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: The bond between two hydrogen atoms and one oxygen atom in a water molecule (H2O).

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

Additional info: Visual representations 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.

• Formula:

• Low pH = high H+ concentration (acidic); high pH = low H+ concentration (basic).

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 whether a reaction is spontaneous.

• Formula:

• If , the reaction is spontaneous.

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 the mitochondria and is converted to acetyl-CoA. Products: NADH, CO2, acetyl-CoA.

3. Citric Acid Cycle (Krebs Cycle): Acetyl-CoA is oxidized; occurs in the mitochondrial matrix. Products: 2 ATP, 6 NADH, 2 FADH2, 4 CO2 (per glucose).

4. Oxidative Phosphorylation: Includes the electron transport chain and chemiosmosis; occurs in the inner mitochondrial membrane. Products: ~28 ATP, water.

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

• Electron Carriers: NADH and FADH2 transport electrons to the electron transport chain.

Photosynthesis

Main Stages and Processes

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

1. Light Reactions: Occur in the thylakoid membranes; convert light energy to ATP and NADPH. Reactants: Water, light. Products: Oxygen, ATP, NADPH.

2. Calvin Cycle (Dark Reactions): Occurs in the stroma; uses ATP and NADPH to fix carbon dioxide into glucose. Reactants: CO2, ATP, NADPH. Products: Glucose, ADP, NADP+.

• ATP: Produced in light reactions, consumed in Calvin cycle.

• Electron Carriers: NADPH is produced in light reactions, used in Calvin cycle.

The Cell Cycle

Stages and Checkpoints

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

• Interphase: Includes G1 (cell growth), S (DNA synthesis), and G2 (preparation for mitosis).

• Mitosis: Division of the nucleus; consists of prophase, metaphase, anaphase, and telophase.

• Cytokinesis: Division of the cytoplasm.

• Checkpoints: G1, G2, and M checkpoints ensure proper progression.

Additional info: During mitosis, chromosomes condense, the nuclear envelope breaks down, and spindle fibers attach to chromosomes.

DNA Structure and Replication

Organization and Replication

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

• Nucleosomes: DNA wrapped around histone proteins.

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

• Chromosomes: Highly condensed chromatin visible during cell division.

• Ingredients for Replication: DNA template, DNA polymerase, nucleotides, primers.

• Leading Strand: Synthesized continuously.

• Lagging Strand: Synthesized discontinuously in Okazaki fragments.

Protein Synthesis and Expression

Process and Components

Protein synthesis involves transcription and translation.

• Transcription: DNA is transcribed to mRNA in the nucleus.

• Translation: mRNA is translated into protein at the ribosome in the cytoplasm.

• mRNA: Messenger RNA; carries genetic information from DNA to ribosome.

• tRNA: Transfer RNA; brings amino acids to the ribosome.

• Splicing: Removal of introns (non-coding regions) and joining of exons (coding regions) in mRNA.

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

Additional info: Codon charts are used to determine which amino acid corresponds to each mRNA codon.

Protein Structure

• Primary: Sequence of amino acids.

• Secondary: Alpha helices and beta sheets formed by hydrogen bonding.

• Tertiary: Three-dimensional folding due to interactions among side chains.

Gene Regulation

• Inducer: Molecule that activates gene expression.

• Repressor: Molecule that inhibits gene expression.

• Lac Operon: A gene system in bacteria regulated by inducers and repressors.

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: 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 and Polygenic Inheritance

Punnett squares are used to predict offspring genotypes and phenotypes.

• Single Gene: Example: Bb x Bb

• Polygenic: Example: BbRR x bbRr

• Interpret parent alleles from offspring alleles using Punnett squares.

Key Terms

• Karyotype: The number and appearance of chromosomes in a cell.

• Chromosome Crossover: Exchange of genetic material during meiosis.

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

Example Table: Types of Inheritance