SCB-203 Exam 2 Review: Molecular and Cellular Foundations

Protein Structure and Function

Hydrogen Bonds

Hydrogen bonds are weak interactions that play a crucial role in stabilizing the three-dimensional structure of proteins and nucleic acids.

• Definition: A hydrogen bond forms when a hydrogen atom covalently bonded to an electronegative atom (like oxygen or nitrogen) is attracted to another electronegative atom.

• Importance: Stabilizes secondary, tertiary, and quaternary protein structures.

Amino Acid Structure and R-Group Function

Amino acids are the building blocks of proteins, each with a central carbon, amino group, carboxyl group, hydrogen atom, and a unique R-group (side chain).

• Peptide Bond Formation: Peptide bonds link amino acids via a dehydration synthesis reaction between the carboxyl group of one amino acid and the amino group of another.

• R-Group Function: The R-group determines the chemical properties and reactivity of each amino acid.

Protein Structure Levels

• Primary Structure: Linear sequence of amino acids.

• Secondary Structure: Local folding into alpha-helices and beta-sheets stabilized by hydrogen bonds.

• Tertiary Structure: Three-dimensional folding due to interactions among R-groups.

• Quaternary Structure: Association of multiple polypeptide chains.

• Globular Protein Shape and Solubility: Globular proteins are compact, water-soluble, and function as enzymes, transporters, etc.

Protein Denaturation

Denaturation is the loss of a protein's native structure due to external stress (heat, pH, chemicals), resulting in loss of function.

Nucleic Acid Structure and Function

Nucleotide Structure

• Bonds: Nucleotides are joined by phosphodiester bonds.

• Purines vs. Pyrimidines: Purines (adenine, guanine) have two rings; pyrimidines (cytosine, thymine, uracil) have one ring.

DNA Replication

DNA replication is the process by which DNA makes a copy of itself during cell division.

• Base Pairing: Adenine pairs with thymine (A-T), and cytosine pairs with guanine (C-G).

DNA vs. RNA

• Structure: DNA is double-stranded; RNA is single-stranded.

• Bases: DNA contains thymine; RNA contains uracil.

• Function: DNA stores genetic information; RNA is involved in protein synthesis.

Gene

A gene is a segment of DNA that encodes a functional product, usually a protein.

ATP Structure and Energy Release

ATP (adenosine triphosphate) is the primary energy carrier in cells.

• Structure: Adenine base, ribose sugar, and three phosphate groups.

• Energy Release: Hydrolysis of the terminal phosphate releases energy: $\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i + \text{energy}$

Gene Expression and Protein Synthesis

Transcription vs. Translation

• Transcription: Synthesis of mRNA from a DNA template (occurs in the nucleus).

• Translation: Synthesis of a polypeptide from mRNA (occurs at ribosomes in the cytoplasm).

• Enzymes: RNA polymerase (transcription), ribosomes (translation).

RNA Processing

• Pre-mRNA Modifications: Addition of 5' cap, poly-A tail, and splicing to remove introns.

Protein Targeting

• Signals: Proteins contain signal sequences that direct them to specific cellular locations (e.g., ER, mitochondria).

DNA → mRNA → Amino Acid Sequence

• Central Dogma: Genetic information flows from DNA to RNA to protein.

• Codons: Triplets of nucleotides in mRNA specify amino acids.

Cell Membranes and Transport

Phospholipid Bilayer and Membrane Structure

• Fluid Mosaic Model: Describes the membrane as a fluid combination of phospholipids, cholesterol, and proteins.

• Integral and Peripheral Membrane Proteins: Integral proteins span the membrane; peripheral proteins are attached to the surface.

• Cholesterol: Modulates membrane fluidity and stability.

Membrane Transport Mechanisms

• Diffusion: Movement of molecules from high to low concentration.

• Facilitated Diffusion: Passive transport via membrane proteins.

• Osmosis: Diffusion of water across a selectively permeable membrane.

• Tonicity: Describes the effect of a solution on cell volume (isotonic, hypertonic, hypotonic).

Active Transport

• Primary Active Transport: Direct use of ATP to move substances against their gradient (e.g., Na+/K+ pump).

• Secondary Active Transport: Uses the energy from the movement of one substance down its gradient to move another up its gradient (symport, antiport).

Endocytosis vs. Exocytosis

• Endocytosis: Uptake of materials into the cell via vesicles.

• Exocytosis: Release of materials from the cell via vesicles.

Cellular Organelles and Functions

• Rough ER: Protein synthesis and modification.

• Smooth ER: Lipid synthesis and detoxification.

• Golgi Apparatus: Protein modification, sorting, and packaging.

• Ribosomes: Protein synthesis.

• Lysosomes: Digestion of macromolecules.

• Mitochondria: ATP production via cellular respiration.

Cytoskeleton Components and Cellular Extensions

• Microfilaments, Intermediate Filaments, Microtubules: Provide structural support, cell movement, and intracellular transport.

• Cellular Extensions: Cilia, flagella, and microvilli increase surface area or aid in movement.

Common Mistakes to Avoid

• Reading DNA template strands in the wrong direction (must be 5' → 3').

• Using thymine (T) instead of uracil (U) in mRNA.

• Confusing codons (mRNA) with anticodons (tRNA) when obtaining amino acid sequences.

• Forgetting ATP is required for active transport.

• Reversing ion movement in the sodium-potassium pump.