Biochemistry Themes and Water Properties

Biochemistry

Common unifying themes in biology:
- Cellular basis of life: All living organisms are made up of cells.
- Heritable information: Organisms inherit genetic information from their parents.
- Evolution: Living organisms change over time, adapting to their environment.
- Structure determines function: The shape of a molecule affects how it works.
- Interactions within systems: Biological systems are interconnected and rely on each other.

Introduction to Chemistry of Life (Water)

Water's Properties:
- Polarity: Water molecules have a partial positive charge on the hydrogen atoms and a partial negative charge on the oxygen atom.
- Hydrogen bonds: Water molecules form hydrogen bonds with each other. These hydrogen bonds are weaker than covalent bonds but are crucial for many biological processes.
Water's Dissociation:
- Water can dissociate into hydroxide ions (OH-) and hydronium ions (H+), which is important for maintaining pH.
Acids, Bases, and pH:
- Acids: Substances that donate hydrogen ions (H+)
- Bases: Substances that accept hydrogen ions (H+)
- pH: A measure of the concentration of hydrogen ions in a solution.
  - pH scale: Ranges from 0 to 14, with lower pH values indicating a higher concentration of hydrogen ions.
  - Strong acids: Have a low pH.
  - Strong bases: Have a high pH.
  - Water: pH of 7.

Macromolecules

Important Chemical Groups:
- Hydroxyl group (-OH): Found in alcohols and sugars, and involved in hydrogen bonding.
- Carboxyl group (-COOH): Found in amino acids and fatty acids, and acts as an acid.
- Amino group (-NH2): Found in amino acids and some bases, and acts as a base.
- Phosphate group (-PO4): Found in nucleic acids, and plays a role in energy transfer.
Polymers:
- Monomers: Building blocks of polymers.
- Polymerization: Monomers are joined together to form polymers.
Carbohydrates:
- Monosaccharides: Simple sugars like glucose and fructose.
- Disaccharides: Two monosaccharides joined together.
- Polysaccharides: Long chains of monosaccharides.
Lipids:
- Fats: Store energy, provide insulation, and protect organs.
- Phospholipids: Make up cell membranes, have a hydrophilic head and hydrophobic tails.
- Steroids: Include hormones like cholesterol and testosterone.

Proteins

Protein Functions:
- Enzymes: Catalyze (speed up) chemical reactions.
- Structural components: Provide support and shape to cells and tissues.
- Transport: Carry molecules across membranes or throughout the body.
Amino Acid Structure:
- Amino group (-NH2): Basic, can accept a proton.
- Carboxyl group (-COOH): Acidic, can donate a proton.
- R group (side chain): Gives each amino acid its unique properties.
- Alpha carbon: Central carbon atom in amino acid.
Levels of Protein Structure:
- Primary structure: The linear sequence of amino acids.
- Secondary structure: Local folding of the polypeptide chain into alpha-helices or beta-sheets.
- Tertiary structure: The three-dimensional shape of a single polypeptide chain.
- Quaternary structure: The arrangement of multiple polypeptide chains in a protein complex.

Nucleic Acids

Nucleoide Structure:
- Phosphate group: Provides negative charge and links nucleotides together.
- Sugar: Pentose sugar (ribose in RNA or deoxyribose in DNA).
- Nitrogenous base: Adenine (A), guanine (G), cytosine (C), thymine (T) in DNA, or uracil (U) in RNA.
DNA Structure:
- Double helix: Two antiparallel strands of nucleotides held together by hydrogen bonds.
- Complementary base pairing: Adenine (A) pairs with thymine (T) and guanine (G) pairs with cytosine (C).

