L14: kill me pls

What are proteins made of?

A1: Proteins are polymers made of amino acids.

Q2: What atoms make up an amino acid?

A2: Carbon, hydrogen, nitrogen, oxygen, and sometimes sulfur.

Q3: What roles do proteins play in the body?

A3: Proteins have structural, transport, enzymatic, immune, and contractile roles.

Q4: What is the role of alpha amylase?

A4: Alpha amylase breaks down starch in saliva, aiding in carbohydrate digestion.

Q5: What structural role does collagen serve?

A5: Collagen provides strength and structure to tissues like skin, bones, tendons, and cartilage.

Q6: What is the function of hemoglobin?

A6: Hemoglobin transports oxygen from the lungs to tissues and returns carbon dioxide to the lungs.

Q7: Which proteins are essential for muscle contraction?

A7: Actin and myosin form muscle fibers and are essential for contraction and tissue integrity.

What is the role of antibody proteins?

A8: Antibodies are part of the immune system, defending the body against pathogens.

Q9: Name two enzymes involved in nucleic acid processes.

A9: DNA helicase and RNA polymerase.

What are the main parts of an amino acid?

An amino group (NH₂), a carboxyl group (COOH), a central carbon (alpha carbon), and an R group (side chain).

What distinguishes one amino acid from another?

A: The R group (side chain) attached to the alpha carbon.

Q12: How many different amino acids exist?

A12: 20.

Name the types of amino acids based on side chain properties.

• Hydrophobic (non-polar)

• Hydrophilic (polar)

• Negatively charged (acidic, hydrophilic)

• Positively charged (basic, hydrophilic)

Q13: What kind of side chains do hydrophobic amino acids have?

A13: Non-polar side chains.

Q14: What kind of side chains do hydrophilic amino acids have?

A14: Polar, negatively charged, or positively charged side chains.

What bond joins two amino acids?

A: A peptide bond.

Q15: What type of reaction forms a peptide bond?

A15: A condensation reaction (water is released).

Q: What catalyzes the formation of peptide bonds?

A: Ribosomes.

Q: What breaks a peptide bond to return amino acids to monomers?

A: Hydrolysis.

Q16: Between which groups does a peptide bond form?

A16: Between the carboxyl group of one amino acid and the amino group of another.

Q17: What is the result of many amino acids joined by peptide bonds?

A17: A polypeptide chain.

Q18: What determines the primary structure of a protein?

A18: The specific sequence of amino acids in the polypeptide chain.

What determines the sequence of amino acids in a protein?

A: The mRNA sequence translated by the ribosome.

Q: What is each amino acid called in a polypeptide chain?

A: A residue.

Q: What is the directionality of a protein chain?

A: From N-terminus (amino end) to C-terminus (carboxyl end).

Q19: What is protein folding?

A19: The process by which a polypeptide folds into its functional 3D shape.

What two shapes can amino acid chains form in the secondary structure?

A20: Alpha helices and beta-pleated sheets.

What determines whether a segment forms an alpha helix or beta sheet?

A: The sequence of amino acids.

Q: Describe the alpha helix structure.

A: A spiral shape with 3-4 residues per turn; R groups face outward.

Describe the beta sheet structure.

A: The polypeptide chain folds back and aligns with itself; forms a flat, sheet-like shape.

Q21: What type of bonding holds secondary structures together?

A21: Hydrogen bonds between backbone atoms (not side chains).

Where do hydrogen bonds form in beta sheets?

A: Between carbonyl oxygens and amide hydrogens of adjacent strands.

Q: Where do hydrogen bonds form in alpha helices?

A: Between carbonyl oxygen of one amino acid and amide hydrogen four residues ahead.

Q: What defines a hydrogen bond in protein structure?

A: A weak interaction between a hydrogen attached to nitrogen/oxygen and another electronegative atom.

Q22: What is tertiary structure?

A22: The overall 3D shape of a polypeptide, determined by interactions between R groups.

Q23: Name four types of bonds/interactions in tertiary structure.

A23: Hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions.

Q: What drives the formation of tertiary structure?

A: The chemical properties of amino acids (e.g., hydrophobic effect, ionic bonds).

Q: How are distant residues brought together in tertiary structure?

A: By folding the chain into a compact 3D shape.

Q: What is the hydrophobic effect in protein folding?

A: Hydrophobic residues cluster inside the protein to avoid water; hydrophilic residues are on the surface.

Q24: What is a disulfide bridge?

A24: A strong covalent bond between two cysteine side chains (sulfur-sulfur).

Q: What are globular proteins?

A: Compact, spherical proteins with functional roles (e.g., enzymes, transporters).

Give examples of globular proteins.

A: Alpha amylase, Artemis.

Q: What is the function of the Artemis protein?

A: It is essential in the immune system for antibody production.

Q: What are fibrous proteins?

A: Elongated proteins that provide structural support.

Q: Give examples of fibrous proteins.

A: Collagen and actin filaments.

Q25: What is quaternary structure?

A25: The structure formed when two or more polypeptide chains (subunits) assemble into a functional protein.

Q26: Give an example of a protein with quaternary structure.

A26: Hemoglobin (4 polypeptide subunits).

What defines quaternary protein structure?

A: Two or more polypeptide chains assembling into one functional protein.

Q: How does quaternary structure differ from tertiary structure?

A: Tertiary involves one chain folding; quaternary involves multiple chains.

Q: What is an example of a protein with quaternary structure?

A: Hemoglobin – a tetramer with four subunits.

Q: Describe the structure of Malic Enzyme 2.

A: A dimer of dimers — two dimer units join to form the functional protein.

Q: Do all proteins have a quaternary structure?

A: No, only proteins made of more than one polypeptide chain do.

What are hydrogen bonds in proteins?

A: Weak interactions between hydrogen bonded to nitrogen/oxygen and another electronegative atom.

Q: Why are hydrogen bonds important in proteins?

A: They stabilize alpha helices and beta sheets and assist with enzyme-substrate interaction.

Q: What are electrostatic interactions (salt bridges) in proteins?

A: Bonds between charged amino acids (e.g., lysine and glutamate).

Q: What are disulfide bonds?

A: Covalent bonds between sulfur atoms of two cysteine residues.

Q: Why are disulfide bonds important in proteins?

A: They add strong structural stability, especially in tertiary structure.

Q: What are hydrophobic interactions?

A: Clustering of non-polar side chains away from water inside the protein.

: What is protein denaturation?

A: The loss of secondary and tertiary structure, causing loss of function.

Q: Is denaturation reversible?

A: Generally, no — especially when disulfide cross-links form.

Q: What causes denaturation?

A:

• pH changes (e.g., milk curdling)

• Salt concentration

• Temperature (e.g., cooking eggs)

• Disulfide bond cross-linking

• Hydrophobic aggregation

What happens to hydrophobic amino acids during denaturation?

A: They become exposed and aggregate, forming insoluble clumps.

Q: What problem does disulfide cross-linking cause in denatured proteins?

A: It leads to aggregation and insolubility, preventing refolding.

Q: Can denatured proteins be refolded?

A: Sometimes, with chemical agents like urea and reducing agents, but not typically in living organisms.

Q: What is X-ray crystallography?

A: A method requiring protein crystals exposed to X-rays to determine atomic structure.

Q: What is cryo-electron microscopy (Cryo-EM)?

A: Uses electron beams on frozen protein grids to visualize structure at high resolution.

Q: What is NMR spectroscopy?

A: Uses isotopically labeled proteins and NMR signals to determine structure in solution.