Introduction to Chemistry and Cell Membrane Structure

Matter

Anything with mass and that occupies space (e.g., food, air, water).

Elements

The simplest substances with unique chemical/physical properties that cannot be broken down by ordinary means.

Sodium Chloride (NaCl)

A compound formed when sodium (soft metal) and chlorine (yellow-green gas) combine, which is very different from their individual properties.

Atoms

The smallest units of matter, retaining the properties of an element.

Protons

Positively charged particles found in the nucleus of an atom.

Neutrons

Neutral particles found in the nucleus of an atom.

Electrons

Negatively charged particles that surround the nucleus of an atom.

Atomic Number

The number of protons in an atom's nucleus, which determines the number of electrons in a neutral atom.

Atomic Mass

The total mass of an atom, based on the number of protons and neutrons.

Isotopes

Atoms of the same element with different numbers of neutrons, having the same chemical properties but slightly different atomic masses.

Periodic Table

An organized chart of elements arranged by atomic number.

Key Elements for Life

Four elements that make up 96% of the human body: Carbon, Nitrogen, Oxygen, and Hydrogen.

Carbon Atoms

Atoms that have 6 protons and 6 electrons, with electrons arranged in shells around the nucleus.

Outer Shell

The outermost shell of electrons in an atom that determines atom interactions.

Covalent Bonds

Bonds formed when two atoms share valence electrons to fill their outer shells.

Hydrogen Gas (H₂)

A molecule formed when two hydrogen atoms share electrons.

Structural Formula

A representation of shared electrons in a covalent bond shown by a line.

Lewis Structure

A representation of electrons shown as dots in a molecule.

Polarity in Covalent Bonds

Occurs when electrons are not shared equally, leading to polar or nonpolar bonds.

Electronegativity

The measure of how strongly an atom attracts shared electrons, based on its proton count and electron distance from the nucleus.

Polar Covalent Bond

A bond where one atom pulls electrons more than another, creating partial charges on the atoms.

Ionic Bonds

Bonds formed when one atom donates an electron to another, resulting in charged particles (ions) that attract each other.

Water polarity

Results from polar covalent bonds between oxygen and hydrogen.

Water as a solvent

Due to its polarity, it can dissolve many substances.

Adhesion

Water's ability to stick to other surfaces.

Cohesion

Water molecules stick to each other.

Water's temperature regulation

Hydrogen bonds allow water to resist temperature changes (e.g., water heats slower than metal in a pan).

Carbon's importance

Forms the backbone of organic molecules, making up the majority of the dry mass of cells.

Carbon's versatility

Can form four covalent bonds with other atoms, allowing a wide variety of molecular structures.

Example (methane CH₄)

Carbon shares its four valence electrons with hydrogen to form covalent bonds in a tetrahedral shape.

Hydrocarbons

Molecules made of only carbon and hydrogen, usually nonpolar and hydrophobic.

Isomerism

Different atomic arrangements with the same chemical formula create distinct molecules with different functions (e.g., isoleucine vs. leucine).

Proteins

Diverse functions, including enzymes, immune system components, signaling molecules, and transporters.

Amino acids

Building blocks of proteins; 20 types, each with a unique R group.

Polypeptide formation

Amino acids linked by peptide bonds, forming a protein after folding into its 3D structure.

Nucleic Acids

DNA and RNA: DNA stores genetic information; RNA aids in protein synthesis.

Nucleotides

The building blocks of nucleic acids, composed of a sugar, phosphate group, and nitrogenous base.

DNA structure

Double helix with complementary base pairing (A-T, G-C).

Carbohydrates

Provide energy (e.g., glucose) and form structural components (e.g., cell walls in plants).

Monosaccharides

Simple sugars like glucose, galactose, and fructose.

Polysaccharides

Chains of monosaccharides, like starch (plants) and glycogen (animals).

Glycosidic bonds

Form between monosaccharides during dehydration synthesis.

Cellulose

A polysaccharide with linear glycosidic bonds, important for plant cell walls.

Lipids

Insoluble in water; important for energy storage and cell structure.

Triglycerides

Store long-term energy; made of glycerol and fatty acids.

Phospholipids

Form cell membranes with amphipathic properties (hydrophobic tails, hydrophilic heads).

Steroids

Lipid hormones that aid in communication and structure.

