What is the structure of an atom?

An atom is the basic unit of matter and is made up of three main parts:

Protons positively charged particles found in the nucleus.

Neutrons neutral particles also in the nucleus.

Electrons negatively charged particles that orbit the nucleus in electron shells or energy levels.

What is the structure of an ion?

An ion is an atom or molecule that has gained or lost electrons, giving it a net charge: Cation: positive ion (lost electrons) Anion: negative ion (gained electrons)

Ionic bond

Formed when electrons are transferred from one atom to another.

Typically between a metal and a non-metal. Results in oppositely charged ions that attract each other.

Covalent bond

Formed when atoms share electrons.

Usually occurs between non-metal atoms. Can involve single, double, or triple electron pairs.

Hydrogen bond

A weak attraction between a hydrogen atom (already covalently bonded to something electronegative like oxygen or nitrogen) and another electronegative atom. Important in stabilizing biological structures like DNA and proteins.

Nonpolar covalent bonds

Electrons are shared equally between atoms.

Happens when atoms have similar or identical electronegativities (ability to attract electrons).

There is no partial charge on the atoms.

Key Feature:

Molecule has no poles (no distinct positive or negative ends).

Polar covalent bonds

Electrons are shared unequally.

One atom attracts electrons more strongly (is more electronegative), creating:

a slightly negative (6-) end (where electrons hang out more) and a slightly positive (5*) end.

Ex: In water, oxygen is more electronegative than hydrogen, so electrons spend more time near oxygen.

Key Feature:

Molecule has positive and negative poles, like a magnet.

Why Are lons and Polar Molecules Soluble in Water?

Water is a polar molecule: It has a partial negative charge near oxygen and a partial positive charge near the hydrogen atoms.

Polar molecules and ions are attracted to the opposite charges on water molecules. This attraction helps break them apart (dissolve them) in water.

Acid

A substance that releases H + (hydrogen ions) in solution.

Increases the concentration of hydrogen ions in a solution.

Acidic/ Basic

A solution is acidic if it has more H+ ions than OH/ pH is less than 7.

A solution is basic if it has more OH- ions than H+/ pH is greater than 7.

Base

A substance that removes H+ ( hydrogen ions) from a solution or releases OH- (hydroxide ions).

Decreases the concentration of hydrogen ions.

What is pH and how does it relate to the concentration of H+?

pH is a scale that measures how acidic or basic a solution is.

It is based on the concentration of hydrogen ions (H+).

Formula: pH -log[H+]

So, as [H+] increases, pH decreases (more acidic).

As [H+] decreases, pH increases (more basic).

What is a buffer?

a system that resists changes in pH when small amounts of acid or base are added. It usually consists of a weak acid and its conjugate base.

In your body, a key buffer is the bicarbonate buffer system, important for maintaining blood pH around 7.35-7.45.

The Bicarbonate buffer pair

In your body:

Carbonic acid (H₂CO₃-)= weak acid

Bicarbonate ion (HCO₃-) = weak base

They work together to keep your blood from getting too acidic or too basic.

If the blood becomes too acidic:

The bicarbonate ion (HCO₃-) picks up the extra H+. Then carbonic acid breaks down into water and carbon dioxide, which is breathed out.

If the blood becomes too basic (too much OH-): The carbonic acid gives up a hydrogen ion to neutralize the OH-.

How Carbon bonds with other atoms and itself?

