MMSC450 Medical Biochemistry

True or false? Pepsinogen is produced in all three sections of the stomach.

True

What are the three major zones of the stomach?

Cardiac zone
Body of stomach
Pyloric zone

What is the intestinal phase?

Begins when digestive products enter the duodenum

What is the gastric phase?

It is initiated by distention caused by food entry into stomach. Involves Hal release from parietal cells and gastrin.

What is the neurogenic phase?

It is initiated by sight, smell, and the taste of food. Involves H2-receptor antagonists and proton pump inhibitors.

What are the three phases of the digestive process?

Neurogenic phase
Gastric phase
Intestinal phase

How many genes does E. coli have?

3000

How many genes does yeast have?

6000

How many genes do humans have?

30,000

What kind of functions are proteins responsible for?

Enzymes, transporters, signal transduction, neural transmission, immune defense, structure

What are proteins made of?

Linear strings of amino acids

What are the amino acids in protein linked by?

Peptide bonds

True or false? All amino acids have the same backbone.

True

What is an amino group represented by?

NH3

What is a carboxyl group represented by?

COO

What is a peptide bond?

Covalent bond between two amino acids

How are peptide bonds formed?

Dehydration synthesis; the loss of a water molecule

What is considered the "mother" of all amino acids?

Glycine

What are the classifications of amino acids?

Non-polar (aliphatic and aromatic)
Polar (acid, basic, and hydroxyl)
Sulfur-containing

What are polar amino acids?

Serine
Threonine
Tyrosine
Asparagine
Glutamine

What are basic amino acids?

Lysine
Arginine
Histidine

What are acidic amino acids?

Aspartic acid
Glutamic acid

True or false? Amino acids are dipolar and can serve as buffers.

True

True or false? The lower the pH of an amino acid, the higher the charge.

True

True or false? The higher the pH of an amino acid, the lower the charge.

True

True or false? The ionization of amino acids is altered by the pH of its environment.

True

True or false? The dipolar form of amino acids predominates near its physiological pH.

True

True or false? The pI is defined as the isoelectric point and is the pH at which the amino acid is essentially neutral and there is no net migration in an electric field.

True

What is the Henderson-Hasselbalch equation?

pH = pKa + log [base]/[acid]

What is the equation to calculate pI?

pI = (pKa1+pKa2)/2

What does protease do?

Breaks down proteins into amino acids

What does chymotrypsin do?

Digests proteins

What does trypsin do?

It hydrolyzes proteins to small fragments (proteases, peptones and peptides).

What are the four structures of proteins?

Primary
Secondary
Tertiary
Quaternary

What is the main characteristic of a primary protein structure?

Amino acid sequence

What is the main characteristic of a secondary protein structure?

Alpha-helix
Beta-sheet
Random coil

What is the main characteristic of a tertiary protein structure?

Overall polypeptide structure

What is the main characteristic of a quaternary protein structure?

Subunit structure

What is a hydrogen bond?

The attraction between a hydrogen atom with a partial positive charge and another atom with a partial negative charge.

What is an ionic interaction?

The attraction of ions or molecules with full permanent charges of opposite signs.
ex. sodium fluoride

What is a hydrophobic interaction?

The relations between water and hydrophobes (low water-soluble molecules).
ex. the folding of the tertiary structure in proteins and the specific double helical structure of DNA.

What is a van der Waals interaction?

The residual attractive or repulsive forces between molecules or atomic groups that do not arise from covalent bonds, nor ionic bonds.
ex. water

How does polarity affect protein conformation?

The hydrophobic core region of the protein contains non-polar side chains while the outside is made of polar side chains which can form hydrogen bonds to water.

How do hydrogen bonds play a role in maintaining secondary protein structure?

Hydrogen bonds are formed between the atoms of two peptide bonds. Hydrogen bonds are formed between atoms of a peptide bond and an amino acid side chain. Hydrogen bonds are formed between two amino acid side chains.

How many residues are there per turn in an alpha helix?

3.6 residues

What is a residue?

Another name for an amino acid subunit

True or false? All helices found in proteins are right-handed.

True

Besides proteins, what other biological structures do helices occur in?

Nucleic acids

What is the benefit of two or more helices?

It can form a coiled coil which has great mechanical strength. This structure is seen in myosin in muscle, fibrin in blood clots, and keratin in hair.

What conditions can induce denaturation of proteins?

Chemical conditions such as pH and physical conditions such as temperature.

True or false? A denatured protein has no function.

True

What do the reagents urea and guanidinium chloride do when added to protein?

They can disrupt non-covalent bonds, causing the protein to denature.

What do the reagents beta-mercaptoethanol and dithiothreitol do when added to protein?

Disulfide bonds are cleaved, causing the protein to denature.

What is formed when there is excess beta-mercaptoethanol introduced to a protein?

Disulfide bridges are converted to sulfhydryls.

Where are most hydrophobic amino acids found in myoglobin?

Inside the structure

What purpose do domains serve in proteins?

They are important structural and functional units in the folding of a protein.

What is a domain in a protein?

A compact, local, semi-independent unit within a polypeptide chain.

How long are protein domains typically?

40-100 amino acids in length

How many domains is Src protein kinase made up of?

4

What are motifs in proteins?

They are small structures recurring in proteins but do not serve a purpose in predicting biological function. They share amino acid sequence homology, which is termed the consensus sequence.

What is a consensus sequence?