DNA Replication

Semi-conservative replication: Each new DNA molecule consists of one original strand and one newly synthesized strand.
Replication Fork: The site where the DNA double helix is unwound and new strands are synthesized.
Key Proteins involved in DNA replication:
- Helicase: Unwinds the DNA double helix.
- Topoisomerase: Relieves the stress on DNA caused by unwinding.
- DNA polymerase: Adds nucleotides to the new strand.
- Primase: Synthesizes a short RNA primer that DNA polymerase can then extend.
- Leading strand: Synthesized continuously in the direction of the replication fork.
- Lagging strand: Synthesized discontinuously in short fragments (Okazaki fragments).

Transcription

Central dogma of molecular biology: Information flows from DNA to RNA to protein.
Transcription: The process of copying genetic information from DNA to RNA.
Key players involved in transcription:
- RNA polymerase: An enzyme that synthesizes RNA.
- Template strand: The DNA strand that is used as a template for RNA synthesis.
- Coding strand: The DNA strand that has the same sequence as the RNA transcript.
- Promoter site: A region of DNA where RNA polymerase binds to begin transcription.
- Initiation complex: The complex of RNA polymerase and other proteins that assemble at the promoter site.
- Elongation: The process of adding nucleotides to the growing RNA chain.
- Termination: The process of stopping transcription.

RNA Processing (Modification)

5' cap: A modified guanine nucleotide added to the 5' end of pre-mRNA, protecting it from degradation and helping it bind to ribosomes.
3' poly A tail: A string of adenine nucleotides added to the 3' end of pre-mRNA, protecting it from degradation and signaling to the ribosome that the transcript is mature.
Splicing: The process of removing introns (non-coding regions) from pre-mRNA and joining exons (coding regions).

Translation

Translation: The process of converting the genetic information in mRNA into a protein. It involves the ribosome, mRNA, tRNA, and rRNA.
Ribosome: The site of protein synthesis in the cytoplasm.
Messenger RNA (mRNA): Carries the genetic code from DNA to the ribosome.
Transfer RNA (tRNA): Transports amino acids to the ribosome.
Ribosomal RNA (rRNA): A component of ribosomes.
Translation Initiation: The small and large ribosomal subunits bind to mRNA, with tRNA carrying the start codon (AUG) at the initiation site.
Translation Elongation: The ribosome adds amino acids to the growing polypeptide chain, moving along the mRNA in a 5' to 3' direction.
Translation Termination: The ribosome encounters a stop codon (UAA, UAG, or UGA), causing release of the polypeptide chain.

Genetic Code

Codon: A three-base-pair sequence on mRNA that specifies a particular amino acid.
Genetic code: The set of rules that relates codons to amino acids. It is universally applicable to all living organisms.
Start codon (AUG): Initiates translation, also codes for methionine.
Stop codons (UAA, UAG, UGA): Terminate translation.

Cell Biology

Cell Structures and Functions
- Nucleus: Contains genetic material (DNA), controls cell activities
- Cytoplasm: Gel-like substance surrounding the nucleus, contains organelles and cytosol
- Ribosomes: Produce proteins
- Endoplasmic reticulum (ER): Network of membranes that synthesize lipids and proteins, modifies proteins
- Golgi apparatus: Modifies, sorts, and packages proteins
- Mitochondria:
  - Powerhouses of the cell
  - Produce ATP (energy) through cellular respiration
- Lysosomes: Break down cellular waste and debris
- Peroxisomes: Break down fatty acids
- Cell membrane: Controls what enters and exits the cell
- Cytoskeleton: Provides structure and support to the cell, aids in movement
Cell Transport
- Passive transport: Movement of molecules across a membrane without requiring energy.
  - Diffusion: Movement from high to low concentration.
  - Osmosis: Diffusion of water across a semipermeable membrane.
- Active transport: Movement of molecules across a membrane requiring energy.
Cellular Communication:
- Reception: A signal molecule binds to a receptor protein on the target cell.
- Transduction: The signal is converted into a form that can be relayed inside the cell.
- Response: The cell produces a specific response to the signal, such as changes in gene expression, enzyme activity, or cell behavior.