Notes on Molecules and Cells (Sections 1.1–1.2)

1.1 MOLECULES

• Organic vs inorganic compounds
  • Inorganic compounds: generally do not contain carbon (e.g., water, salts, many acids and bases)
  • Organic compounds: contain carbon and are characteristic of living organisms; four major classes:
  • Carbohydrates (glucides)
  • Lipids
  • Proteins
  • Nucleic acids

1.1.2 GLUCIDES (Carbohydrates)

• General formula: $C<em>n(H</em>2O)_m$
• General question: What is the general formula for disaccharides? (Text shows andDiscussed in class) → typical example: $C<em>{12}H</em>{22}O_{11}$ (two monosaccharides minus one water)
• Key monosaccharides shown: glucose, fructose, galactose, deoxyribose, ribose
• Monosaccharides: building blocks of larger carbohydrates; can form cyclic structures
• Disaccharides: formed by dehydration synthesis (condensation) between two monosaccharides; examples include sucrose (glucose + fructose), lactose, maltose
• Polysaccharides: long polymers of sugars
• Synthesis and digestion: disaccharides are too large to cross membranes and must be hydrolyzed to monosaccharides during digestion

1.1.3 Monosaccharides

• Definition: single cyclic structure (pentose or hexose)
• They are the basic units of other carbohydrates
• Examples: glucose (the main sugar in blood plasma), deoxyribose (in DNA)

1.1.4 Disaccharides

• Definition: double sugars (e.g., glucose + fructose → sucrose)
• Occur in diet as sucrose, lactose, maltose
• Too large to cross cell membranes; must be hydrolyzed to monosaccharides during digestion

1.1.5 Polysaccharides

• Definition: long chains of identical sugars (polymers)
• Starch (amidon) stored in plants
• Glycogen stored in animal tissues (liver, muscles)
• Degradation to glucose provides a rapid glucose source

1.1.6 Functions of Carbohydrates

• Major function: glucose as a fuel for ATP synthesis
• Other functions: structural roles via glycolipids, glycoproteins, and nucleic acids

1.1.7 LIPIDS (Introduction to lipids via structure)

• Lipid structures include glycerol with phosphate groups and fatty acid chains; glycerol can form triglycerides with three fatty acids
• Key forms:
  • Phospholipids: glycerol + phosphate group + two fatty acid tails; polar head (phosphate-containing) and non-polar tail; essential components of cell membranes; also assist lipid transport in plasma; abundant in nervous tissue
  • Triglycerides (neutral fats): glycerol + 3 fatty acids; energy storage; formation involves release of 3 water molecules (condensation)
• Visual note: triglyceride structure shows three fatty acid chains attached to a glycerol backbone with a condensation reaction producing 3 H2O

1.1.8 Fatty acids and triglycerides in adipose tissue

• Neutral fats stored in adipose tissue serve as a major energy reserve, provide insulation and protection for organs

1.1.9 Phospholipids (in membranes)

• Main components of cellular membranes; help transport lipids in blood; abundant in nervous tissue
• Structural evolution: polar head (phosphate-containing) and non-polar tails create a bilayer

1.1.10 Steroids

• Cholesterol: key steroid, essential component of cell membranes; precursor to steroid hormones, vitamin D, and bile salts
• True/false prompts from slide:
  • “The source of cholesterol is necessarily dietary because our cells cannot synthesize it.” → False (cells synthesize cholesterol)
  • “Like neutral fats, cholesterol can be used by cells as an energy source.” → False (cholesterol is not a primary energy source)

1.1.11 Other lipid-soluble substances

• Eicosanoids: group derived from a 20-carbon fatty acid; important membrane components and chemical messengers; e.g., prostaglandins
• Lipoproteins: complexes of lipids and proteins; transport triglycerides and cholesterol in the blood

1.1.12 PROTEINS and PEPTIDE BONDS

• Proteins are built from amino acids linked by peptide bonds
• Simple representation: dipeptide formation through a dehydration synthesis, with release of a water molecule; peptide bond formation links C=O of one amino acid to the N of the next
• Hydrolysis breaks peptide bonds to release amino acids
• The heme group is present in some proteins (e.g., hemoglobin)

1.1.13 Levels of protein structure

• Primary, secondary, tertiary, and quaternary structures (not fully detailed in the slide, but implied by figures)

1.1.14 Proteins: characteristics and functions

• Fibrous proteins: structural, long and filamentous; insoluble in water; very stable; provide support and movement; examples include collagen, keratin, elastin, actin, myosin
• Globular proteins: compact and spherical; soluble in water; active in metabolism; examples include enzymes, hemoglobin, lipoproteins, peptide hormones, antibodies
• Enzymes: biological catalysts; most enzyme names end with -ase (e.g., hydrolase, kinase, ATPase)

1.1.15 ENZYMES

• Role: catalyze biochemical reactions; specificity and active sites; regulate metabolic pathways

1.1.16 NUCLEIC ACIDS: Nucleotides

• Basic unit: nucleotide (nitrogenous base + five-carbon sugar + phosphate group)
• Example: DNA and RNA

1.1.17 DNA vs RNA

• DNA (ADN):
  • Structure: double helix; sugar = deoxyribose; bases = A, T, C, G
  • Localized mainly in nucleus
  • Encodes genes; replicates before cell division; governs protein synthesis
• RNA (ARN):
  • Structure: single strand; sugar = ribose; bases = A, U, C, G
  • Localized mainly in cytoplasm
  • Executes protein synthesis following instructions from DNA

1.1.18 What is a gene?

• Simple definition: a segment of DNA that carries instructions for building a polypeptide chain
• Big questions from the slide:
  • How many genes per molecule of DNA?
  • How many DNA molecules per nucleus?
  • How many genes are activated in a cell?

