Unit One

Atom

Smallest natural form of matter (Stable)

• basic building blocks of substances

Structure: Consists of a nucleus ( with protons and neutrons) and electrons orbiting it

Biological importance: Atoms combine to form molecules, like water, DNA and proteins

Electron

Subatomic particle

• negative electric charge

• No mass

• Essential in chemical bonding and energy transfer in living organisms.

Isotope

Unstable, higher atomic mass, more neutrons than normal (med)

Isomer

Same chemical formula, different structural formula

Hydrophilic

Water loving, glycerol part of lipids

Hydrophobic

Water hating, fatty acid part of lipids

Polar

No symmetry, different electronegativities of atoms- water

Non polar

Symmetrical, methane, solvent electronegativities

Buffer

Resists change to pH (Hemoglobin in blood)

Denature

Proteins, change from level 4°- 3°-2° to 1°- Change Shape

Enzyme

Protein, lowers activation energy of chemical reactions

Dehydration Reactions

a chemical process where two smaller molecules join together by removing a water molecule (H₂O).

How It Works:

• One molecule loses an –OH group.

• Another molecule loses a –H atom.

• These combine to form water (H₂O).

• The two molecules then bond to form a larger molecule.

Hydration Reaction

Hydration reactions are when water is added to molecules, helping change their structure or break bonds.

Why It’s Important:

• Helps convert molecules into forms that cells can use.

• Important in digestion and metabolism.

• Plays a role in chemical changes inside cells

How It Works:

• Water adds across a double bond (or another reactive site) in a molecule.

• The molecule absorbs the H and OH from water.

• This changes the molecule’s structure.

Condensation Reactions

also called dehydration synthesis) is a chemical reaction where two smaller molecules join together to form a larger molecule, with the removal of a water molecule (H₂O).

🔬 How It Works:

• Two molecules each lose a part of a water molecule:

  • One loses –OH

  • The other loses –H

• These parts combine to form water, which is removed.

• The two molecules bond together.

• Builds complex molecules from simpler ones.

• Essential for growth, repair, and storage in living organisms.

• Opposite of hydrolysis reactions.

Hydrolysis Reactions

a chemical reaction where water is used to break down a larger molecule into smaller parts.

• It's how cells break polymers (like proteins and starch) into monomers.

• It’s the reverse of dehydration synthesis (which builds molecules by removing water).

• "Hydro" = water

• "Lysis" = to break

Like Dissolves Like

"Like dissolves like" is a phrase used to describe how solubility works — especially in biological systems.

• Polar substances dissolve in polar solvents

• Nonpolar substances dissolve in nonpolar solvents

Shape is Essential

shape = function. The shape of a molecule or structure determines how it works and how it interacts with other molecules. If the shape is wrong, the function may be lost or impaired.

Deamination

Removal of an amino group- Alternative Pathways

Decarboxylation

Removal of a carbon (forms CO2g)

Redox Reduction

a chemical reaction involving the transfer of electrons between molecules

• Oxidation = loss of electrons

• Reduction = gain of electrons

Noncompetitive Inhibition

when a molecule (the inhibitor) binds to an enzyme at a site other than the active site (called an allosteric site).

• This changes the shape of the enzyme, so the active site no longer works properly.

• The substrate can still bind, but the enzyme can't carry out the reaction.

• This slows down or stops the enzyme's activity.

Substance blocks allosteric site (Dangerous)

Competitive Inhibition

happens when a molecule (inhibitor) that looks like the substrate binds to the active site of an enzyme.

• substance blocs Active Site

• The inhibitor competes with the substrate for the active site.

• If the inhibitor is in the site, the substrate can't bind — so the reaction slows down.

• It can be overcome by adding more substrate.

Carbohydrates

Type	Description	Examples
Monosaccharides	Single sugar units	Glucose, ribose, fructose, galactose
Disaccharides	Two monosaccharides joined	Sucrose (table sugar), maltose
Polysaccharides	Long chains of monosaccharides	Starch, glycogen, cellulose

Proteins

Proteins are macromolecules made of long chains of amino acids, which are their monomers (building blocks).

Monomers of Proteins:

• The monomer of a protein is an amino acid.

• Functions of Proteins:

Function	Example
Enzymes	Amylase, DNA polymerase
Transport	Hemoglobin (carries oxygen)
Structure	Collagen (skin, bone)
Movement	Actin, myosin (muscles)
Defense	Antibodies
Hormones	Insulin

4 LEVELS of PROTEIN

Level	Description
Primary	Sequence of amino acids
Secondary	Coiling (alpha helix) or folding (beta sheet)
Tertiary	3D shape due to R-group interactions
Quaternary	Multiple polypeptides working together

Myoglobin

protein found in muscle cells that helps store and carry oxygen. It gives muscle tissue its reddish color.

