w2 slides fc Flashcards
What characteristic of amino acid side chains (R groups) determines their classification?
(A) Their molecular weight
(B) Their ability to form peptide bonds
(C) Their polarity and charge properties
(D) Their ability to form covalent bonds with DNA
Answer: (C) (Amino acids are classified as nonpolar, polar uncharged, acidic, or basic based on R group properties.)
How does cysteine contribute uniquely to protein stability?
(A) It is the only amino acid with an amide-containing side chain.
(B) It forms disulfide bonds, which stabilize tertiary and quaternary structure.
(C) It participates in β-sheet formation but not α-helices.
(D) It does not contribute to stability.
Answer: (B) (Cysteine forms covalent disulfide bonds, reinforcing protein structure.)
What is the primary structure of a protein?
(A) The overall 3D shape of the protein
(B) The sequence of amino acids connected by peptide bonds
(C) The arrangement of α-helices and β-sheets
(D) A complex of multiple polypeptide chains
Answer: (B) (Primary structure is the linear sequence of amino acids in a polypeptide chain.)
Which of the following best describes the interactions that stabilize secondary structures like α-helices and β-sheets?
(A) Hydrogen bonding between backbone amide and carbonyl groups
(B) Disulfide bridges between cysteine residues
(C) Hydrophobic interactions between nonpolar side chains
(D) Ionic bonding between charged R groups
Answer: (A) (Secondary structures are stabilized by hydrogen bonds between backbone atoms.)
What is the driving force for protein folding into its tertiary structure?
(A) Formation of peptide bonds
(B) Hydrophobic interactions that minimize water exposure
(C) RNA guidance mechanisms
(D) ATP-dependent helicase activity
Answer: (B) (Hydrophobic residues cluster inside the protein, driving folding.)
What role do chaperone proteins play in protein folding?
(A) They covalently bond to the protein to hold it in the correct shape.
(B) They guide misfolded proteins to degradation pathways.
(C) They help proteins fold correctly by preventing incorrect interactions.
(D) They facilitate peptide bond formation.
Answer: (C) (Chaperones assist in proper protein folding and prevent aggregation.)
How do protein domains contribute to protein function?
(A) They allow proteins to fold randomly.
(B) They function independently and can evolve separately.
(C) They are only found in prokaryotic proteins.
(D) They prevent proteins from interacting with other molecules.
Answer: (B) (Domains have distinct structures and functions within a protein.)
How do protein families evolve?
(A) By retaining identical amino acid sequences over generations
(B) Through gene duplication and sequence divergence
(C) By eliminating all structural domains
(D) By binding only to DNA
Answer: (B) (Protein families arise from gene duplication and evolutionary divergence.)
What interaction stabilizes quaternary protein structures?
(A) Noncovalent interactions between polypeptide subunits
(B) Single peptide bonds
(C) Phosphodiester linkages
(D) Watson-Crick base pairing
Answer: (A) (Subunits interact via hydrogen bonding, ionic bonds, and hydrophobic interactions.)
Why do some proteins form multiprotein complexes?
(A) To increase their molecular weight
(B) To facilitate specific biological functions requiring multiple components
(C) To prevent degradation by proteases
(D) To increase the solubility of hydrophobic amino acids
Answer: (B) (Multiprotein complexes enable coordinated function, such as ribosomes or transcription factors.)
What is the primary advantage of X-ray crystallography in protein studies?
(A) It provides high-resolution 3D structures of proteins.
(B) It determines protein primary sequence.
(C) It only works for membrane proteins.
(D) It requires liquid-phase proteins.
Answer: (A) (X-ray crystallography is a powerful tool for determining precise atomic structures.)
How does mass spectrometry contribute to protein research?
(A) It identifies amino acid sequences based on mass-to-charge ratios.
(B) It measures protein solubility.
(C) It sequences DNA encoding the protein.
(D) It provides live imaging of proteins inside cells.
Answer: (A) (Mass spectrometry helps determine protein identity and modifications.)
How does proteomics differ from studying a single protein?
(A) It focuses on all proteins within a cell or tissue, rather than one protein at a time.
(B) It examines DNA sequences rather than proteins.
(C) It only studies extracellular proteins.
(D) It ignores protein-protein interactions.
Answer: (A) (Proteomics analyzes large-scale protein expression and interactions.)
What is a major challenge of studying the proteome?
(A) Proteins are highly dynamic and can undergo modifications.
(B) Proteins have the same properties as DNA.
(C) The proteome is constant across all cell types.
(D) All proteins function independently.
Answer: (A) (Post-translational modifications and variability make proteomics complex.)
Why do some proteins require chaperonins rather than regular chaperone proteins?
(A) Chaperonins help proteins that cannot fold properly on their own by isolating them in a specialized chamber.
(B) Chaperonins only degrade misfolded proteins.
(C) Chaperonins are responsible for forming peptide bonds.
(D) Chaperonins prevent the formation of disulfide bonds.
Answer: (A) (Chaperonins provide an isolated environment for proper protein folding.)