(Via Covalent bonds, max = 4 bonds)

Other Carbons- Forms chains, rings, or branches. Can make single (-), double (=), or triple (=) bonds

Hydrogen (H)- Forms simple C-H bonds Found in fuels like methane (CH4)

Oxygen (O)- Can form: C-0 (single bond) or C=0 (double bond)

Nitrogen (N)- Can form: C-N (single bond) or C=N (triple bond)

Different types of Carbohydrates

Monosaccharides (simple sugars)

One sugar unit, Quick energy source

Examples: Glucose, Fructose, and Galactose

Disaccharides (two sugar units)

Ex: Sucrose = glucose + fructose, Lactose = glucose + galactose, and Maltose= glucose + glucose

Polysaccharides (many sugar units)

Long chains of sugars that are used for energy storage or structure

Examples: Starch, Glycogen, and Cellulose

Different types of lipids

Fats and Oils (Triglycerides)

Made of 1 glycerol + 3 fatty acids

Saturated Fats [Fats solid at room temp (animal fat)]

Unsaturated Fats [Oils = Iiquid at room temp (olive oil)]

Phospholipids

Main part of cell membranes

Have a water-loving head and a water-hating tail

Example: Phospholipids in your cell walls

Steroids

Ring-shaped lipids that are used as hormones or cholesterol

Examples:

Cholesterol (in cell membranes)

Testosterone and estrogen

Dehydration synthesis (build up) of Carbohydrates and Lipids

In Monosaccharides (simple sugars like glucose) join to form disaccharides or polysaccharides.

Example: Glucose + Glucose -> Maltose + Water What happens: An -OH (hydroxyl) group from one sugar and an H from another sugar are removed. They form H₂O (water). The sugars bond via a glycosidic bond.

In Triglycerides (fats): Made by joining 1 glycerol and 3 fatty acids.

Example: Glycerol +3 Fatty Acids -> Triglyceride + 3 Water

What happens: Each fatty acid attaches to glycerol by removing a water molecule. The bond formed is called an ester bond.

Hydrolysis (break down) of Carbohydrates and Lipids

In Carbohydrates:

Breaks polysaccharides into monosaccharides.

Example: Maltose + Water -> Glucose + Glucose

What happens: A water molecule is added. The glycosidic bond is broken.

In Triglycerides:

Breaks fats into glycerol + 3 fatty acids.

Example:

Triglyceride + 3 Water -> Glycerol + 3 Fatty Acids

What happens:

Water helps break the ester bonds.

Describe the nature of Phospholipids

Found in cell membranes.

Made of: 2 fatty acid tails (hydrophobic – "water-fearing"), 1 phosphate group head (hydrophilic – "water-loving") and 1 glycerol backbone

Nature:

Amphipathic: Has both hydrophobic and hydrophilic parts.

In water, they form bilayers, which are the basis of cell membranes.

The hydrophobic tails face inward, away from water, while hydrophilic heads face outward, toward water.

Describe the nature of Prostaglandins

Derived from fatty acids

Not part of membranes—these act more like hormone-like messengers.

Have a five-membered carbon ring and two side chains.

Hydrophobic but work in watery environments

Nature: Act locally, not throughout the body (unlike hormones).

• Involved in: Inflammation, Pain, Fever, Blood clotting, Smooth muscle contraction (e.g., in uterus and lungs)

Description of amino acids

the building blocks of proteins.

Each amino acid has the same basic structure: Amino group (—NH₂), Carboxyl group (—COOH), Hydrogen atom (—H), and R group (side chain) – varies between amino acids and determines their properties.

All four parts are bonded to a central carbon (called the alpha carbon).

There are 20 common amino acids, each with a unique R group.

How peptide bonds are formed?

A peptide bond links amino acids together to form proteins or polypeptides.

Amino acid 1's —COOH (carboxyl group) + Amino acid 2's —NH₂ (amino group)
↓ ↓
(remove H₂O → dehydration synthesis)
↓
Result: —CO—NH— (peptide bond)

How are peptide bonds broken down?

To break a peptide bond, water is added (hydrolysis)

The bond is broken, restoring the original —COOH (carboxyl group) and —NH₂ groups (amino group) on the separate amino acids.

The Four Orders of protein structures

Primary Structure

The sequence of amino acids in a polypeptide chain. It is held by Peptide bonds.

• Importance: Like letters in a sentence — the exact order matters for the final function.

