BIO1 Final Exam Review Notes Good

Protein Structure

• Different levels of protein structure:

  • Primary: Sequence of amino acids determined by genetic information; dictates the final folding and function of the protein.

  • Secondary: Localized folding (alpha helices, beta sheets) stabilized by hydrogen bonds between amino acids in the polypeptide chain. Alpha helices are coiled structures, while beta sheets are pleated or corrugated.

  • Tertiary: 3D structure of a single polypeptide chain stabilized by various interactions, including hydrophobic interactions, hydrogen bonds, disulfide bridges, and ionic bonds.

  • Quaternary: Arrangement of multiple polypeptide chains (subunits) to form a protein complex. Not all proteins have a quaternary structure.

Nucleic Acids

• RNA and DNA characteristics:

  • DNA: Double-stranded helix, deoxyribose sugar, thymine (T) base. Carries genetic information and is involved in heredity.

  • RNA: Single-stranded, ribose sugar, uracil (U) base. Involved in gene expression, including mRNA, tRNA, and rRNA.

Ribosomes

• Free vs. membrane-bound ribosomes:

  • Free: Synthesize proteins for use within the cell, such as enzymes and structural proteins.

  • Membrane-bound: (ER) Synthesize proteins for secretion or insertion into membranes, including plasma membrane and organelle membranes.

Organelles

• Function-to-organelle matching: Be able to identify organelles based on their functions.

Cytoskeleton

• Cytoskeleton and cargo movement: Microtubules (involved in chromosome separation during cell division and intracellular transport), microfilaments (involved in muscle contraction and cell motility), intermediate filaments (provide structural support).

Cell Membrane

• \Cell membrane permeability: Small, nonpolar molecules cross easily; large, polar, and charged molecules require transport proteins such as channels and carriers.

Solutions and Cells

• Animal/plant cells in solutions: Isotonic (no net movement of water), hypertonic (cell shrinks), hypotonic (cell swells and may burst).

Membrane Lipids

• Saturated and unsaturated fats in cell membrane: Unsaturated fats increase membrane fluidity due to kinks in hydrocarbon tails, which prevent tight packing of lipids. Saturated fats decrease membrane fluidity.

Free Energy

• Free energy and $\Delta G$: $\Delta G$ is the change in free energy.

  • Negative $\Delta G$: Exergonic reaction (releases energy), spontaneous.

  • Positive $\Delta G$: Endergonic reaction (requires energy), non-spontaneous.

Enzymes

• Enzymes: Speed up chemical reactions by lowering activation energy. They are biological catalysts.

• Inhibitors:

  • Competitive: Bind to active site, preventing substrate binding.

  • Noncompetitive: Bind to allosteric site, changing enzyme shape and reducing its activity.

Cellular Respiration

• Aerobic cellular respiration: Oxygen is the final electron acceptor in the electron transport chain, producing water and ATP.

Photosynthesis

• Light reaction of photosynthesis: Converts light energy into chemical energy (ATP and NADPH) in the thylakoid membrane.

• Electron movement:

  • Photosynthesis: Electrons move from water to NADPH, generating oxygen as a byproduct.

  • Respiration: Electrons move from glucose to oxygen, generating water and ATP.

Cell Cycle

• Cell cycle checkpoints: G1 (checks for DNA damage), G2 (checks for DNA replication), M checkpoints (checks for chromosome alignment).

• Mitotic phase stages: Prophase, metaphase, anaphase, telophase, cytokinesis. Each stage has distinct events.

Redox Reactions

• Oxidation and reduction:

  • Photosynthesis: Water is oxidized, carbon dioxide is reduced.

  • Respiration: Glucose is oxidized, oxygen is reduced.

Enzymes and Free Energy

• $\Delta G$ and enzymes: Enzymes do not affect $\Delta G$, only the rate of reaction by lowering the activation energy.

Organelles Specific to Cell Types

• Organelles in animal/plant cells: Cell wall and chloroplasts in plant cells; centrioles in animal cells.

Chromosomes

• Homologous chromosomes: Chromosome pairs (one from each parent) with genes for the same traits at the same loci.

Cell Division

• Mitosis vs. meiosis:

  • Mitosis: Produces two identical diploid cells for growth and repair.

  • Meiosis: Produces four unique haploid cells for sexual reproduction.

Chromosome Types

• Autosomes and sex chromosomes: Autosomes are non-sex chromosomes; sex chromosomes determine sex (e.g., X and Y in humans).

• Ploidy: Diploid (2n) and haploid (n) cells. Diploid cells have two sets of chromosomes; haploid cells have one set.

Meiosis

• Crossing over in meiosis: Exchange of genetic material between homologous chromosomes during prophase I, leading to genetic variation.

• Somatic and gamete chromosome number: Somatic cells are diploid; gametes are haploid; gametes fuse to form a diploid zygote during fertilization.

Reproduction

• Sexual vs. asexual reproduction: Sexual reproduction involves genetic variation, asexual does not. Sexual reproduction produces diverse offspring, while asexual reproduction produces genetically identical offspring.

