Module 1 notes.2

Module 1 Biology Review — Complete Study Notes1. Atoms and ElementsAtom

Atoms are made of:

  • Protons (+)

  • Neutrons (0)

  • Electrons (-)

Element

  • Matter containing only one type of atom.

  • Elements have abbreviations, such as:

    • O = oxygen

    • Fe = iron

Atomic Number

  • The number of protons in an atom.

  • Defines which element the atom is.

Mass Number

Mass number = protons + neutrons

Isotopes

  • Atoms of the same element that have different mass numbers.

  • Important in:

    • Radiation-based diagnostics

    • Therapies

    • Bone scans

Electron Shells

  • Electrons are arranged in shells.

  • Most shells can hold up to 8 electrons.

  • The smallest shell holds 2 electrons.

  • Atoms can bond together to form compounds.

2. Molecules and Covalent BondsMolecules

  • Molecules are compounds formed when atoms share electrons.

  • This sharing forms a covalent bond.

Why Atoms Bond

  • Atoms share electrons to fill their outer shells and become more stable.

Covalent Bonds

  • Electrons are shared in pairs.

  • 1 pair = single bond

  • 2 pairs = double bond

Important Biological Molecules

Living things contain molecules such as:

  • Carbohydrates

  • Lipids

  • Proteins

  • Nucleic acids

3. WaterPolarity

  • The main important feature of water is its polarity.

Hydrogen Bonds

  • Hydrogen bonds form between hydrogen and an atom with an unshared or lone electron pair.

  • Oxygen and nitrogen can participate in hydrogen bonding.

Water Mixtures

Water can form:

  • Solutions

  • Suspensions

  • Colloids

Solubility

A molecule's ability to dissolve in water depends on:

  • Polarity

  • Charge

  • Number of polar groups

4. Ions and Oxidation-Reduction ReactionsIon

An ion is an atom or molecule with an overall:

  • Positive charge

  • Negative charge

Oxidation

  • Loss of electrons

  • Makes the atom/molecule more positive.

Reduction

  • Gain of electrons

  • Makes the atom/molecule more negative.

Memory Trick: OIL RIG

  • Oxidation Is Loss

  • Reduction Is Gain

Ionic Bonding

  • Ions can combine through ionic bonding.

  • Some ionic compounds are associated with:

    • Teeth

    • Bones

    • Kidney stones

Solubility of Ionic Compounds

  • Some ionic compounds dissolve easily in water.

  • Example: NaCl

  • Some are poorly soluble.

  • Bone is an example of a poorly soluble ionic compound.

5. Chemical ReactionsDefinition

Chemical reactions are rearrangements of atoms that form new chemical combinations.

During a reaction, bonds may be:

  • Broken

  • Formed

  • Rotated

Reactants

  • What you start with.

Products

  • What you make.

Example

Hydrogen + Oxygen → Water

2H₂ + O₂ → 2H₂O

  • Reactants:

    • Hydrogen

    • Oxygen

  • Product:

    • Water

Another Example

Glucose + Oxygen → Water + Carbon Dioxide

C₆H₁₂O₆ + 6O₂ → 6H₂O + 6CO₂

6. pHWater Can Form

  • H₃O⁺ = hydronium

  • OH⁻ = hydroxide

Neutral

  • H₃O⁺ = OH⁻

  • pH = 7

Acidic

  • H₃O⁺ > OH⁻

  • pH below 7

Basic

  • H₃O⁺ < OH⁻

  • pH above 7

Neutralization

  • Acids and bases can neutralize each other.

Buffers

  • Buffers resist changes in pH.

7. EnergyEnergy

The capacity to:

  • Do work

  • Produce heat

Kinetic Energy

  • Energy of movement.

Potential Energy

  • Stored energy.

Chemical Energy

  • A common form of potential energy in cells.

8. Exergonic and Endergonic ReactionsExergonic

  • Gives off energy as heat.

Endergonic

  • Requires energy to run.

Metabolism

The sum of all:

  • Exergonic reactions

  • Endergonic reactions

occurring in the cell.

9. Catabolism and AnabolismCatabolism

  • Breaks down/disassembles molecules.

  • Molecules can be used as:

    • Energy sources

    • Raw materials for other molecules

  • Generally exergonic.

