Chemistry in Biology

Types of Chemical Bonds

Chemical bonds are essential for the structure and function of biological molecules. The three main types are ionic, covalent, and hydrogen bonds.

• Ionic Bonds: Formed when electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other. Example: NaCl (sodium chloride).

• Covalent Bonds: Formed when two atoms share one or more pairs of electrons. Example: H2O (water).

• Hydrogen Bonds: Weak attractions between a hydrogen atom (covalently bonded to an electronegative atom like oxygen or nitrogen) and another electronegative atom. Example: Bonds between water molecules.

Additional info: Diagrams typically show electron transfer (ionic), electron sharing (covalent), and dotted lines for hydrogen bonds.

pH and Hydrogen Ion Concentration

The pH scale measures the concentration of hydrogen ions (H+) in a solution.

• Acidic solutions have high H+ concentration (pH < 7).

• Basic solutions have low H+ concentration (pH > 7).

• Neutral solution: pH = 7.

Formula:

Types of Reactions

• Dehydration Synthesis: Builds larger molecules by removing water.

• Hydrolysis: Breaks down molecules by adding water.

Laws of Thermodynamics & Gibbs Free Energy

• First Law: Energy cannot be created or destroyed, only transformed.

• Second Law: Entropy (disorder) increases in spontaneous processes.

• Gibbs Free Energy: Determines if a reaction is spontaneous.

Formula:

Where is change in free energy, is change in enthalpy, is temperature in Kelvin, and is change in entropy.

Cellular Respiration

Overview and Steps

Cellular respiration is the process by which cells extract energy from glucose. It consists of four main stages:

1. Glycolysis: Occurs in the cytoplasm. Glucose is split into two pyruvate molecules. Products: 2 ATP, 2 NADH, 2 pyruvate.

2. Pyruvate Oxidation: Pyruvate enters mitochondria and is converted to acetyl-CoA. Products: NADH, CO2, acetyl-CoA.

3. Citric Acid Cycle (Krebs Cycle): Acetyl-CoA is oxidized, producing NADH, FADH2, ATP, and CO2.

4. Oxidative Phosphorylation: Includes electron transport chain and chemiosmosis. NADH and FADH2 donate electrons, leading to ATP production.

Electron-carrying molecules: NADH and FADH2 are produced in earlier steps and used in the electron transport chain.

ATP: Required in glycolysis (investment phase), exported in all stages (net gain).

Summary Table

Additional info: Total ATP yield per glucose is about 30-32.

Photosynthesis

Main Stages

Photosynthesis converts light energy into chemical energy in plants, algae, and some bacteria. It has two main stages:

• Light Reactions: Occur in the thylakoid membranes. Use light to produce ATP and NADPH; oxygen is released.

• Calvin Cycle (Dark Reactions): Occur in the stroma. Use ATP and NADPH to fix CO2 into glucose.

Summary Table

Electron carriers: NADPH is produced in light reactions and used in the Calvin cycle.

The Cell Cycle

Stages of the Cell Cycle

The cell cycle is the series of events that cells go through as they grow and divide. It consists of:

• G1 Phase: Cell grows and prepares for DNA replication.

• S Phase: DNA is replicated.

• G2 Phase: Cell prepares for mitosis.

• M Phase (Mitosis): Cell divides its nucleus and cytoplasm.

Checkpoints: Ensure proper progression; G1, G2, and M checkpoints monitor DNA integrity and division.

Mitosis Stages

• Prophase: Chromosomes condense, nuclear envelope breaks down, spindle forms.

• Metaphase: Chromosomes align at the cell equator.

• Anaphase: Sister chromatids separate and move to opposite poles.

• Telophase: Nuclear envelope reforms, chromosomes decondense.

• Cytokinesis: Cytoplasm divides, forming two daughter cells.

Additional info: Diagrams typically show chromosome movement and spindle formation.

DNA Structure and Replication

Key Components

• Histones: Proteins that package and order DNA into structural units.

• Nucleosomes: DNA wrapped around histone proteins.

• Chromatin: Complex of DNA and proteins; can be euchromatin (active) or heterochromatin (inactive).

• Chromosomes: Condensed chromatin visible during cell division.

DNA Replication Ingredients

• DNA template

• DNA polymerase

• Primers

• Nucleotides (dNTPs)

Leading vs. Lagging Strand

• Leading Strand: Synthesized continuously in the direction of the replication fork.

• Lagging Strand: Synthesized discontinuously as Okazaki fragments, away from the fork.

Protein Synthesis and Expression

General Process

Protein synthesis involves two main steps:

1. Transcription: DNA is copied into mRNA in the nucleus.

2. Translation: mRNA is decoded by ribosomes in the cytoplasm to build a protein.

mRNA vs. tRNA

Splicing, Introns, and Exons

• Splicing: Removal of introns (non-coding regions) from pre-mRNA; exons (coding regions) are joined.

• Introns: Non-coding sequences.

• Exons: Coding sequences.

Amino Acids

• Amino acids: Building blocks of proteins; differ by their side chains (R groups).

• Codon chart: Used to determine which amino acid corresponds to each mRNA codon.

Protein Structure

• Primary: Sequence of amino acids.

• Secondary: Alpha helices and beta sheets.

• Tertiary: 3D folding of the protein.

Gene Regulation

• Inducer: Activates gene expression.

• Repressor: Inhibits gene expression.

• Lac operon: Classic example of gene regulation in bacteria.

Genetics and Heredity

Inheritance Patterns

• Autosomal Dominant: Trait appears in every generation; only one allele needed.

• Autosomal Recessive: Trait appears only when both alleles are recessive.

• Sex-linked Dominant/Recessive: Traits linked to sex chromosomes (usually X); males and females affected differently.

Codominance vs. Incomplete Dominance

• Codominance: Both alleles are fully expressed (e.g., AB blood type).

• Incomplete Dominance: Heterozygote shows intermediate phenotype (e.g., pink flowers from red and white parents).

Punnett Squares

Punnett squares are used to predict offspring genotypes from parental alleles.

• Single gene: Example: Bb x Bb

• Polygenic: Example: BbRR x bbRr

Additional info: Interpreting parent alleles from offspring genotypes involves working backward using known ratios.

Key Terms

• Karyotype: Chromosome profile of an individual.

• Chromosome crossover: Exchange of genetic material during meiosis.

• Linkage: Genes located close together on a chromosome tend to be inherited together.