General Biology Final Exam Study Guide: Chemistry, Cellular Processes, Genetics, and Molecular Biology

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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.

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 if a reaction is spontaneous.
Formula:

Cellular Respiration

Overview and Steps

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

Glycolysis: Occurs in the cytoplasm; glucose is split into two pyruvate molecules. Products: 2 ATP, 2 NADH, 2 pyruvate.
Pyruvate Oxidation: Pyruvate enters mitochondria and is converted to acetyl-CoA. Products: NADH, CO2, acetyl-CoA.
Citric Acid Cycle (Krebs Cycle): Acetyl-CoA is oxidized; Products: 2 ATP, 6 NADH, 2 FADH2, 4 CO2 (per glucose).
Oxidative Phosphorylation: Includes electron transport chain and chemiosmosis; 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 Products

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

Light Reactions: Occur in the thylakoid membranes; use light to produce ATP and NADPH, release O2.
Calvin Cycle (Dark Reactions): Occur in the stroma; use ATP and NADPH to fix CO2 into glucose.

ATP: Produced in light reactions, consumed in Calvin cycle.
Electron Carriers: NADPH produced in light reactions, used in Calvin cycle.

The Cell Cycle

Stages and Checkpoints

The cell cycle is the sequence of events in cell growth and division. It includes:

G1 Phase: Cell grows, 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; main checkpoints are at G1, G2, and M phases.

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, spindle fibers, and nuclear envelope changes.

DNA Structure and Replication

Chromatin Organization

Histones: Proteins around which DNA winds.
Nucleosomes: DNA-histone complexes; basic unit of chromatin.
Chromatin: DNA and protein complex; can be loosely (euchromatin) or tightly (heterochromatin) packed.
Chromosomes: Condensed chromatin visible during cell division.

DNA Replication Ingredients

DNA template
DNA polymerase
Primase
Nucleotides (dNTPs)
Other enzymes: Helicase, ligase, topoisomerase

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:

Transcription: DNA is copied into mRNA in the nucleus.
Translation: mRNA is decoded by ribosomes in the cytoplasm to build proteins.

mRNA vs. tRNA

Feature	mRNA	tRNA
Function	Carries genetic code from DNA	Transfers amino acids to ribosome
Structure	Single-stranded	Cloverleaf, with anticodon
Location	Nucleus & cytoplasm	Cytoplasm

Splicing, Introns, and Exons

Splicing: Removal of introns from pre-mRNA; exons are joined to form mature mRNA.
Introns: Non-coding regions removed during splicing.
Exons: Coding regions retained in mature mRNA.

Amino Acids and Codon Chart

Amino Acids: Building blocks of proteins; differ by their side chains (R groups).
Codon Chart: Used to translate mRNA codons into amino acids.

Protein Structure

Primary: Sequence of amino acids.
Secondary: Alpha helices and beta sheets (hydrogen bonding).
Tertiary: 3D folding due to side chain interactions.

Gene Regulation: Inducers and Repressors

Inducer: Activates gene expression (can be active/inactive).
Repressor: Inhibits gene expression (can be active/inactive).
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 (X or Y).

Codominance vs. Incomplete Dominance

Type	Description	Example
Codominance	Both alleles fully expressed	AB blood type
Incomplete Dominance	Intermediate phenotype	Pink snapdragons

Punnett Squares and Polygenic Inheritance

Punnett Square: Diagram to predict offspring genotypes from parental alleles.
Single Gene: Example: Bb x Bb
Polygenic: Example: BbRR x bbRr

Genetic Terms

Karyotype: Chromosome chart for an individual.
Chromosome Crossover: Exchange of genetic material during meiosis.
Linkage: Genes located close together on a chromosome tend to be inherited together.