Structure And Function Of Proteins

Question 1

What are the functions of globular proteins?

Answer 1

Catalysts: enzymes

Regulatory: hormones

Defense: antibodies

Transport in blood: albumin

Oxygen in delivery: hemoglobin

Question 2

Give examples of structural proteins

Answer 2

Extracellular matrix: collagen, elastin

Contractile: actin and myosin

Signal transduction

Question 3

Describe the four levels of protein organization

Answer 3

Primary: sequence of amino ac8ds in a protein

Secondary structure: elements which can be found repeatedly in the 3D structure of proteins. They include commonly a-helicase and B-sheets which are stabilized by hydrogen bonds

Tertiary structure: description of the locomotion of all atoms in a protein in Space due to amino acid side-chain interactions. This includes domains which are the functional 3D structural units of polypeptides

Quaternary: describes the composition of a protein that consists of two or more polypeptide chains

Question 4

Describe the covalent bonds for proteins

Answer 4

They are strong larger than 50kcal mol-1

Ex: peptide binds and disulfide bonds are formed and are not meant to be broken other than during degradation

Question 5

Describe non covalent bonds for proteins

Answer 5

Noncovalent bonds are weaker and range from 1-2 kcal/mol. These “weak attractive forces” specify protein folding and conformational changes:

Hydrophobic interactions: 2-3 kcal/mol

Hydrogen bonds: 1-7 kcal/mol

Ionic bonds: 1-20 kcal/mol

These forces may be additive, so in aggregates they may provide a string stabilizing force

Question 6

Explain the hydrophobic interactions of proteins

Answer 6

Amino acids with nonpolar side chains can associate with other hydrophobic amino acids

Nonpolar amino acids tend to be located in the interior of the folded protein

Water is excluded

The branched chain amino acids (valine, leucine, isoleucine ), alanine and phenylalanine are commonly found to participate in hydrophobic interactions

Question 7

Describe the hydrogen bond interactions between proteins.

Answer 7

A hydrogen donor (-OH or -NH) must interactive with a hydrogen acceptor (-O or -N)

Hydrogen bonds between peptide bonds stabilize the secondary structures of a-helix and B-sheet

Hydrogen bonds between between amino acid side chains stabilize the tertiary structure of proteins

Example: the serine side chain can form a hydrogen bond with:
-the charged side chain of glutamate or Aspartate

-the uncharged polar side chain of an aspargine or glutamine

Question 8

Describe ionic bonds (electrostatic attraction)

Answer 8

Ionic bonds are formed between negatively and positively charged side chains of amino acid residues

• Negatively charged side chains are found in Aspartate and glutamine residues
• Positively charged side residues are found in lysine, arginine and histidine residues

Question 9

Describe the a-helix structure as a secondary structure

Answer 9

A specific right-handed wound around an imaginary axis. The core of the a-helix is packed tightly such that the Van der Waal forces (weak bonds less than 1kcal/mol)can take place between atoms

• The spiral has 3.6 residues per turn
• Hydrogen bonds are parallel to the direction of the imaginary axis and are formed between peptide bonds
• The side chains project to the outside of the cylinder

Proline or glycine residues often terminate the a-helix

The a-helix is interrupted by electrostatic repulsion (or attraction) between charged amino acid side chains or due to steric hindrance by bulky side chains

Question 10

What are a-helix structures stabilized by ?

Answer 10

Hydrogen bonds and Van deer waal forces

Question 11

What are Beta pleated sheets as a secondary structure?

Answer 11

• Hydrogen bonds between the peptide bonds stabilize the B-pleated sheet which is formed by two or more peptide chains
• Amino acid side chains alternative above and below the plane of the pleated sheet
• The protein strands can be anti-parallel or parallel
• The B-turn involves four successive amino acid residues and permit changes of direction of the peptide chain

Question 12

What are Beta pleated sheets stabilized by?

Answer 12

Stabilized by hydrogen bonds

Question 13

What are tertiary structures?

Answer 13

Describes the arrangement of all atoms in a protein in space due to amino acid side chain interactions. This includes domains which are the functional 3D structural units of polypeptides

Ribonuclease

Lysozyme

Myoglobin

Question 14

Describe quaternary structure

Answer 14

Hemoglobin is found only in RBC. It has a quaternary structure with 2 a and 2 B subunits

• The a and B subunits form a stable aB dimer which is held together primarily by hydrophobic interactions
• Hb can be seen as composed of two identical dimers (aB)1 and (aB)2 which are held together by weak ionic and hydrogen bonds

Question 15

Describe the polarity of the side chains play an important role in protein folding and function

Answer 15

Water soluble proteins- fold into three-dimensional structures with nonpolar side chains to the inside: “hydrophobic core”

Membrane proteins- fold into a membrane-spanning structure that can interact with nonpolar amino acid side chains with the fatty acids of a cell membrane

Question 16

What are chaperones?