What is the primary consequence of protein misfolding in diseases like Alzheimer’s or Parkinson’s?
(A) Misfolded proteins disrupt transcriptional regulation.
(B) Misfolded proteins aggregate into amyloid fibrils, causing cellular toxicity.
(C) Misfolded proteins fail to be translated properly.
(D) Misfolding alters DNA methylation patterns.
Answer: (B) (Amyloid fibrils accumulate and contribute to neurodegenerative disease.)
How do post-translational modifications affect protein function?
(A) They alter protein activity, localization, or interactions by adding chemical groups.
(B) They always reduce protein function.
(C) They occur exclusively in prokaryotic cells.
(D) They replace amino acids in the primary sequence.
Answer: (A) (Modifications like phosphorylation or glycosylation regulate protein activity.)
Which of the following best describes phosphorylation as a post-translational modification?
(A) It is the addition of a phosphate group, often regulating enzyme activity.
(B) It always inhibits protein function.
(C) It involves breaking peptide bonds.
(D) It is only found in prokaryotic cells.
Answer: (A) (Kinases add phosphate groups, affecting protein function.)
What is the primary function of an enzyme in a biological reaction?
(A) Lower the activation energy, increasing reaction speed.
(B) Change the equilibrium constant of the reaction.
(C) Alter the thermodynamics of a reaction.
(D) Act as a reactant in the reaction.
Answer: (A) (Enzymes speed up reactions by lowering activation energy.)
How does an enzyme-substrate complex lower activation energy?
(A) By stabilizing the transition state, reducing energy barriers.
(B) By supplying extra reactants.
(C) By permanently binding the substrate.
(D) By increasing the temperature.
Answer: (A) (Enzymes provide an optimal environment to stabilize intermediates.)
How do ubiquitin-proteasome systems regulate protein levels?
(A) Ubiquitin tags proteins for degradation in the proteasome.
(B) Ubiquitin acts as a structural component of proteins.
(C) The proteasome repairs unfolded proteins.
(D) Proteins with ubiquitin are stored in the Golgi apparatus.
Answer: (A) (Ubiquitin signals proteins for degradation in proteasomes.)
What happens to proteins degraded by the proteasome?
(A) They are broken into short peptides, which can be recycled or further degraded.
(B) They are refolded into their original shape.
(C) They become part of new DNA molecules.
(D) They are permanently inactivated but remain inside cells.
Answer: (A) (Proteasomes break proteins into small peptides for further processing.)
Why are protein-protein interactions important for cellular function?
(A) They enable complex processes like signal transduction and enzymatic pathways.
(B) They prevent proteins from functioning.
(C) They only occur in extracellular proteins.
(D) They increase RNA transcription rates.
Answer: (A) (Proteins interact to regulate cellular functions.)
What is a key feature of a protein interaction domain?
(A) It allows proteins to bind specific partners through complementary shapes and charges.
(B) It prevents proteins from interacting.
(C) It catalyzes peptide bond formation.
(D) It only exists in ribosomal proteins.
Answer: (A) (Domains facilitate selective binding between proteins.)
How do prions cause disease?
(A) Prions induce abnormal protein folding, leading to aggregates.
(B) Prions directly damage DNA.
(C) Prions function as enzymes that break down proteins.
(D) Prions stimulate excessive protein translation.
Answer: (A) (Prions misfold normal proteins, forming aggregates seen in diseases like CJD and mad cow disease.)
Which disease is characterized by protein misfolding and aggregation in neurons?
(A) Alzheimer’s disease
(B) Cystic fibrosis
(C) Sickle-cell anemia
(D) Huntington’s disease
a
What is the primary advantage of SDS-PAGE in protein analysis?
(A) It separates proteins based on size by applying an electric field.
(B) It sequences amino acids.
(C) It measures enzymatic activity.
(D) It detects protein-DNA interactions.
Answer: (A) (SDS-PAGE separates proteins by molecular weight.)
Why is Western blotting used in protein research?
(A) It detects specific proteins using antibodies after SDS-PAGE.
(B) It measures RNA levels.
(C) It determines DNA sequence.
(D) It quantifies enzyme activity.
a
What is the significance of cryo-electron microscopy in protein research?
(A) It allows visualization of large protein complexes at near-atomic resolution.
(B) It sequences proteins directly.
(C) It replaces X-ray crystallography completely.
(D) It only works on membrane proteins.
Answer: (A) (Cryo-EM is a powerful technique for structural biology.)
Why is understanding protein structure critical for drug design?
(A) Drugs often target specific protein active sites or allosteric sites.
(B) Drugs only affect DNA sequences.
(C) Protein structure does not influence drug function.
(D) Protein folding is irrelevant to pharmaceutical applications.
a
function of the r group
the r group is variable and determines the type of amino acid
cysteine (disulphide bonds)
-nonpolar amino acid
-depending on where the protein ends up, oxidation conditions in the cell will favour forming disulfide bonds
-SH: forms strong covalent bonds
-reducing conditions in the cell will favour disulfide bonds being broken –> SH bonds
-cell controls whether disulfide bridges are formed or broken
which type of bond are r groups not involved in?
