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)

Stage

Description

Initiation

Small subunit binds 5′ cap, scans for AUG; large subunit joins

Elongation

tRNA enters A site → peptide bond forms → ribosome shifts

Termination

Stop codon triggers release factor; ribosome disassembles

  • 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

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

    • A. In ER

    • B. Secreted

    • C. In cytoplasm ✅

    • D. In lysosome

  2. 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

  1. 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

  1. 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.