Frederick Griffith's Experiment (1920s)

Studied Streptococcus pneumoniae bacteria: smooth strain (virulent) and rough strain (non-virulent).

Oswald Avery, Colin MacLeod, and Maclyn McCarty (1944)

Extended Griffith's experiment with enzymes (RNAse, protease, DNase). DNase prevented transformation, showing DNA is responsible for transferring genetic material.

Hershey and Chase's Bacteriophage Experiment (1952)

Used bacteriophages (viruses that infect bacteria) to track DNA and protein.

Watson and Crick's DNA Structure Discovery (1953)

Proposed DNA's double helix structure using Rosalind Franklin's X-ray crystallography data.

DNA Structure

DNA resembles a twisted rope ladder: sugar-phosphate backbone forms the outer rails, nitrogenous bases form the rungs.

Base pairing

A-T (2 hydrogen bonds), G-C (3 hydrogen bonds).

Directionality

Critical for processes like DNA replication and transcription.

Central Dogma of Molecular Biology

Describes the flow of genetic information: DNA → RNA → Protein.

Transcription

DNA information is copied into RNA.

Translation

RNA is used to produce proteins that perform cellular functions.

Transcription Process

RNA polymerase binds to promoter to initiate transcription.

RNA polymerase

Reads DNA and synthesizes RNA (A-U, T-A, G-C, C-G).

Terminator sequence

Marks the end of transcription.

Prokaryotes

Transcription and translation occur simultaneously.

Eukaryotes

RNA is processed before translation.

Gene Regulation

Transcription factors bind to promoter to initiate transcription.

Transcription factors

Eukaryotes have multiple transcription factors; prokaryotes only one (sigma factor).

Transcriptional activators

Bind to enhancer sequences upstream of genes.

5' cap

Added to the RNA for protection and signaling.

Poly A tail

Added to the 3' end to prevent degradation and help RNA exit the nucleus.

Splicing

Removes introns and joins exons.

Alternative splicing

Allows for different mRNA products from the same gene, producing different proteins.

Proteins (Polypeptides)

Linear polymers of amino acids folded into 3D shapes.

Primary Structure

Simple: linear sequence of amino acids linked by peptide bonds.

Amino acids

Have amino group, carboxyl group, and unique R group.

Secondary Structure

Involves local folding due to interactions between peptide backbone groups.

Alpha Helix

Twisted shape due to hydrogen bonds between every fourth amino acid.

Beta Sheet

Folded, pleated sheet stabilized by hydrogen bonds between amino and carboxyl groups.

Tertiary Structure

Overall 3D shape determined by interactions between amino acid R groups.

Quaternary Structure

Present in proteins with multiple polypeptide chains (subunits).

Denaturation

Disrupts protein structure and function.

Codons

Triplets of nucleotides in mRNA, each specifying an amino acid.

Genetic code

Is redundant (e.g., multiple codons for the same amino acid).

Codon Wobble

Redundancy in the third codon position.

Universal Genetic Code

Same codons for amino acids across species (e.g., GFP in mice or human insulin in bacteria).

Start codon

AUG marks translation start.

Translation Steps

Initiation, Elongation, Termination.

mRNA

Template carrying genetic information.

tRNA

Reads mRNA codons, brings corresponding amino acids.

rRNA

Key part of the ribosome, facilitates peptide bond formation.

Aminoacyl-tRNA synthetases

Charge tRNA with the correct amino acid, ensuring accuracy in translation.

Monocistronic mRNA

Eukaryotic mRNA that contains one gene per mRNA.

Polycistronic mRNA

Prokaryotic mRNA that contains multiple genes per mRNA.

Shine-Dalgarno sequence

Allows translation initiation at various points in prokaryotes.

Initiation

Stage where ribosome binds to mRNA and finds the start codon.

Elongation

Stage where amino acids are added to the growing polypeptide chain.

Termination

Stage where stop codon releases the polypeptide.

Translation

Essential for protein synthesis, with differing mechanisms in prokaryotes and eukaryotes.

Cell Membrane

All cells are defined by the presence of a cell membrane.

Regulation of Molecules

Regulates what molecules enter and exit the cell.

Phospholipids

Major lipid type in the cell membrane.

Van der Waals Forces

Neighboring phospholipids interact via Van der Waals forces between fatty acid tails.

Membrane Fluidity

Membrane is fluid and flexible, moving horizontally within the plane of one layer of the lipid bilayer.