Anabolism

  • Builds/assembles molecules.

  • Requires:

    • Parts

    • Energy

  • Generally endergonic.

Reaction Coupling

  • A catabolic reaction can power an endergonic reaction.

10. Biomolecules

Major biological molecules:

  1. Carbohydrates

  2. Lipids

  3. Proteins

  4. Nucleic acids

  5. High-energy molecules

Monomers

  • Smaller building blocks.

Polymers

  • Larger molecules made from monomers.

Dehydration Synthesis

  • Builds molecules through the loss of water.

Hydrolysis

  • Breaks molecules apart by splitting water.

11. CarbohydratesMonosaccharides

  • Single sugars.

  • Usually a 3–6 carbon chain or ring.

  • Contain hydrogen and oxygen.

  • Oxygen is often present as alcohol groups.

Functions

  • Energy

  • Building blocks for larger molecules

  • Metabolic intermediates

Disaccharides

Two monosaccharides joined together.

Examples:

  • Sucrose = glucose + fructose

  • Lactose = glucose + galactose

Polysaccharides

Long chains of monosaccharides.

Storage PolysaccharidesAmylose

  • Unbranched.

  • Examples:

    • Red potatoes

    • Basmati rice

Amylopectin

  • Branched.

  • Examples:

    • White potatoes

    • Sticky rice

Glycogen

  • Found in animals.

  • Extensively branched.

Structural Polysaccharides

Used for structure and support:

  • Cellulose

  • Chitin

Carbohydrate Interactions

  • Carbohydrates have many polar groups.

  • Especially alcohol groups.

  • They interact mainly through dipole interactions.

12. LipidsFunctions

  • Storage of metabolic fuel

  • Transport of metabolic fuel

  • Structural component of membranes

  • Components of some hormones

Fatty Acids

Can be:

  • Saturated

  • Unsaturated

  • Polyunsaturated

Glycerides

  • Monoglycerides

  • Diglycerides

  • Triglycerides

These involve fatty acids attached to glycerol.

Other Lipids

  • Sterols

  • Phospholipids

Lipid Interactions

  • Lipids may have some ionic charge.

  • Main attraction is through weak London dispersion forces.

  • Tightly packed molecules experience stronger interactions.

Saturated Fats

  • Described as straighter.

  • Have higher melting points.

  • More solid at room temperature.

13. ProteinsPolypeptide

  • A chain of amino acids.

Protein

  • One or more polypeptide chains with a structure that allows a specific function.

Humans have more than 100,000 different kinds of proteins.

Protein FunctionsStructural

Examples:

  • Tendons

  • Bone

Defense

  • Immune system antibodies.

Transport

Examples:

  • Hemoglobin

  • Membrane proteins

Contractility

Examples:

  • Actin

  • Myosin

Involved in muscle and cell contraction.

Metabolic Regulation

Enzymes can:

  • Assemble

  • Disassemble

  • Isomerize

  • Transfer

14. Levels of Protein Structure1. Primary Structure

  • Sequence of amino acids.

2. Secondary Structure

  • Folding and hydrogen bonding.

3. Tertiary Structure

Determined by:

  • Side chains

  • Sulfide bridges

  • Hydrophobic reactions

4. Quaternary Structure

  • Two or more polypeptide chains.

Protein Attractions

Can involve:

  • Ionic charge

  • Polarity

  • Amino acid attractions

  • Hydrogen bonds

15. Nucleic AcidsNucleotide

Made of:

  • Phosphate group

  • Pentose sugar

  • Nitrogenous base

RNA

  • Contains ribose.

  • Forms a single chain.

  • Bases:

    • A

    • G

    • C

    • U

  • RNA never contains T.

DNA

  • Contains deoxyribose.

  • Forms a double chain.

  • Bases:

    • A

    • G

    • C

    • T

  • DNA never contains U.

  • Forms a double helix.

DNA Base Pairing

  • A–T

  • G–C

These base pairs use hydrogen bonds.

16. High-Energy MoleculesATP

Adenosine triphosphate

  • Primary energy carrier in cells.

  • Energy is primarily associated with the ADP–P bond.

GTP

Guanine triphosphate

  • Used in the Krebs cycle.