• It acts as an oxygen reserve when oxygen levels are low.

• Crucial in aerobic respiration, allowing muscles to keep producing ATP.

Hemoglobin

Hemoglobin is a protein found in red blood cells (RBCs) that carries oxygen from the lungs to the body and returns carbon dioxide back to the lungs to be exhaled.

• Globular protein made of 4 polypeptide chains:

  • 2 alpha (α) chains

  • 2 beta (β) chains

Factors that affect enzyme

Enzymes are proteins — anything that changes their shape affects their function!

• Temperature

  • ↑ Temp = ↑ activity (to a point)

  • Too hot = denatures enzyme

• pH

  • Each enzyme has an optimal pH

  • Too acidic/basic = denaturation

• Substrate Concentration

  • ↑ Substrate = ↑ rate (until saturation)

• Enzyme Concentration

  • More enzyme = faster reaction (if substrate is available)

• Inhibitors

  • Competitive: Block active site

  • Noncompetitive: Change enzyme shape

Lipids

Lipids are not true polymers, but they are built from two main types of monomers:

• Glycerol – a 3-carbon alcohol

• Fatty acids – long chains of carbon and hydrogen with a carboxyl group (–COOH)

Glycerol and Fatty Acids

• Glycerol:

  • Has 3 hydroxyl (–OH) groups

  • Acts as the "backbone" of lipids

• Fatty Acids:

  • Long hydrocarbon chains (can be saturated or unsaturated)

  • Join to glycerol via ester bonds in a dehydration reaction

Functions of Lipids

Function	Explanation

Energy storage

Long-term energy reserve (more energy per gram than carbs)

Insulation and protection

Fat cushions organs and insulates the body

Cell membrane structure

Phospholipids form the bilayer of all cell membranes

Hormone production

Steroids like estrogen and testosterone

Waterproofing

Waxes on plant leaves or animal fur

Hemoglobin vs. Myoglobin:

Feature	Hemoglobin	Myoglobin
Found in	Red blood cells	Muscle cells
Structure	4 chains (quaternary)	1 chain (tertiary)
Oxygen binding	4 O₂ molecules	1 O₂ molecule
Function	Transport of O₂ and CO₂	Storage of O₂

Catalase

enzyme found in nearly all living organisms that are exposed to oxygen.

helps protect cells from oxidative damage by breaking down hydrogen peroxide (H₂O₂) — a toxic byproduct of metabolism.

Nucleic Acids

large, complex macromolecules that store and transmit genetic information in all living things.

1. Monomers of Nucleic Acids

• The monomer (building block) of nucleic acids is the nucleotide.

• Nucleotides join together to form long chains: DNA or RNA.

🔹 2. Nucleotide Structure

Each nucleotide is made of 3 parts:

1. Phosphate group

2. Pentose sugar

3. Nitrogenous base

Difference between organic families

. Hydrocarbons

Family	Functional Group	Description	Example
Alkanes	None	Only single bonds (C–C)	Methane (CH₄)
Alkenes	C=C double bond	One or more double bonds	Ethene (C₂H₄)
Alkynes	C≡C triple bond	One or more triple bonds	Ethyne (C₂H₂)
Aromatic	Benzene ring	Alternating double bonds in a ring	Benzene (C₆H₆)

Oxygen-Containing Families

Family	Functional Group	Description	Example
Alcohols	–OH (hydroxyl)	Polar, forms hydrogen bonds	Ethanol (C₂H₅OH)
Ethers	R–O–R	Oxygen between 2 carbon chains	Dimethyl ether
Aldehydes	–CHO (carbonyl on end)	Double bond O on terminal carbon	Formaldehyde
Ketones	–C=O (carbonyl inside)	Double bond O in middle of chain	Acetone
Carboxylic Acids	–COOH	Acidic; has both carbonyl and hydroxyl	Acetic acid (vinegar)
Esters	–COO–	Sweet smell; from alcohol + acid	Methyl acetate

Nitrogen-Containing Families

Family	Functional Group	Description	Example
Amines	–NH₂ (or R–NH₂)	Basic; found in amino acids	Methylamine
Amides	–CONH₂	Has both carbonyl and amine groups	Acetamide
Nitriles	–C≡N	Triple bond between C and N	Acetonitrile

Endocytosis and Exocytosis

Endocytosis – “Entering the Cell”

Definition:
The process where the cell takes in materials by engulfing them in a vesicle formed from the plasma membrane.

Exocytosis – “Exiting the Cell”

Definition:
The process where vesicles fuse with the plasma membrane to release substances outside the cell.