1.1.19 ADENOSINE TRIPHOSPHATE (ATP)

• Energy stored in the phosphate bonds; hydrolysis releases energy
• Adenosine structure includes adenine + ribose + phosphate groups (AMP, ADP, ATP)
• Diagrammatic progression: AMP ⇄ ADP ⇄ ATP with increasing phosphate groups
• Chemical depiction:
  • ATP: $ext{Adenosine} ext{ + } ext{P}_{ ext{(3)}}$
  • ADP: $ext{Adenosine} ext{ + } ext{P}_{ ext{(2)}}$
  • AMP: $ext{Adenosine} ext{ + } ext{P}_{ ext{(1)}}$

1.1.20 ATP in cellular work

• ATP powers cellular work: transport, mechanical work (contraction/movement), and chemical work (driving reactions)
• Example: energy use in three types of work (Fig. 2.27 in the slides)

1.2 CELLS AND THEIR STRUCTURES

1.2 Animation and overview

• Cell types mentioned (from the animation): fibroblasts, erythrocytes, epithelial cells, skeletal muscle cells, smooth muscle cells, adipocytes, macrophage, neuron, sperm
• The science of cells is Cytology

1.2.1 Key definitions in the cell

• Cytosol
• Plasma membrane
• Nucleus
• Cytoplasm: cytosol, organelles, inclusions

1.2.2 CYTOPLASMIC ORGANELLES (pp. 96-103)

• Mitochondria

  • Two membranes; inner membrane folds (cristae)
  • Own DNA; can replicate by fission; function: ATP production
  • True/false prompts from slides:
  • Oxygen use for ATP production only inside mitochondria → False (also occurs in mitochondria, but depends on overall metabolism; the statement is a simplification)
  • ATP production only inside mitochondria → False (more nuanced: mitochondria are major sites, but some ATP is produced elsewhere via glycolysis)
  • All cells contain mitochondria → False (some cell types have few or none)

• Ribosomes and endoplasmic reticulum (ER)

  • Rough ER with ribosomes; smooth ER lacking ribosomes
  • Functions:
  • Rough ER: protein synthesis for membranes and secretion; glycosylation; protein processing in cisternae; vesicular transport
  • Smooth ER: lipid synthesis; detoxification; calcium storage in muscle
  • The ER is part of the continuous network extending from the nuclear envelope

• Golgi apparatus

  • Modifies, concentrates, and packages products from the ER into vesicles
  • Three vesicle destinies: secretory vesicles; membrane/organellar vesicles; lysosomes
  • Proteins from the ER pass through cisternae, are processed, and packed for their final destination

• Lysosomes and Peroxisomes

  • Lysosomes: contain digestive (hydrolase) enzymes
  • Peroxisomes: contain oxidases and catalases for detox and metabolism

1.2.3 THE CYTOSKELETON

• Network of fibrous elements that provide structure, shape, and movement
• Three components:
  • Microfilaments (actin)
  • Intermediate filaments
  • Microtubules (tubulins)
• Functions of the cytoskeleton include maintaining shape, aiding organelle movement, forming cilia/flagella, and helping in cell division

1.2.4 THE NUCLEUS

• Envelope: double membrane with nuclear pores; outer membrane continuous with rough ER
• Nucleolus: site of ribosomal subunit synthesis; within nucleus
• Chromatin: DNA + histones; forms chromosomes during division
• Nucleosome: fundamental unit of chromatin; DNA wrapped around histone octamer
• RBCs are anucleate (lack nucleus) due to maturation process; questions on how they reproduce and synthesize new proteins

Additional notes on nucleus and chromatin

• The nuclear envelope consists of an inner and outer membrane with large pores to allow movement of large particles (RNA, ribosomal subunits) between nucleus and cytoplasm
• Chromatin condenses into chromatids during cell division
• Nucleosome: basic unit of chromatin, ~147 bp of DNA wrapped around a histone octamer

Notes on cross-links and connections

• Principles: cellular metabolism relies on the flow of energy from nutrients through ATP; chemical reactions are organized by enzymes; macromolecules (proteins, nucleic acids, carbohydrates, lipids) underpin structure and function of the cell
• Real-world relevance: lipids form membranes; carbohydrates provide energy; proteins and enzymes drive metabolism; nucleic acids carry genetic information; the cytoskeleton and organelles enable intracellular transport and cell movement
• Ethical/philosophical implications: understanding cellular energy, genetic information, and manipulation of enzymes and genes raises questions about biomedical applications, gene therapy, and the governance of biotechnology

Key equations and formulas to remember

• Carbohydrate general formula: $C<em>n(H</em>2O)_m$
• Disaccharide formula (example): $C<em>{12}H</em>{22}O_{11}$ (glucose + fructose minus one water)
• Dehydration synthesis (monosaccharide linkage): monomer + monomer → disaccharide + $ext{H}_2 ext{O}$
• ATP hydrolysis (energy release): ext{ATP} + ext{H}2 ext{O} ightarrow ext{ADP} + ext{P}i + ext{energy}
• Triglyceride formation (condensation of glycerol with 3 fatty acids): glycerol + 3 fatty acids → triglyceride + 3 H2O
• Nuclear basics: nucleotide = base + sugar + phosphate; DNA uses deoxyribose and bases A, T, C, G; RNA uses ribose and bases A, U, C, G