  • Can be quickly converted to ATP.

Electron Carriers

  • NADH

  • FADH₂

CELL BIOLOGY17. Cellular Contents

Cells can have many different:

  • Shapes

  • Functions

Cytosol

  • Translucent fluid portion of the cell.

  • Not enclosed within membrane-bound organelles.

  • Makes up approximately 70% of cell volume.

Contains:

  • Water

  • Salts

  • Cytoskeleton

  • Soluble proteins

  • Ribosomes

Organelles

Membrane-bound compartments with specific functions.

Examples:

  • Mitochondria

  • Rough ER

  • Smooth ER

  • Golgi apparatus

  • Peroxisomes

  • Lysosomes

Cytoplasmic Inclusions

Insoluble substances suspended in the cytosol.

Examples:

  • Glycogen granules

  • Lipid droplets

18. Plasma MembraneFunctions

  • Isolation and regulation of exchange

  • Selective permeability

  • Sensitivity to the external environment

  • Provides structure and boundaries

Fluid Mosaic ModelPhospholipid Bilayer

  • Most of the membrane is fluid.

  • Consistency is compared to olive oil.

  • Consistency depends partly on saturation of fats.

Membrane Proteins

Functions:

  • Transport

  • Enzymes

  • Receptors

  • Recognition

  • Cell adhesion

  • Cytoskeleton attachment

Peripheral Proteins

  • Proteins that cling to only one side of the membrane.

Membrane Carbohydrates

Can form:

  • Glycoproteins

  • Glycolipids

Functions:

  • Anchor the cell

  • Act as receptors

  • Aid in cell recognition

Membrane Steroids

  • Another important component of the plasma membrane.

19. Cell Junctions

Cell junctions can be:

  • Sheets = fascia

  • Rings = zonula

  • Spots = macula

Tight/Occluding Junctions

  • Fused membranes.

  • Water/ion tight.

  • Often form a ring near the free surface.

  • Can also occur in sheets in capillaries.

Desmosomes

  • Anchoring junction.

  • Strong and flexible.

  • Involves proteoglycan and protein filaments.

Hemidesmosomes

  • Anchoring junction.

  • Similar to a “half” desmosome.

  • Attach cells to basement membranes.

Gap Junctions

  • Interlocked membrane proteins.

  • Allow passage from cell to cell.

  • Examples include cells except:

    • Skeletal muscle

    • Blood

20. Passive TransportPassive Transport

  • No energy is expended by the cell.

What Can Cross the Membrane?Oxygen and Carbon Dioxide

Can cross because they are:

  • Small

  • Uncharged

  • Nonpolar

Fatty Acids

  • Can dissolve through the membrane because it is fatty.

Triglycerides

  • Cannot cross directly because they are too large.

Sugars and Amino Acids

Cannot dissolve through the membrane because they are:

  • Too polar

  • Often too large

Ions

  • Ions such as Na⁺ cannot cross directly through the membrane.

Proteins and Starches

  • Too large to cross.

21. Diffusion

  • Particles move independently.

  • Overall movement tends to go:

High concentration → Low concentration

  • This occurs because particles are randomly bombarded by other particles, especially water molecules.

  • This process is called diffusion.

  • Diffusion influences the direction of movement across membranes.

22. OsmosisOsmosis

  • The movement of water across a membrane.

Tonicity

You need to understand how osmotic changes affect cells.

Important terms:

  • Isotonic

  • Hypotonic

  • Hypertonic

  • Osmotic pressure

  • Hydrostatic pressure

Possible cellular effects include:

  • Crenation

  • Lysis

23. Facilitated Diffusion

  • Does not require cellular energy.

  • Uses membrane proteins.

Examples include movement of:

  • Sugars

  • Amino acids

  • Ions through specific membrane proteins

24. Active Transport

  • Requires energy.

  • Uses selective membrane proteins.

  • Can move substances independently of their concentration gradient.

Examples:

  • Hydrogen ion pumps

  • Sodium-potassium exchange pump powered by ATP

25. Bulk TransportPhagocytosis

  • Taking in large particles.

Pinocytosis

  • Taking in extracellular fluid.

Receptor-Mediated Transport

  • Selective for specific chemicals.

