Structural Biochemistry/Final Review/Midterm III

How does carbon dioxide affect hemoglobin?
Carbon dioxide decreases the affinity of hemoglobin for oxygen. This is because CO2 reacts with water, with the help of carbonic anhydrase, to form carbonic acid. this lowers the pH, which in turn lowers the affinity of oxygen to hemoglobin.

What are the differences between myoglobin and hemoglobin?
Hemoglobin -tetramer with beta and alpha subunits with a Fe metal center at the active site

-more efficient O2 carrier from lungs to rest of the body due to easy release of ligand (O2)

-weaker hold on and lower affinity for O2

-cooperative molecule with two distinct states: T (tense) and R (relaxed)

-as pH decreases the O2 affinity decreases and vice versa

-better release of ligand when low pH inside red blood cells

Myoglobin

-single polypeptide with Fe metal center at active site

-controls reactivity of Heme group to prevent release of reactive O2

-stronger hold on and higher affinity for O2

-better carrier choice in muscle cells

-Fe gets oxidized from II to III through binding of O2

-works better if remains in dioxygen form and not superoxide

Describe the catalytic mechanism of chymotrypsin?
1. Binding of substrate

2. A nucleophilic attack of serine on the peptide carbonyl group

3. Collapse of the tetrahedral intermediate

4. The release of the amine component

5. Water binds (hydrolysis)

6. Nucleophilic attack of water on the acyl-enzyme intermediate

7. Collapse of the tetrahedral intermediate

8. Release of the carboxylic acid component

What is a zymogen, why are they created by the body?
A zymogen is an inactive precursor of an enzyme. The reason for cells to secrete inactive enzymes is to prevent unwanted destruction of cellular proteins.

What are the two models for the formation of Golgi complex?
1. CISTERNAE MATURATION describes that golgi was made from scratch and that proteins from the ER fused and matured to create the specific compartments.

2. VESICULAR SHUTTLE MODEL describes that golgi was a pre-existing structure within the cell and that its function is to continue the processing of proteins after the ER.

Carbohydrates
Sugars or saccharides CnH2nOn Monosaccharides are chiral molecules An aldehyde or a ketone can react with an alcohol to yield a hemiacetal or a hemiketal.

Anomeric Carbon
- In a ring structure it is the hemiacetal or hemiketal that is bound to an alcohol group and an ester bond

Formation of Glycosidic Bond
- In ring form of glucose molecule, the anomeric carbon and a hemiacetal group react with alcohol group - It releases water then forms glycosidic bond - Can be either an alpha or beta bond

Reducing Sugars
- Reducing sugars are hemiacetals and have a reactive carbonyl group - Reducing sugars can be made longer and longer - Examples: glucose, maltose, lactose

Non-reducing Sugars
- Cannot form glycosidic bond - There is no anomeric carbon available since they are fixed in a bond already

Polysaccharides
- Homo-polysaccharides take one sugar and the rest of chain is made of the same sugar - Hetero-polysaccharides are chains made up of different sugars - Both can be branched or unbranched

Glycosylation
- Glycoproteins are formed when a carbohydrate is attached to a protein - Main goal is to make protein more soluble - Makes it easier for protein to be in solution because of the added hydroxyl group - Often results in a branched oligosaccharide - Occurs in the endoplasmic reticulum then is transported to the Golgi - TWO TYPES
 * N-linked: Only happens with amino acid, Asparagine
 * Begins in the endoplasmic reticulum then continues to Golgi


 * O-linked: Only happend with amino acids, Serine and Threonine
 * Takes place exclusively in Golgi

Lipids
- Fatty acid component
 * Hydrocarbon chains
 * Saturated or unsaturated
 * Carboxylic group at end

Phospholipids
- Consists of:
 * Glycerol molecule
 * Fatty acid attached to glycerol
 * Phosphate group and alcohol also attached to glycerol

- They are also amphipathic molecules