• Meiosis I and II: Meiosis I separates homologous chromosomes; Meiosis II separates sister chromatids, similar to mitosis.

Genetics

• Independent assortment: Random alignment of homologous chromosomes during metaphase I, leading to different combinations of alleles in gametes.

• Genotype and Phenotype:

  • Homozygous dominant: Two dominant alleles (e.g., AA).

  • Homozygous recessive: Two recessive alleles (e.g., aa).

  • Heterozygous: One dominant and one recessive allele (e.g., Aa); dominant allele is expressed. (e.g., in a Punnett square).

Mendelian Genetics

• Mendel’s laws:

  • Law of independent assortment: Alleles of different genes assort independently during gamete formation.

  • Law of segregation: Allele pairs separate during gamete formation, so each gamete carries only one allele for each gene.

• Blood types: ABO blood groups and Punnett squares to determine inheritance patterns. Includes A, B, AB, and O blood types.

• Dominance:

  • Complete dominance: One allele masks the other (e.g., Aa expresses the dominant trait).

  • Incomplete dominance: Blending of traits (e.g., red and white flowers produce pink flowers).

  • Codominance: Both alleles are expressed (e.g., AB blood type expresses both A and B antigens).

  • Epistasis: One gene affects the expression of another (e.g., coat color in Labrador Retrievers).

  • Polygenic inheritance: Multiple genes affect a trait (e.g., skin color, height).

  • Pleiotropy: One gene affects multiple traits (e.g., Marfan syndrome).

Chromosomes

• Chromatids and centromeres: Sister chromatids are joined at the centromere; centromere is the region where spindle fibers attach during cell division.

Nucleic Acids

• RNA and DNA nucleotides: Adenine, guanine, cytosine, thymine (DNA), uracil (RNA). A, G, C are common to both.

• Complementary base pairing:

  • DNA: A-T, G-C.

  • RNA: A-U, G-C.

DNA

• DNA replication:

  • Process of copying DNA. Requires enzymes such as DNA polymerase, helicase, and ligase. Occurs during the S phase of the cell cycle.

Gene Expression

• Transcription: DNA to RNA in the nucleus.

• Prokaryotic vs. eukaryotic chromosomes: Eukaryotic chromosomes are linear and in the nucleus; prokaryotic chromosomes are circular and in the cytoplasm without a nucleus.

• Translation: RNA to protein in the ribosome.

Protein Synthesis

• Gene expression: Eukaryotic vs. prokaryotic cells. Eukaryotic gene expression involves RNA processing (splicing, capping, tailing) and occurs in multiple cellular locations.

• Triplet vs. codon vs. anticodon: Triplet (DNA), codon (mRNA), anticodon (tRNA). These are involved in the process of translating mRNA into a protein sequence.

• Translation in prokaryotes vs. eukaryotes. Prokaryotic translation can occur simultaneously with transcription, while eukaryotic translation occurs separately after RNA processing.

Mutations

• Mutation types: Point mutations (substitutions), frameshift mutations (insertions or deletions), etc. Mutations can be harmful, beneficial, or neutral.

Cancer

• Oncogenes vs. proto-oncogenes: Oncogenes promote cancer; proto-oncogenes are normal genes that can become oncogenes through mutation or increased expression.

• Tumor-suppressor genes: Inhibit cell division; loss-of-function mutations can lead to cancer. Examples include p53 and Rb.

• Tumor viruses: Can insert oncogenes or disrupt tumor-suppressor genes, leading to uncontrolled cell growth.

Viruses

• Viral replication types: Lytic (host cell destruction) and lysogenic (integration into host genome).

• Retroviruses: Use reverse transcriptase to convert RNA to DNA, which is then integrated into the host cell's genome (e.g., HIV).

• Phage types: Lytic and lysogenic cycles in bacteriophages (viruses that infect bacteria).

• Viral DNA incorporation: When viral DNA integrates into host cell DNA, it can disrupt normal gene function or be replicated along with the host cell's DNA.

RNA Processing

• RNA processing: Splicing (removal of introns), capping (addition of a 5' cap), tailing (addition of a poly-A tail).

Macromolecules

• Polysaccharides, monosaccharides, disaccharides: Types of carbohydrates. Examples include starch, glucose, and sucrose.

• Fat types: Saturated, unsaturated, trans fats. Differ in their chemical structure and effects on health.

Bacteria

• Bacteria types: Gram-positive (thick peptidoglycan layer) and Gram-negative bacteria (thin peptidoglycan layer and outer membrane).

Protists

• Protists and movement: Cilia, flagella, pseudopods. Various methods used for locomotion.

• Host/protist relationships: Some protists are parasitic and can cause diseases (e.g., malaria).

Animal Development

• Body Cavities: Pseudocoelomate, coelomate, acoelomate, diploblastic, triploblastic. Different body plans in animals.

• Segmentation in animals: Repeating body segments (e.g., annelids).

• Phylum Porifera: Sponges; lack true tissues.

• Animal body plans: Bilateral and radial symmetry.

Evolution

• Charles Darwin's observations and inferences: Natural selection and adaptation of species over time.