and side chain interactions
Quaternary

Question 18

Tertiary structures basic

Answer 18

3-D arrangements of all amino acids in polypeptides

Functional proteins at this levels will not do any further folding

What proteins naturally do
Polypeptide chains fold spontaneously so that majority of its hydrophobic side chains are buried interiorly, and majority of its hydrophilic, polar and charged side chains are on the surface. (water loving will face outwards and water hating will face inwards)
They maintain conformation by hydrophobic interactions, electrostatic forces, hydrogen bonding and disulfide bonds which determines 3-D structure.

Interactions between amino acids residues result in protein taking a stable, compact arrangement.

Question 19

Secondary structures and Amino acids in Tertiary structure

Answer 19

Involves the way the random coils, alpha helices and beta sheets fold in respect to each other.

Amino acids that were distant in the primary structure may now become very close to each other after the folding has taken place

It may be globular or fibrous. It now has its functional shape or conformation.

Question 20

A structural domain

Answer 20

A structurally independent region in a tertiary polypeptide
Each domains has its specific function
Blue, Orange and Green domain have its own domain.
Different domains impart different functions to the protein.
The bigger the protein, the more domain a protein can contain
Can be transferred as a domain into other proteins by genetic engineering

Question 21

Fibrous proteins

Answer 21

• more beta pleaded
• insoluble in water
• form used by connective tissues such as collagen, silk and alpha keratin
• usually span a long distance in cell
• 3-D structure is usually long and rod-shaped

Question 22

Globular proteins

Answer 22

• more alpha helices
• water soluble
• formed used by cell proteins such as albumin and immunoglobulin
• Tertiary 3-D structure
• Compact shape like a ball with irregular surfaces

Question 23

Quaternary structure

Answer 23

consist of several polypeptides grouped together

• interaction of 2 or more tertiary polypeptide chains to form a larger molecule
• they are a combination of many polypeptide strains
• come together to form a even bigger protein molecule
• held by weak, no-covalent bonds, hydrogen bonds, ionic bonds, hydrophobic bonds and disulfide bonds

Example of quaternary protein structure is hemoglobulin
It has 4 polypeptide chain 2 alpha and 2 beta
Each of the 4 contains iron.

Question 24

Overview of the 4 levels

Answer 24

Primary is a single sequence
Secondary is beta-pleaded and alpha helix
Tertiary is many many beta-pleaded and alpha helix,, interactions between R group.
Quaternary is where more than 1 tertiary polypeptide come together

Question 25

Hemoglobin

Answer 25

Hemoglobin is the iron containing oxygen transport metalloprotein in the red blood cell.

Consist of 4 subunits,
2 alpha globin chains
2 beta globin chains
4 heme groups (bind to 4 oxygen)

Question 26

What happened in sickle cell anemia

Answer 26

Hb represents normal
Hbs represents sickle
Glutamic acid is substituted with valine
It affects the hydrophobicity of the protein as glutamic acid is polar, negatively charged and valine is non-polar
and hydrophobic.

Question 27

Pathophysiology of sickle cell anemia

Answer 27

• it is caused by a point mutation in the beta-chain of hemoglobulin
• This mutation leads to a hydrophobic area on the surface of the hemoglobin and causes it to become sticky and polymerize into long fiber-like chains => the RBC is distorted into a sickle shape.
• Glutamic acid mutated to valine at the 6th position
• In low oxygen levels cause polymerization of mutant beta chain and alpha chain, leading to sickling of red blood cells
• Distortion of RBC, from a donut-like shape to a sickled shape, reducing its elasticity
• ## Repeat sickling of RBC cause blocked capillaries

Question 28

Difference between normal and sickled red blood cells

Answer 28

Normal red blood cells are smooth, round and flexible, able to squeeze into capillaries and blood vessels.
Sickled red blood cells are inflexible and tend to clump in the blood vessels, leading to blockage of blood flow.
Sickle red blood cells also have a shorter lifespan than normal red blood cells and the blood marrow is unable to replace the red blood cells quickly enough.
Individuals will experience low oxygen levels as the sickled red blood cells reduces the rate of oxygen transport instead of delivering oxygen to the cells

Question 29

Factors affecting rate of protein folding in cells

Answer 29

Spontaneous synthesis in cells, proteins are folded quickly

Environmental factors
Body salt concentration, pH of buffer
Temperature, high temperature reduce rate of protein folding
Molecular chaperones, assist proteins in folding

Question 30

Molecular chaperones

Answer 30

Example of a group of chaperones are heat shock proteins expressed in response to cellular factors and stress factors.
Help assist in protein folding and unfolding.
Help prevent denaturation such as during high temperature during fever

Question 31

How molecular chaperones fold

What are native proteins and aggregates?

Answer 31

There is a normal pathway where U, the newly synthesized protein form partially folded intermediates and then form native proteins.
U can also form aggregates or chaperone complex with U.
Chaperone complex with U can form chaperone complex with intermediate to form native..
Partially folded intermediate can form with chaperone to form chaperone complex with intermediates. It can also be aggregates.

Aggregates are deposited and clumping of misfolded proteins which are not cleared by the body.

Native state are functional proteins.

Basically chaperones can help partially folded intermediates and chaperone complex with newly synthesized protein to become native proteins.
Aggregates can form from partially folded intermediates and newly synthesized proteins, and cannot be saved by chaperones,