Cellular Metabolism, Cell Cycle, DNA Replication, and Protein Synthesis: Key Concepts and Terminology

General Terminology in Human Biology

Metabolism

Metabolism refers to all chemical reactions that occur within living organisms to maintain life. These reactions are broadly classified into two categories:

• Anabolism: The synthesis of complex molecules from simpler ones, requiring energy input. Example: Protein synthesis from amino acids.

• Catabolism: The breakdown of complex molecules into simpler ones, releasing energy. Example: Cellular respiration breaking down glucose.

Product: The final molecule(s) produced in a metabolic reaction.

Substrate: The reactant molecule(s) upon which an enzyme acts.

Co-enzyme: Non-protein molecules that assist enzymes in catalyzing reactions (e.g., NAD+, FAD, Coenzyme A).

Concentration gradient: The difference in the concentration of a substance between two regions, often driving diffusion or active transport.

Active transport: The movement of molecules across a membrane against their concentration gradient, requiring energy (usually ATP).

Endocytosis: The process by which cells engulf external substances, bringing them into the cell enclosed in a vesicle.

Cellular Respiration and ATP Production

Overview of ATP Production

ATP (adenosine triphosphate) is the primary energy currency of the cell. Cellular respiration is the process by which cells extract energy from glucose to produce ATP. The process occurs in several stages:

1. Glycolysis: Occurs in the cytoplasm; glucose is split into two molecules of pyruvate, producing a net gain of 2 ATP and 2 NADH.

2. Preparatory Step (Link Reaction): Pyruvate is converted to acetyl-CoA, producing NADH and releasing CO2.

3. Citric Acid Cycle (Krebs Cycle): Acetyl-CoA enters the cycle, generating NADH, FADH2, ATP, and CO2.

4. Electron Transport System (ETS): Electrons from NADH and FADH2 are transferred through protein complexes in the inner mitochondrial membrane, driving ATP synthesis via ATP synthase.

Aerobic respiration requires oxygen and produces the most ATP. Anaerobic respiration (e.g., lactic acid fermentation) occurs without oxygen, yielding less ATP.

Key Intermediates: Pyruvate, α-ketoglutarate, succinate, fumarate, oxaloacetate, G3P (glyceraldehyde-3-phosphate), citric acid.

Key Enzymes: ATP synthase (produces ATP), dehydrogenases, coenzymes (NAD+, FAD).

Inner mitochondrial membrane space and cristae are structural features important for the electron transport system.

Phosphorylation: The addition of a phosphate group to a molecule, often regulating activity or storing energy.

ATP Yield at Each Stage

Stage	ATP Produced (per glucose)	Other Products
Glycolysis	2 (net)	2 NADH, 2 pyruvate
Preparatory Step	0	2 NADH, 2 CO2
Citric Acid Cycle	2	6 NADH, 2 FADH2, 4 CO2
Electron Transport System	~28	H2O
Total	~32

Additional info: The exact ATP yield can vary depending on cell type and shuttle systems used.

The Cell Cycle

Phases and Activities

The cell cycle is the series of events that cells go through as they grow and divide. It consists of interphase and the mitotic phase:

• G1 phase: Cell grows and carries out normal functions.

• S phase: DNA replication occurs.

• G2 phase: Cell prepares for division; checks for DNA errors.

• G0 phase: Resting phase; cells may exit the cycle and stop dividing.

• Mitotic phase (M phase): Includes mitosis (nuclear division) and cytokinesis (cytoplasmic division).

Interphase includes G1, S, and G2 phases.

DNA Structure, Replication, and Repair

DNA Structure

• DNA (deoxyribonucleic acid): Double helix composed of nucleotides (A, T, C, G).

• Chromatin: DNA wrapped around histone proteins.

• Chromosomes: Condensed chromatin visible during cell division.

• Chromatid: Each of the two identical halves of a duplicated chromosome.

• Complimentary strand: The sequence of bases that pairs with another strand (A with T, C with G).

DNA Replication

DNA replication is the process by which a cell duplicates its DNA before cell division. It is semiconservative, meaning each new DNA molecule consists of one old and one new strand.

• Initiation: Begins at origins of replication, forming a replication bubble.

• Enzymes involved:

  • Helicase: Unwinds the DNA double helix.

  • Single stranded binding proteins: Stabilize unwound DNA.

  • Primase: Synthesizes RNA primers.

  • DNA Polymerase: Adds nucleotides to the growing DNA strand.

  • Ligase: Joins Okazaki fragments on the lagging strand.

  • Repair enzymes: Correct errors in DNA.

• Leading strand (3’): Synthesized continuously.

• Lagging strand (5’): Synthesized in short segments called Okazaki fragments.

Mutations: Changes in DNA sequence; can be caused by errors in replication or environmental factors.

Restriction enzymes: Cut DNA at specific sequences; important in genetic engineering.

Protein Synthesis and Structure

Transcription and Translation

Protein synthesis involves two main processes:

1. Transcription: DNA is used as a template to synthesize messenger RNA (mRNA).

   • Promoter: DNA sequence where RNA polymerase binds to start transcription.

   • RNA polymerase: Enzyme that synthesizes RNA from DNA template.

   • 1° transcript: The initial RNA transcript before processing.

   • Introns: Non-coding regions removed from mRNA.

   • Exons: Coding regions that remain in mRNA.

   • Elongation: RNA strand grows.

   • Termination: RNA synthesis ends.

2. Translation: mRNA is decoded to build a polypeptide (protein) at the ribosome.

   • mRNA: Carries genetic code from DNA.

   • rRNA: Forms part of the ribosome.

   • tRNA: Brings amino acids to the ribosome; contains anticodon that pairs with mRNA codon.

   • Codon: Three-nucleotide sequence on mRNA specifying an amino acid.

   • Polypeptide: Chain of amino acids linked by peptide bonds.

   • Initiation, elongation, termination: Stages of translation.

   • Ribozymes: RNA molecules with enzymatic activity.

Protein Structure

• Primary structure: Sequence of amino acids.

• Secondary structure: Local folding into alpha helix or beta sheet due to hydrogen bonding.

• Tertiary structure: Overall 3D shape of a single polypeptide.

• Quaternary structure: Association of multiple polypeptide chains.

Summary Table: Key Enzymes and Their Functions

Enzyme	Function	Process
ATP synthase	Produces ATP from ADP and Pi	Cellular respiration
DNA polymerase	Synthesizes new DNA strands	DNA replication
RNA polymerase	Synthesizes RNA from DNA template	Transcription
Helicase	Unwinds DNA double helix	DNA replication
Ligase	Joins DNA fragments	DNA replication
Primase	Synthesizes RNA primers	DNA replication
Repair enzymes	Correct DNA errors	DNA repair
Restriction enzymes	Cut DNA at specific sites	Genetic engineering

Additional Key Concepts

• Linear pathway: Series of reactions where the product of one is the substrate for the next.

• Cyclic pathway: Series of reactions that regenerate the starting molecule (e.g., Citric Acid Cycle).

• Energy investment: Initial input of energy (ATP) required to start a metabolic pathway (e.g., glycolysis).

• Semiconservative replication: Each new DNA molecule contains one old and one new strand.