Chapter 6: Protein Analysis

What makes up the structure of a protein?

Amino acids and peptide bonds

What is the central c

Structural hub for every amino acid

What is the carboxyl group?

Provides acidic character, releases H+ ions and creates negatively charged -COO

What is the R group?

Variable side chain of an amino acid that determines its identity and chemical properties.

What does the hydrogen atom in the protein structure do?

Complete the amino acid’s structure and allows proper bonding and folding of the protein.

How is a peptide bond formed?

Dehydration (condensation) reaction.

What is the ionization process?

An atom or molecule gains or loses electrons (or protons), becoming electrically charged.

What is the Zwitterion?

A molecule that has both a positive and a negative charge at the same time but is overall electrically neutral.

How does the primary structure of a protein look?

Linear chain of amino acids joined together by peptide bonds in a sequence determined by DNA codons.

How do alpha helices and beta sheets fold the protein?

By forming regular, stable patterns through hydrogen bonds between the backbone atoms.

How is the tertiary structure of a protein described?

Three-dimensional shape, formed when its secondary structures fold further and interact through hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions between side chains (R groups).

What is the quaternary structure of a protein?

Arrangement and interaction of multiple polypeptide chains (subunits) into a single functional protein.

What are examples of protein misfolding diseases?

Alzheimers and prions disease

How does sickle cell anemia occur?

Single amino acid substitution

What are the non polar amino acids?

side chains (R groups) are hydrophobic, meaning they do not interact well with water. These include glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, and proline.

What are the polar amino acids?

Polar amino acids have side chains that can form hydrogen bonds with water, making them hydrophilic, such as serine, threonine, cysteine, tyrosine, asparagine, and glutamine.

What are the ionic (charged amino acids)?

Ionic (charged) amino acids have side chains that are positively or negatively charged at physiological pH; positively charged: lysine, arginine, histidine; negatively charged: aspartic acid, glutamic acid.

What are the essential amino acids?

histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.

What are examples of amino acid disorders

Phenylketonuria, maple syrup urine disease, and homocystinuria

Why is it clinically relevant important to understand amino acid diseases?

Understanding amino acid diseases is important because defects in amino acids or protein folding can cause disorders, guiding diagnosis and treatment.

What are the stabilizing forces in proteins?

Hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions.

How do proteins affect Alzheimer’s and cystic fibrosis?

In Alzheimer’s, misfolded proteins form toxic brain aggregates, and in cystic fibrosis, a misfolded CFTR protein disrupts chloride transport.

What are some medical interventions that can affect protein related diseases?

Medical interventions for protein-related diseases include enzyme replacement therapy, chaperone drugs to aid folding, gene therapy, and medications that prevent protein aggregation.

What are Alpha helix regions

multiple helical segments distributed throughout the folded proteins

What are Proline-Induced Bends?

Sharpe kinks or turns in the polypeptide chain

What is a disulfide bridge

Two cysteine residues

What is an ionic bond

Electrostatic attraction

What is the hydrophobic core

Nonpolar amino acids cluster together away from aqueous.

What are Van Der Waals Forces?

Weak interactions between atoms in close proximity

What is the alpha chain

One type of polypeptide subunit

What is the beta chain?

Second type of polypeptide subunits

What is the Heme Group

Enables oxygen transport from lungs to tissues

How does sickle cell disease occur

Single amino acid substitution (glutamate to valine)

How do Prion diseases occur

Tertiary conformations

How can protein structures influence drug design

Enabling the identification of binding sites and the optimization of drug candidates for maximum affinity, specificity, and safety

What are enzymes

Proteins that act as catalysts

Why is it important to understand enzyme properties

They act as essential biological catalysts, speeding up life-sustaining reactions (digestion, respiration, DNA replication) by millions of times

What metabolic diseases are caused by enzyme deficiency

Phenylketonuria (PKU), Maple Syrup Urine Disease (MSUD), Tay-Sachs, Gaucher disease, and various glycogen storage diseases like Pompe

What is a substrate

reactant molecule

What is the enzyme-substrate complex?

Temporary molecular structure formed when a specific substrate molecule binds to an enzyme's active site.

What occurs at the active site

The substrate binds to the enzyme

What is the lock and key

The precise fit into the activity site

What is a non-substrate molecule

Incompatible shape that cannot bind to the active site

What is the bound substrate

Substrate secured in the active site

What is competitive inhibition

Inhibitor competes directly with substrateś active site

What is noncompetitive inhibition

Inhibitor binds without competing with another substrate

What is allosteric regulation

Inhibitor that binds ends up changing the shape of the active site

How do enzyme mechanisms enable targeted drug development

providing highly specific, druggable active sites that allow inhibitors to precisely modulate disease-related pathways, minimizing off-target effects and maximizing efficacy.

What is a Holoenzyme

Active form of an enzyme that consists of an apoenzyme and its cofactor or coenzyme.

What is a cofactor binding site

A specific region on an enzyme where cofactors or coenzymes bind to facilitate enzyme activity.

What is a nicotinamide ring

A component of NAD+ and NADH, crucial for redox reactions in metabolism.

What are hydrogen positions

Specific locations on biomolecules where hydrogen atoms are bound, influencing molecular interactions.

What is NAD+ Reduction mechanism

The process of NAD+ gaining electrons to form NADH, playing a key role in cellular respiration.

What is FAD Structure and Function

FAD (Flavin Adenine Dinucleotide) acts as a redox cofactor and is involved in various enzymatic reactions.

What is protein electrophoresis used for

A laboratory technique for separating proteins based on their size and charge.

Describe Native Page

A type of electrophoresis that preserves the native structure of proteins while separating them.

What is Sodium Dodecyl Sulfate

A detergent used in SDS-PAGE to denature proteins and impart a uniform negative charge.

How does SDS affect protein structure

SDS disrupts non-covalent bonds, leading to protein denaturation.

What are reducing agents used for

Substances that donate electrons to other molecules, often used to break disulfide bonds in proteins.

What is a polyacrylamide gel

A gel medium used for electrophoresis that provides a porous structure for protein separation.

What are the steps in SDS-PAGE procedure

1. Sample preparation, 2. Gel casting, 3. Loading samples, 4. Running the gel, 5. Staining to visualize proteins.

What is the Coomassie Brilliant Blue staining used for

A dye used to visualize proteins in gels following electrophoresis.

How are molecular weights determined

By comparing the migration distance of proteins in a gel to a standard molecular weight marker

What is a protein purity assessment

Analyzing protein samples to determine the presence of contaminants or impurities.

What is a Western Blotting

A method used to detect specific proteins in a sample using antibodies.

How is Western Blotting used today

In research and clinical labs for protein detection and quantification.

What is capillary action

The ability of a liquid to flow in narrow spaces without the assistance of external forces.

What is the hybridization probe

A nucleic acid probe used to detect specific sequences within a DNA or RNA molecule.

What is an autoradiogram

A photographic or digital image created using radiation emitted from radiolabeled samples.

What is the difference between western blotting and southern blotting

Western blotting detects proteins, whereas southern blotting is used to identify specific DNA sequences.

What Is a heterogenous protein sample

A mixture containing different types of proteins, often requiring fractionation for analysis.

What is a buffer

A solution that resists changes in pH when small amounts of acid or base are added.