Chapter 5

I. Amino Acids: The Building Blocks

• Structure (Slide 4):

  1. Central (α) carbon

  2. Amino group (–NH₂)

  3. Carboxyl group (–COOH)

  4. Hydrogen atom

  5. R group (variable, gives chemical identity)

• Amino Acid Classification (Slides 6–8):

  • Hydrophobic: nonpolar side chains (inside of proteins)

  • Hydrophilic:

    • Polar uncharged

    • Acidic (- charge)

    • Basic (+ charge) (e.g., histones are rich in lysine & arginine)

• Special Amino Acids (Slide 9):

  • Glycine: flexible

  • Proline: rigid; causes bends

  • Cysteine: forms disulfide bridges

II. Protein Structure and Folding

• Primary Structure (Slide 15):

  • Linear chain of amino acids (polypeptide)

  • Determines all higher levels of structure

• Secondary Structure (Slides 16–17):

  • α-Helix: right-handed, H-bonds within chain

  • β-Sheet: pleated sheet; H-bonds between chains

• Tertiary Structure (Slide 18):

  • 3D shape due to interactions:

    • H-bonds

    • Ionic bonds

    • Van der Waals

    • Disulfide bridges

  • Slide 19 confirms: “All of these” forces are involved

• Quaternary Structure (Slide 26):

  • Multiple polypeptide subunits form a functional protein (e.g., hemoglobin)

• Denaturation & Chaperones (Slide 22):

  • Proteins lose shape/function with pH, temp changes

  • Chaperones help refold or protect

III. Translation: RNA to Protein

A. Key Players

• mRNA: template

• tRNA (Slides 32, 34):

  • Has an anticodon that pairs with mRNA codon

  • Carries specific amino acid on 3′ end

• Ribosome (Slide 29):

  • Large + small subunits

  • Reads mRNA 5′ → 3′

  • Has A, P, and E sites (Slide 31)

B. Genetic Code (Slide 35)

• Redundant: multiple codons for one amino acid

• Unambiguous: each codon codes for only one amino acid

• Start codon = AUG (methionine)

• 3 Stop codons = UAA, UAG, UGA

C. Process of Translation (Slides 38–47)

• Peptide bond catalyzed by rRNA, not a protein (Slide 42 = True)

D. Reading Frame (Slide 30)

• Must read codons non-overlapping, in correct triplets.

• Frameshift mutations disrupt all downstream codons.

IV. Protein Sorting and Targeting

Signal Recognition Particle (SRP) (Slides 52–54)

• Proteins with signal sequence are recognized by SRP

• SRP pauses translation, directs complex to ER membrane

• Translation resumes into ER lumen or membrane

If SRP is mutated → proteins remain in cytosol (Slide 56)

V. Protein Evolution (Slides 59–62)

• Proteins evolve via mutations in DNA

• Folding domains (~2,500) can recombine across proteins

• Leads to ~25,000 protein families with shared ancestry

🧠 Sample Test Questions

🧬 Conceptual

1. Which level of protein structure is determined solely by gene-encoded amino acid order?

   • A. Primary ✅

   • B. Secondary

   • C. Tertiary

   • D. Quaternary

2. Which bonds stabilize secondary structure in proteins?

   • A. Disulfide

   • B. Ionic

   • C. Hydrogen ✅

   • D. Peptide

🔗 Connection-Based

3. A mutation prevents SRP binding. Where would the affected proteins end up?

   • A. In ER

   • B. Secreted

   • C. In cytoplasm ✅

   • D. In lysosome

4. Why is the genetic code called “redundant but not ambiguous”?

   • A. Each codon codes for multiple amino acids

   • B. Each amino acid has multiple codons ✅

   • C. Codons overlap

   • D. Start codons are variable

🧩 Prediction

5. mRNA Codon: 5′-GAA-3′ → What is the anticodon?

   • A. 5′-CUU-3′

   • B. 3′-CUU-5′ ✅

   • C. 3′-GAA-5′

   • D. 5′-UUC-3′

⚠ Frameshift Question

6. A deletion of 1 base near the start codon will:

   • A. Stop translation immediately

   • B. Remove 1 amino acid

   • C. Shift all downstream codons ✅

   • D. Only affect the start codon

1. Amino Acid

• Definition: The basic building block of proteins.

• Each has a central carbon bonded to:

  • An amino group (–NH₂)

  • A carboxyl group (–COOH)

  • A hydrogen

  • An R group (side chain that varies)

2. R Group (Side Chain)

• The variable part of each amino acid.

• Determines the amino acid’s:

  • Polarity (polar/nonpolar)

  • Charge (acidic/basic)

  • Hydrophobicity (water-hating) or hydrophilicity (water-loving)

3. Peptide Bond

• A covalent bond that links two amino acids.

• Formed via dehydration synthesis (water is removed).

• Joins the carboxyl group of one amino acid to the amino group of the next.

4. Primary Structure

• The linear sequence of amino acids in a protein (written from N → C terminus).

• Determines all higher-level folding and function.

5. Secondary Structure

• Local folding patterns in the polypeptide due to hydrogen bonding:

  • Alpha helix: spiral shape

  • Beta sheet: folded or pleated sheet

6. Tertiary Structure

• The complete 3D folded shape of a single polypeptide chain.

• Stabilized by interactions among R groups:

  • Hydrogen bonds

  • Ionic bonds

  • Disulfide bridges

  • Hydrophobic interactions

  • Van der Waals forces

7. Quaternary Structure

• Protein structure formed when multiple polypeptide chains (subunits) assemble into a functional protein (e.g., hemoglobin).

8. Denaturation

• The loss of a protein’s shape (and function) due to heat, pH, or chemicals.

• Often irreversible.

9. Ribosome

• A molecular machine that reads mRNA and assembles proteins.

• Made of rRNA and proteins.

• Contains:

  • A site: accepts new tRNA

  • P site: holds growing polypeptide

  • E site: tRNA exits

10. tRNA (Transfer RNA)

• A small RNA molecule that:

  • Matches an anticodon to the mRNA codon

  • Carries the corresponding amino acid to the ribosome

• Structure includes a cloverleaf shape and 3′ end for amino acid attachment.

11. Codon

• A triplet of mRNA bases (e.g., AUG) that codes for a specific amino acid.

• There are 64 possible codons:

  • 1 start codon (AUG)

  • 3 stop codons

  • 61 code for amino acids

12. Anticodon

• A triplet of bases on tRNA that pairs complementarily and antiparallel to the mRNA codon.

13. Reading Frame

• The way nucleotides are grouped into codons during translation.

• Shifts in the reading frame (frameshift mutations) cause all downstream codons to change, altering the protein.

14. Redundant Genetic Code

• More than one codon can code for the same amino acid.

  • Example: GAA and GAG both = glutamic acid.

15. Unambiguous Genetic Code

• Each codon codes for only one amino acid — no confusion.

16. Signal Peptide (Signal Sequence)

• A short amino-terminal sequence on a new polypeptide that signals the ribosome to go to the endoplasmic reticulum (ER).

17. Signal Recognition Particle (SRP)

• A protein-RNA complex that:

  • Recognizes the signal peptide

  • Pauses translation

  • Directs the ribosome to the ER

18. Folding Domain

• A part of a protein that folds independently into a stable structure.

• Often shared across multiple proteins with similar functions.

19. Protein Family

• A group of proteins that are evolutionarily related and have similar structure and function due to shared domains or sequences.