Exocytosis

  • Vesicles release their contents from the cell.

26. Major OrganellesMitochondria

  • Major organelle involved in cellular energy processes.

Ribosomes

  • Involved in protein production.

Rough Endoplasmic Reticulum

  • Connected with the nuclear envelope.

  • Associated with protein synthesis.

Smooth Endoplasmic Reticulum

  • A major organelle.

Golgi Apparatus

Functions:

  • Completes protein processing

  • Often adds sugars

  • Packages products

  • Produces cell membrane and associated proteins

27. NucleusNuclear Envelope

  • Surrounds the nucleus.

  • Contains pores.

Nucleolus

  • Produces ribosomes.

Chromatin

  • DNA wraps around histones to form chromatin.

28. Cytoskeleton

The cytoskeleton is a strong and flexible protein framework.

ComponentsActin Filaments

  • Help form microvilli.

Microtubules

  • Made of tubulin.

  • Important for:

    • Cell movement

    • Cell division

Intermediate Filaments

  • Another component of the cytoskeleton.

29. Cell Movement StructuresPseudopodia

Used for:

  • Crawling

  • Engulfing

Cilia and Flagella

  • Hairlike membrane-bound extensions.

  • Contain microtubules.

Microvilli

  • Associated with actin filaments.

30. Cell DivisionDNA Replication

  • Occurs during interphase before cell division.

Mitosis Phases1. Prophase2. Metaphase3. Anaphase4. Telophase5. Cytokinesis

31. Meiosis

  • Produces haploid gametes.

  • Involves two divisions.

  • Results in a reduction of chromosome number.

32. Protein ProductionTranscription

  • Uses a DNA template to produce RNA.

Types of RNA

  • mRNA

  • tRNA

  • rRNA

Translation

  • Uses mRNA as a template.

  • Constructs polypeptides.

33. Glycolysis

  • Occurs in the cytosol.

  • Breaks monosaccharides down into two molecules of pyruvate.

Pyruvate can:

  • Enter a mitochondrion

  • Be fermented

34. Fermentation

  • Uses pyruvate as a dumping site for electrons from NAD:H.

  • Can occur when an organism:

    • Does not have the enzymes needed for the Krebs cycle or beyond, or

    • Runs out of oxygen or another electron sink

BIG PICTURE STUDY MAPChemistry

Atoms → Elements → Molecules → Ions → Chemical Reactions → pH → Energy

Biomolecules

Carbohydrates + Lipids + Proteins + Nucleic Acids + High-Energy Molecules

Cell Biology

Cell Contents → Plasma Membrane → Cell Junctions → Diffusion/Osmosis → Facilitated Diffusion → Active Transport → Bulk Transport

Cell Structures

Organelles → Nucleus → Cytoskeleton → Cell Movement

Cell Reproduction and Genetics

DNA → Transcription → RNA → Translation → Protein

Interphase → Mitosis

Meiosis → Haploid Gametes

Cellular Energy

Glycolysis → Pyruvate → Mitochondria OR Fermentation

  1. NADH brings electrons (e⁻) to the electron transport chain.

  2. The electrons move through the proteins in the inner mitochondrial membrane.

  3. As the electrons move, the proteins use their energy to pump H⁺ (hydrogen ions) into the intermembrane space.

  4. Now there are a LOT of H⁺ outside and fewer H⁺ inside the matrix.

    • This creates a gradient (basically pressure).

  5. H⁺ wants to get back into the matrix, so it flows through a protein called ATP synthase.

  6. ATP synthase uses that movement to make:

ADP + P → ATP ⚡

  1. At the very end, oxygen (O₂) catches the electrons and H⁺.

  2. This produces H₂O (water).

The whole thing in one line:

NADH → electrons → H⁺ gets pumped → H⁺ flows through ATP synthase → ATP is made → O₂ makes water

What the important words mean:

  • Matrix = inside of the mitochondria

  • Intermembrane space = space between the two mitochondrial membranes

  • H⁺ = hydrogen ions

  • NADH = carries high-energy electrons

  • ATP synthase = the protein that makes ATP

  • ADP + P → ATP = energy gets stored in ATP

  • O₂ = final electron acceptor

  • Aerobic respiration = cellular respiration using oxygen