Answer 16

Chaperones are specialized proteins:

• Help fold proteins that are not spontaneously folded
• Bind to aggregated proteins
• Unfold and refold misfolded proteins
• Direct proteins to degradation in proteosome and lysosomes

Question 17

What are the functions if HSP 70 and HSP 60?

Answer 17

HSP 70 prevents the aggregation of unfolded protein
-It binds to hydrophobic regions of an extended polypeptide and prevents premature folding of a protein

HSP 60 proteins have a barrel shape and are required for correct folding of cellular proteins that do not fold spontaneously

- HSP 60 can be used to aid refolding of a protein after it has crossed a cellular membrane.
- This process needs ATP

Question 18

Describe protein turnover: ubiquitin-proteosome complex

Answer 18

Misfolded or defective proteins are normally tagged by the small protein ubiquitin and degraded in the ubiquitin-proteosome system

• The linkage of ubiquitin is an ATP-dependent process
• The ubiquitinated proteins are degraded in the cytosolic proteosome and ubiquitin is recycled
• The proteosome unfolds and cuts the target protein into fragments that are farther degraded by cytosolic proteases

Question 19

Explain essential amino acids

Answer 19

9 of 20 amino acids required to synthesize body proteins cannot be synthesized in humans and are therefore said to be essential

-Dietary proteins provide essential amino acids

-However, some amino acids can become conditionally essential
For example, outcome in patients with trauma, postoperative infections and immunosuppression has been shown to improve by supplementation with glutamine and arginine

Question 20

Explain how Creutzfeldt-Jakob disease works

Answer 20

Cause: Creutzfeldt-Jakob disease is caused by abnormal proteins called prions that aren’t killed by standard methods for sterilizing surgical equipment

-As prions build up in cells, the brain slowly shrinks and the tissue fills with holes until it resembles a sponge

Consequences: those affected lose the ability to think and to move properly and suffer from memory loss. It is always fatal, usually within one year of onset of illness

Question 21

Explain prion disease: transmissible spongiform encephalopathy (TSE)

Answer 21

This disease has different names:

Kuru(cannabilism)-New Guinea 1950s

Bovine Spongifirm enencephalopathy (BSE) and discovery of prions 1980s

Creuzptzfeld-Jacob (CJD)

Scrapie in sheep

“Mad-cow” disease outbreak 1996

Question 22

Explain the prion(proteinaceous infectious agent)

Answer 22

The infectious agent is a single protein that isn’t complexed to nucleic acid

The prion protein is normally found in the brain and is encoded by the human genome and is found on the surface of neurons in all mammals.

No primary structure differences or alternate translational modifications of the disease-causing form of the prion protein has been discovered

The key of becoming infectious results from changes in the 3d conformation due to changes in secondary structures

The infectious prion has more B-sheets. The a-helices of the normal prion protein are changed to B-sheets

Question 23

Discuss the abnormal PrP (PrPSc)

Answer 23

Illness (prion disease)occurs when the normal cellular PrP (PrPSc) occurs in the altered form PrPSc (sc for scrapie)

• PrPSc acts like a template and leads to conversion of prp to large aggregates of PrPSc
  
  • Sometimes called a “catalytic” process

-The abnormal protein is highly infective and is not destroyed by the human ubiquitin-proteosome complex and neither by sterilization of surgical instruments

Question 24

What are the routes of transmission of prion disease?

Answer 24

• Sporadic (most cases)
• Genetic predisposition (mutations)

Acquired:
-Ingestion of contaminated meat (brain)

• Blood transfusion
• Invasive brain surgeries and procedures
• Injection of contaminated human growth hormone

Question 25

How does protein denaturation occur in the body?

Answer 25

A protein is denatured when it’s native 3D structure is lost by by breaking noncovalent bonds and disulfide bonds without hydrolyzing the peptide bonds

Denaturation May be reversible or irreversible. Chaperones facilitate the refolding of proteins

Examples fir protein denaturation:

• Enzymatic degradation of insulin by cleavage of the disulfide bonds in the liver
• Dietary proteins are denatured by the gastric juice at below pH

Question 26

How can we denature proteins in the laboratory ?

Answer 26

• intentional denaturation of proteins is often used as a means of disinfection
• Hydrogen bonds are broken by an unphysiological high temperature, 5-10 M urea or salt
• Ionic bonds and hydrogen bonds are broken by strong acids or bases
• Hydrophobic interactions are broken by 1-2% of the detergent sodium dodecyl sulfate (SDS)
• Disulfude bonds are broken by B-mercaptoethanol