Peptide bonds
-carboxyl group reacting with amino group to make peptide bond and water
residues
take AA and make peptide bond and join it to another AA = residue
–AA part of protein
–numbered from AMINO end (starts there)
the alpha helix
secondary structure
-R groups NOT involved in forming this structure
the beta sheet
-H-bonding between carbonyl oxygen (C=O) of 1 aa and amide hydrogen (N-H) of aa in neighboring strand
-R groups not involved but they alternately project up and down
-polypeptide arrows always pointing TWD carboxyl terminus
amyloids
-stacked beta sheets
-part of neurogenerative diseases
H-bonding in secondary structures
-Which atoms are H-bonded?
carbonyl oxygen, amide hydrogen in peptide backbone
H-bonding in secondary structures
Alpha helices
4 AA’s apart and within the SAME segment of polypeptide chain
H-bonding in secondary structures
Beta sheet
between AA’s in different segments or strands of polypeptide chain
Coiled coil
-has to be amphipathic (type of alpha helix) to form a coiled coil
–(amphipathic: both hydrophobic and hydrophilic areas in SAME molecule)
-hydrophobic force will push R groups (?)
tertiary structure - forces
3D overall structure of a protein
held tg by:
-hydrophobic interactions
-non-covalent bonds
-covalent disulfide bonds
-water pushes side groups into middle of molecule
tertiary structure (proteins)
1) proteins generally fold into the conformation that’s MOST energetically favourable
2) proteins will fold into the shape dictated by their AA sequence, but CHAPERONE proteins help make the process more efficient and reliable
chaperone proteins
-aids in folding
-if it folds incorrectly…
—won’t be able to correct itself
protein domains
-specialized for different functions
-portion of a protein that has its own tertiary structure, often functioning in semi-independent manner
-eukaryotic proteins often have 2 or more domains connected by intrinsically DISORDERED sequence (flexible part of polypeptide)
-domains important for the evolution of proteins
quaternary structure: hemoglobin
1) hemoglobin protein formed from separate subunits: 2a, 2B
2) each subunit= separate pp (held by noncovalent bonds)
3) sickle cell anemia is caused by a mutation in the B subunit
-hemoglobin can’t carry oxygen and changes RBC shape to a sickle cell
scaffold protein
-non-enzymatic, multi-domain proteins that organize and coordinate signaling pathways by bringing together multiple interacting proteins
-serve as molecular platforms that control signal transduction, structural organization, and intracellular communication
proteomics
-study of proteins
–protein-protein interactions, regulation and their position within a pathway
-location within a cell or tissue
difference between the structures of protein
Imagine a protein like a LEGO set:
🟩 Primary Structure → The individual LEGO pieces
🟦 Secondary Structure → How those pieces snap together (walls, bridges)
🟥 Tertiary Structure → How the entire LEGO set looks when complete
🟨 Quaternary Structure → How multiple LEGO sets combine into a giant castle
polar vs nonpolar AA
Amino acids are categorized as:
Nonpolar (hydrophobic) → Think oil, avoids water (e.g., valine, leucine)
Polar uncharged → Loves water but doesn’t carry a charge (e.g., serine)
protein folding
Primary Structure: The Blueprint (Amino Acid Sequence)
Secondary Structure: Local Folding (Alpha Helices & Beta Sheets)
-these structures are stabilized by hydrogen bonds between atoms in the protein backbone
Alpha helix (spiral staircase)→ Found in hair, keratin
-Beta sheet (folded paper) 📄 → Found in silk, spider webs
-Exam Tip: Beta sheets can be parallel or anti-parallel.
Tertiary Structure: 3D Folding (Functional Shape!)
Now the protein gets its final functional shape, stabilized by:
✅ Hydrogen bonds (weak but important)
✅ Ionic bonds (salt bridges)
✅ Hydrophobic interactions (water-fearing amino acids clump together)
✅ Disulfide bonds (covalent “bridges” by cysteine)
💡 Key Concept: Chaperone proteins help proteins fold correctly! Without them, misfolded proteins can cause diseases like Alzheimer’s.
🟨 Quaternary Structure: When Multiple Proteins Work Together
Some proteins work alone, but others team up into giant molecular machines.
Example:
🩸 Hemoglobin → 4 protein subunits work together to carry oxygen in blood!
🚨 Exam Tip: Sickle cell anemia happens due to one mutation in hemoglobin, causing red blood cells to become rigid and sickle-shaped.
important takeaways
1️⃣ Protein function depends on its 3D shape, which depends on the amino acid sequence!
2️⃣ Misfolded proteins = disease (e.g., Alzheimer’s, sickle cell anemia).
3️⃣ Peptide bonds hold amino acids together, but hydrogen, ionic, and disulfide bonds shape the protein.
4️⃣ Chaperones help proteins fold correctly.
5️⃣ Proteins can work alone or as giant molecular machines (e.g., hemoglobin).
What type of bond stabilizes an alpha helix?
Hydrogen bond ✅