📤 Used for:

• Secreting hormones (e.g., insulin)

• Releasing waste

• Sending neurotransmitters in nerve cells

Comparison Table:

Feature	Endocytosis	Exocytosis
Direction	Into the cell	Out of the cell
Uses vesicles?	Yes	Yes
Requires energy?	Yes (ATP)	Yes (ATP)
Membrane action	Membrane folds in	Vesicle fuses with membrane
Example	White blood cell eating bacteria	Insulin being secreted

Phagocytosis, Pinocytosis and receptor mediated transport

Phagocytosis – “Cell Eating”

• What it is: The cell engulfs large solid particles like bacteria or debris.

• How: The membrane wraps around the particle and forms a vesicle (called a phagosome).

Pinocytosis – “Cell Drinking”

• What it is: The cell takes in liquids and dissolved solutes.

• How: The membrane forms small vesicles filled with extracellular fluid.

Receptor-Mediated Endocytosis

• What it is: The cell uses specific receptors on its membrane to bring in targeted molecules.

• How: Molecules bind to receptors → membrane forms a coated vesicle.

Saturated vs. Unsaturated Fatty Acids

Feature	Saturated Fatty Acids	Unsaturated Fatty Acids
Bonds	All single C–C bonds	One or more double C=C bonds
Shape	Straight chains	Kinked chains due to double bonds
Source	Animal fats (butter, lard)	Plant oils (olive oil, sunflower oil)
State at Room Temp	Solid	Liquid
Health Impact	Too much = ↑ risk of heart disease	Healthier for the heart

Cholesterol and Steroids

• Steroids: Lipids made of 4 fused carbon rings

  • Not made from glycerol + fatty acids

  • Examples: Cholesterol, testosterone, estrogen

• Cholesterol:

  • Found in cell membranes (adds flexibility & stability)

  • Precursor to vitamin D and steroid hormones

ATP

ATP – Adenosine Triphosphate

• ATP is a modified nucleotide.

• Structure: Adenine + Ribose + 3 Phosphate groups

• Function: Primary energy carrier in cells

• When ATP breaks down (ATP → ADP + P), it releases energy for cell processes.

Shape of DNA

• DNA is a double helix, like a twisted ladder.

• The sugar-phosphate backbone forms the sides.

• The nitrogenous bases form the "rungs" through base pairing:

  • A pairs with T

  • C pairs with G

Antiparallel Structure

• The two strands of DNA run in opposite directions:

  • One strand runs 5′ → 3′

  • The other runs 3′ → 5′

• This arrangement is called antiparallel.

• It's essential for replication and transcription.

Purines vs. Pyrimidines

Type	Bases Included	Structure
Purines	Adenine (A), Guanine (G)	2 rings
Pyrimidines	Cytosine (C), Thymine (T), Uracil (U)	1 ring

• Purines pair with pyrimidines to keep the DNA helix evenly spaced:

  • A (purine) pairs with T (pyrimidine)

  • G (purine) pairs with C (pyrimidine)

Deamination

• Deamination is the removal of an amino group (–NH₂) from a nitrogenous base.

• It can alter DNA, potentially causing mutations.

• Example: Cytosine deaminates to become uracil (which shouldn't be in DNA).

• Cells have enzymes to repair deamination damage.

Function of the endomembrane

a network of membrane-bound organelles inside eukaryotic cells that coordinate the production, processing, and transport of proteins and lipids.

Main Functions:

1. Synthesize proteins and lipids

2. Modify and sort molecules

3. Transport materials

4. Digest and recycle waste

5. Store substances

6. Export cell products

How water dissolves organic matter

Water is a Polar Molecule

• Water (H₂O) has partial positive charges on the hydrogen atoms and a partial negative charge on the oxygen.

• This makes water polar, meaning it has opposite charges on opposite ends.

• Water dissolves polar and charged (ionic) substances well.

• Many types of organic matter (like sugars, proteins, and some small molecules) have polar groups (e.g., –OH, –COOH, –NH₂).

• These groups interact with water molecules through hydrogen bonding or ion-dipole interactions.

How Dissolving Happens:

1. Attraction:
   Water molecules are attracted to the polar or charged parts of the organic molecule.

2. Hydrogen Bonding:
   Water forms hydrogen bonds with the organic molecule’s polar groups (like hydroxyls –OH).

3. Surrounding (Solvation):
   Water surrounds the organic molecules, separating and dispersing them into solution.

4. Dissolution:
   The molecules become evenly distributed in the water, forming a solution.

Properties of Water

Properties of Water – Quick Summary

1. Cohesion – Water sticks to itself (surface tension).

2. Adhesion – Water sticks to other surfaces (capillary action).

3. High Specific Heat – Resists temperature changes.

4. High Heat of Vaporization – Cooling through evaporation (sweat).

5. Ice is Less Dense – Ice floats, protects aquatic life.

6. Great Solvent – Dissolves polar and ionic substances.

7. Polar Molecule – Allows hydrogen bonding; key to all properties.