A sequence of DNA having similar structure and function in different organisms.

What are molecular chaperones?

Proteins that assist the conformational folding or unfolding and the assembly or disassembly of other macromolecular structures.

What are the roles of molecular chaperones?

- Suppress aggregation during folding and unfolding
- Influence the production of folded proteins
- Prevent denaturation
- Translation of proteins to golgi or mitochondria
- Facilitate degradation
- Programmed cell death (apoptosis)

What are some diseases that are the result of misfolded proteins?

Alzheimer's, ALS, Huntington's disease, Mad Cow disease, and Parkinson's disease.

What is a common feature of the diseases that result from misfolded proteins?

The correctly folded protein being converted into aggregated forms which accumulate in insoluble fibrils or plaques.

What causes protein misfolding?

DNA mutation, which causes the production of a protein that cannot fold when initially produced by the ribosome.

What can mutations cause?

It can cause the production of a protein that is destabilized and thus unfolds easier once folded.

What happens when a protein is stressed or damaged during its lifetime?

The protein can modify, resulting in it destabilizing and unfolding.

What is protein aggregation?

When proteins are unfolded either partially or completely, they are more susceptible to aggregation.

How do we recognize the protein we are looking for?

Through the use of a test called "assay" which can tell when the protein is present and possibly active.

What is differential centrifugation?

Separation of cellular components by centrifugation. Denser material will form a pellet at the bottom at lower centrifugal force. These isolated fractions can be used to further purification.

What is the separation process that is based on size?

Gel filtration chromatography. Larger proteins fall through gel faster while smaller proteins fall through gel slower.

What is the separation process that is based on charge?

Ion-exchange chromatography. Negatively charged proteins will flow through while positively charged proteins bind to the negatively charged beads.

What is the separation process that is based on specific protein interaction?

Affinity chromatography. Glucose-binding proteins attach to the glucose residues on the beads. Glucose is added, which results in the release of glucose-binding proteins.

What does sodium dodecyl sulfate do?

It is a detergent that disrupts all protein structure. Reducing agents are added to break all disulfide bonds.

What is isoelectric focusing?

A technique where proteins are separated on the basis of their relative content of acidic or basic residues. Separation of different isoelectric forms of certain medically relevant proteins have important clinical applications.

What is two-dimensional gel electrophoresis?

The protein sample is initially fractionated in one dimension by isoelectric focusing. The IEF gel is then loaded on an SDS-PAGE gel and electrophoresis is performed in the second dimension.

What is adult hemoglobin A composed of?

Four polypeptide chains, two alpha and two beta.

What do the polypeptide chains in hemoglobin A contain?

Each chain contains a heme prosthetic group, which the ability to bind oxygen depends on.

What is myoglobin?

An oxygen carrier found in muscle. It is made up of a single polypeptide chain and contains a single heme group.

True or false? Binding of the ligand to a subunit changes the conformation of that subunit.

True

True or false? The binding of the ligand to a subunit affects the affinity of the remaining subunits for the ligand.

True

How many potential oxygen binding sites does hemoglobin have?

Four

True or false? The binding of oxygen to three of the four potential binding sites increases the affinity of the remaining site 20-fold.

True

True or false? Cooperative enzymes display sigmoidal curves.

True

What are the two alpha and beta chains in hemoglobin held together by?

Noncovalent bonds

How many helical alpha segments do the alpha and beta chains of hemoglobin contain?

Eight

How many amino acids are in the alpha chain of hemoglobin?

141

How many amino acids are in the beta chain of hemoglobin?

146

True or false? In deoxyhemoglobin, the sixth coordination site of Fe2+ is unoccupied.

True

True or false? Upon binding oxygen, iron rearranges its electrons, thereby becoming smaller.

True

What is the Bohr effect?

Hydrogen ions and carbon dioxide decrease the affinity of hemoglobin for oxygen. The pH of active muscle tissue is lowered while the pCO2 is elevated. These factors promote pickup of oxygen in the lungs and release in active muscle tissue.

Where is the single copy of the beta globin gene located?

Chromosome 11

Where are the two copies of the alpha globin gene found?

Chromosome 16

What does the regulation of beta and alpha globin genes do?

It produces a molecule with two alpha chains and two beta chains and four heme groups.

What does fetal hemoglobin (HbF) consist of? How does it change during development?

Two alpha globin and two gamma globin chains. After birth, gene expression changes where 99% of Hb is in the form of alpha2 beta2.

Describe the affinity of the gamma chain in fetal hemoglobin. What effect does this have?

It has a significantly reduced affinity for 2,3-BPG (lack of His143). It results in an increased oxygen affinity of fetal Hb relative to that of the maternal and plays a pivotal role in the transfer of oxygen from the maternal to fetal cells.

How can beta thalassemia be treated?

Red cell transfusions and Fe chelating therapy. Bone marrow transplantation and drug (e.g. hydroxyurea) activation of HbF gene. Potential therapy involves lentivirus vector delivery of antisense RNA to correct the errors in the beta globin gene.

What causes sickle cell anemia?

A single point mutation in the beta chain of hemoglobin. Glucose is replaced by Val at the amino acid beta 6 position because of this mutation.
HbA -> -Pro-Glu-Glu
HbS -> -Pro-Val-Glu
HbC(mild disease) -> -Pro-Lys-Glu

What was the first genetic disease to be characterized at the molecular level?

Sickle cell anemia