Secondary Structure

Local folding of the chain into α-helices (coils) and β-pleated sheets (folds) . It is held by Hydrogen bonds between nearby backbone atoms.

• Importance: Provides flexibility and shape.

Tertiary Structure

The overall 3D shape of a single polypeptide. It is held by: Hydrogen bonds, Ionic bonds, Disulfide bridges, Hydrophobic interactions

• Importance: Determines the protein’s functional shape.

Quaternary Structure

• Definition: When two or more polypeptide chains come together to form one protein. It is held by: Same interactions as tertiary.
• Examples: Hemoglobin (has 4 polypeptide chains)

The different functions of proteins

Enzymes: Speed up chemical reactions. Ex: Amylase, DNA polymerase

Transport: Carry substances across membranes or through blood. Ex: Hemoglobin, ion channels

Structural: Provide support and shape to cells and tissues. Ex: Collagen, keratin Defense: Fight infection. Ex: Antibodies (immunoglobulins)

Signaling: Carry messages between cells. Ex: Insulin, growth hormone

Movement: Help cells or muscles move. Ex: Actin, myosin

Storage: Store ions or amino acids. Ex: Ferritin (iron storage)

How Structure Gives Function Specificity?

A protein's shape = function.

The 3D structure of a protein allows it to fit like a lock and key with its specific target (like a substrate for an enzyme).

Even a small change in the amino acid sequence (primary structure) can change the folding, shape, and destroy or alter the function.

Ex: Enzyme active sites are shaped to bind only to specific molecules.

• If the structure is damaged (by heat, pH change, or mutation), it becomes denatured and no longer works.

Describe the structure of a nucleotide

the basic building block of nucleic acids (DNA and RNA).
Each nucleotide has three parts:

Phosphate group (PO₄³⁻)

Sugar

• DNA: Deoxyribose
• RNA: Ribose

Nitrogenous base

• Purines: Adenine (A) and Guanine (G)
• Pyrimidines: DNA: Cytosine (C) and Thymine (T) or RNA: Cytosine (C) and Uracil (U)

The structural differences between DNA and RNA

What is the law of complementary base pairing?

states that in DNA, specific nitrogenous bases always pair with each other in a consistent way:

Adenine (A) always pairs with Thymine (T)

Cytosine (C) always pairs with Guanine (G)

How does the law of complementary base pairing work between DNA strands?

DNA is made of two strands twisted into a double helix. These strands are held together by hydrogen bonds between the bases.

A–T form 2 hydrogen bonds

C–G form 3 hydrogen bonds

Because of this rule:

One strand determines the sequence of the other.
For example: Strand 1: A - T - G - C
Strand 2: T - A - C - G

It ensures accurate DNA replication—each strand serves as a template, maintains genetic stability over generations and prevents random or mismatched pairing, which would lead to mutations.

Describe the structure of the plasma (cell) membrane

Function: Acts as a selective barrier, controlling what enters and leaves the cell.

Structure: Made of a phospholipid bilayer

Hydrophilic heads (face water) and Hydrophobic tails (face inward)

Contains: Proteins (for transport, signaling, and structure), Cholesterol (adds stability and fluidity), and Carbohydrates (for cell recognition and communication)

Key Feature:

• Fluid Mosaic Model: Membrane is flexible and proteins float like "tiles" in a fluid lipid "sea."

Describe the structure of cilia

Function: Move fluids across the surface of cells (e.g., mucus in the respiratory tract) and can also play sensory roles.

Structure: Short, hair-like projections, made of microtubules in a 9 + 2 arrangement:

9 pairs of microtubules around the outside and 2 single microtubules in the center

• Anchored to the cell by a basal body (like a foundation)

Describe the structure of flagella

Function: Move the entire cell (like sperm cells swimming)

Structure: Long, tail-like projection, the same 9 + 2 microtubule structure as cilia and also anchored by a basal body

Amoeboid Movement

A type of movement used by cells like amoebas and white blood cells.

The cell forms pseudopods (“false feet”) by extending part of its cytoplasm. The cytoplasm flows into the pseudopod, pulling the cell forward. This is driven by the cytoskeleton (especially actin filaments).

Function: Allows crawling movement and helps cells hunt or move through tissues.

Phagocytosis ("Cell Eating")

A form of endocytosis where the cell engulfs large particles (e.g., bacteria, dead cells).

The membrane wraps around the target and forms a vesicle called a phagosome. The phagosome then fuses with a lysosome, which digests the material.

Function : Used by immune cells like macrophages to destroy invaders

Pinocytosis ("Cell Drinking")

Another form of endocytosis where the cell takes in fluids and small molecules. The membrane pinches inward, forming a small vesicle of fluid.

Function: Helps cells take in nutrients and maintain fluid balance.

Receptor-Mediated Endocytosis

A selective form of endocytosis.

Receptors on the cell surface bind to specific molecules (like cholesterol or hormones). Once bound, the membrane folds inward to form a vesicle.

Function: Allows cells to take in specific substances in concentrated amounts.

Exocytosis

Opposite of endocytosis.

A vesicle inside the cell fuses with the plasma membrane, releasing its contents outside the cell. Used to remove waste or release hormones, enzymes, or neurotransmitters.

Function: Secretes important substances and maintains membrane balance.

The structure and functions of cytoskeleton

Structure: A network of protein fibers inside the cell.

Made of:

Microfilaments (actin): thin, flexible fibers

Intermediate filaments: medium-sized, rope-like

Microtubules: thick, hollow tubes (made of tubulin)

Functions: Supports cell shape, helps with movement (inside and outside the cell), guides organelle positioning and transport, and forms cilia and flagella

The structure and functions of lysosomes

Structure: Small, membrane-bound vesicles filled with digestive enzymes

Functions: Break down worn-out cell parts, bacteria, and macromolecules, known as the cell’s "recycling center" and important for immune responses and cell cleanup

The structure and functions of peroxisomes

Structure: Small, membrane-bound organelles (like lysosomes) and contain enzymes (like catalase) that break down toxins

Functions: Break down fatty acids, detoxify harmful substances (e.g., hydrogen peroxide into water and oxygen), and protect cells from oxidative damage

The structure and functions of mitochondria

Structure: Bean-shaped organelles with double membranes

Outer membrane: smooth

Inner membrane: folded into cristae for surface area

Inside: matrix (fluid-filled space)

Functions: Produce ATP (cell’s energy) through cellular respiration, known as the “powerhouse” of the cell and also involved in apoptosis (controlled cell death)

The structure and functions of ribosomes

Structure: Small, round structures made of RNA and proteins

• Found: Free in cytoplasm,and attached to rough ER

Functions: Make proteins by linking amino acids together using instructions from mRNA

• Free ribosomes → proteins for use inside the cell
• ER-bound ribosomes → proteins for membranes or export

The structures and functions of the endoplasmic reticulum

Rough ER (RER)

Structure: A network of flattened membranes with ribosomes attached to the surface.

Function: Makes proteins (with the help of ribosomes), modifies proteins (e.g., adds sugar chains), and sends proteins to the Golgi in transport vesicles

Smooth ER (SER)

Structure: Similar to rough ER, but no ribosomes and more tubular in shape

Function: Makes lipids (fats, oils, steroid hormones), detoxifies drugs and alcohol, and stores calcium in muscle cells

The structure and functions of the Golgi Complex (Golgi Apparatus)

Structure: A stack of flattened, membrane-bound sacs (like pancakes)

Function: Receives proteins and lipids from the ER, modifies them (e.g., adds sugar or phosphate groups), sorts and packages them into vesicles, and send them to their final destinations (inside or outside the cell)

How do the ER and Golgi Apparatus work together?

Proteins/lipids are made in the ER

• Proteins in rough ER and Lipids in smooth ER

Transport vesicles carry them from the ER to the Golgi

• In the Golgi: Molecules are modified, sorted, and repackaged
• The Golgi sends finished products: To the plasma membrane (for secretion or membrane use), to lysosomes, to other parts of the cell

The structure of the nucleus

Function: Controls the cell's activities and stores genetic information (DNA).

Structure:

Nuclear envelope: Double membrane that surrounds the nucleus; has pores to let things in/out.

Nucleoplasm: Jelly-like fluid inside the nucleus.

Nucleolus: Dense area that makes ribosomes.

Chromatin: DNA + proteins

The structure of chromatin

Chromatin = DNA + histone proteins

• Found inside the nucleus. DNA wraps around histones to stay organized and compact.
• Chromatin exists in two forms:
• Euchromatin: Loosely packed, light-staining, an Active DNA (being used for RNA)
• Heterochromatin: Densely packed, dark-staining an Inactive DNA (not being used)

The types of RNA

How DNA directs the synthesis of RNA in genetic transcription?

Transcription is the process by which a gene on DNA is copied into RNA.
It’s the first step in making a protein (DNA → RNA → Protein).

Steps of Transcription

Initiation: The enzyme RNA polymerase binds to a promoter (a specific DNA sequence at the start of a gene). This signals where transcription should start.

Elongation: RNA polymerase unzips the DNA strand (just one section).

• It reads one strand of DNA (called the template strand) and builds a complementary RNA strand.
  • DNA A → RNA U
  • DNA T → RNA A
  • DNA C → RNA G
  • DNA G → RNA C
• RNA is built in the 5′ to 3′ direction.

Termination: When RNA polymerase reaches a termination sequence, it stops. The new RNA strand (usually mRNA) detaches.The DNA zips back up.

The Key Players in Transcription

• DNA template- Holds the gene code
• RNA polymerase- Enzyme that builds RNA
• Promoter- Start signal for transcription
• Terminator- Stop signal for transcription
• mRNA- Messenger RNA copy that leaves the nucleus

How RNA directs the synthesis of proteins in genetic translation?

Translation is the process where the genetic code in mRNA is used to build a protein (a chain of amino acids).

It’s the second step of gene expression:
DNA → RNA → Protein

mRNA is read in groups of 3 bases called codons. Each codon codes for one amino acid.

Steps of Translation

Initiation: The ribosome attaches to the start codon (AUG) on the mRNA. The first tRNA brings the amino acid methionine.

Elongation: The ribosome reads the next codon on the mRNA. A tRNA with the matching anticodon brings the correct amino acid. The ribosome links amino acids together with peptide bonds to form a chain.

Termination: When the ribosome reaches a stop codon (e.g., UAA, UAG, UGA), translation stops. The protein chain is released and folded into its final shape.

The Key Players in Translation

How proteins are modified after translation?

After a protein is made through translation, it often needs to be modified to become functional. These changes are called post-translational modifications.

Folding: Protein folds into its correct 3D shape (often with help from chaperone proteins)

Cleavage: A piece of the protein is cut off to activate it

Phosphorylation: A phosphate group is added (can turn protein on/off)

Glycosylation: Sugar chains are added (important for cell recognition and signaling)

Lipidation: Lipid added for membrane anchoring

Disulfide bonds: Help stabilize protein structure

These modifications happen in the endoplasmic reticulum (ER), Golgi apparatus, or cytoplasm depending on the protein’s role.

How ubiquitin and the proteasome are involved in breaking down proteins?

Sometimes proteins are: Misfolded, Damaged and No longer needed

They must be removed to keep the cell healthy.

Ubiquitin: A small protein that acts like a "tag".

It is attached to proteins that need to be destroyed. The process is called ubiquitination. Multiple ubiquitin tags = “this protein must go!”

Proteasome: A large protein complex (like a molecular paper shredder).

It recognizes and destroys proteins that are tagged with ubiquitin. It breaks them into small peptides or amino acids that the cell can reuse.

Explain the semiconservative replication of DNA in DNA synthesis.

Semiconservative replication means that when DNA is copied, each new DNA molecule contains one original (parent) strand and one new strand.

Steps of DNA Synthesis (Replication)

Unwinding the DNA

The enzyme helicase unzips the double helix by breaking the hydrogen bonds between base pairs. This forms a replication fork (Y-shaped opening).

Priming

Primase lays down a short RNA primer to start the new strand.

Building New Strands

DNA polymerase adds new nucleotides to the exposed bases using base pairing rules:

A pairs with T, C pairs with G, One strand (the leading strand) is built continuously. The other strand (the lagging strand) is built in pieces called Okazaki fragments and later joined by DNA ligase.

Result

Two identical DNA molecules are formed.

• Each has: 1 original strand (from the parent molecule) and 1 newly synthesized strand

The Cell Cycle

the series of stages a cell goes through to grow and divide into two identical daughter cells.

Phases of the Cell Cycle

Interphase – the longest phase (cell prepares to divide)

• G1 phase ("Gap 1") - Cell grows, performs normal functions
• S phase ("Synthesis")- DNA is replicated
• G2 phase ("Gap 2")- Cell continues to grow; checks for errors

Mitotic Phase (M phase) – actual cell division

• Mitosis: Nucleus divides (has 4–5 sub-phases: prophase, metaphase, anaphase, telophase)
• Cytokinesis: Cytoplasm divides, forming 2 new cells

G0 phase – some cells exit the cycle permanently (e.g., nerve cells)

Factors that affect the cell cycle

• Growth factors: Proteins that signal the cell to divide
• Nutrients & energy: Cells need fuel and materials to grow
• Cell size: Too small = keep growing; right size = divide
• DNA damage: Stops the cycle for repair or leads to apoptosis
• Checkpoints: Built-in stops at G1, G2, and M to ensure accuracy
• Hormones: Can stimulate or block cell division

If any errors or damage are detected, the cell can pause the cycle or self-destruct.

The significance of apoptosis

A controlled, safe way for cells to self-destruct when they’re old, damaged, or no longer needed.

Protects the body by removing damaged or cancer-prone cells, Shapes the body during development (e.g., removing webbing between fingers) and Maintains balance between cell growth and death

Failure in apoptosis can lead to: Cancer (if damaged cells survive and divide), Autoimmune diseases (if immune cells that should die survive), and Degenerative diseases (if too many cells die)

The Phases of Mitosis

Purpose: To create two identical diploid cells (same number of chromosomes as the original cell).
Used in: Body (somatic) cells.

Prophase: Chromosomes condense and become visible, Spindle fibers form, and Nuclear envelope breaks down

Metaphase: Chromosomes line up in the middle of the cell

Anaphase: Sister chromatids are pulled apart to opposite sides

Telophase: Chromosomes uncoil, and Nuclear envelopes reform around each set

Cytokinesis (not part of mitosis but follows it)- Cytoplasm divides, forming two identical daughter cells

The Phases of Meiosis

Purpose: To create four genetically unique haploid cells (with half the chromosome number).
Used in: Gametes (sperm and egg cells).

Meiosis I – Separates homologous chromosomes

Prophase I: Chromosomes pair up (synapsis), Crossing over occurs (genes are exchanged)

Metaphase I: Paired chromosomes line up in the middle

Anaphase I: Homologous chromosomes separate (not sister chromatids)

Telophase I & Cytokinesis: Two haploid cells form (each with half the chromosomes)

Meiosis II – Separates sister chromatids (like mitosis)

Prophase II: New spindle fibers form in each haploid cell

Metaphase II: Chromosomes line up in the center

Anaphase II: Sister chromatids are pulled apart

Telophase II & Cytokinesis: Four unique haploid cells are formed

Meiosis vs. Mitosis