bio 200

Information flow:

understand how genetic and environmental information is perceived, transmitted, and interpreted at molecular, cellular, and systemic levels

Structure and function:

analyze how the structure of molecules, cells, and systems is directly related to their biological roles and efficiency

Energy transformations:

study the storage, transfer, and conversion of energy in biological systems under thermodynamic principles

Evolution:

explore the mechanisms (mutation, selection, drift) driving genetic variation and population dynamics over time

Systems:

investigate interconnected biological networks and their adaptive responses to environmental changes, including feedback loops and regulatory mechanisms.

Polar bonds

unequal electronegativity

Nonpolar bonds

equal electronegativity

Polar functional groups (OH, COOH, NH2) are

hydrophilic

Nonpolar functional groups (long alkyl chains, benzene rings) are

hydrophobic

Be able to draw hydrogen bonds between biomolecules

Covalent bonds

Energy Storage: Store energy in bond energy, which is the energy required to break the bond.

Example: Glucose (C₆H₁₂O₆) stores energy in covalent bonds.

Potential Energy: Stronger, shorter bonds store more energy.

Ionic bonds

Energy Storage: Store energy in electrostatic attraction between oppositely charged ions.

Example: Sodium chloride (NaCl) stores energy in the attraction between Na⁺ and Cl⁻.

Potential Energy: Stronger ionic bonds form with larger charges and smaller ions, storing more energy.

Metallic bonds

Energy Storage: Store energy through delocalized electrons in a metallic lattice.

Example: Copper (Cu) stores energy via delocalized electrons, allowing conductivity.

Potential Energy: Distributed over the entire lattice, effective for energy conduction.

Explain why breaking polar bonds releases less energy compared to breaking nonpolar bonds.

Polar bonds involve unequal sharing of electrons, leading to lower bond strength and less energy release upon breaking, while nonpolar bonds have equal sharing and stronger interactions.

Explain how DNA mutations alter protein function and affect fitness.

Genotype refers to an organism’s genetic makeup, and mutations in DNA can alter the phenotype by changing protein function.

The effects on fitness depend on whether the mutation is beneficial, neutral, or harmful. Beneficial mutations can increase fitness, while harmful mutations can reduce it.

Primary protein structure

is the sequence of amino acids in a polypeptide chain, determining the protein's unique characteristics and function.

Secondary protein structure:

hydrogen bonds form between the backbone atoms in a polypeptide chain, leading to the formation of alpha helices and beta sheets.

Tertiary protein structure:

The three-dimensional shape of a protein formed by the folding of the polypeptide chain, stabilized by interactions between side chains.

Quaternary protein structure:

interactions including disulfide bonds and hydrophobic packingbetween multiple polypeptide chains, forming a functional protein complex.

Transcription

Initiation: RNA polymerase binds to the sigma, sigma binds to promotor, helix opens, transcription begins at 1+ site

Elongation: RNA adds bases to 5’ to 3’ end

Termination: terminator sequence ends transcription, sigma dissociates

Translation

Initiation: Ribosome begins at the start codon AUG. Small ribosomal subunit bind to ribosome at Ribosome Binding Site —> codons binds to anticodons—> Large ribosomal subunit binds so that a tRNA is at the p-site

Elongation: tRNA enters A-site —> peptide bonds form between amino acids carried by tRNA —> polypeptides attached to A-site tRNAs ribosomes moving from 5’ to 3’, placing new codon at A-site

Termination: Stop codon enters A-site —> protein finishes folding

Product: protein

Transcription and translation in prokaryotic:

Because prokaryotes lack a nucleus, transcription and translation occurs in the cytoplasm

Transcription and translation in eukaryotes:

Translation occurs in the nucleus, and translation occurs in the cytoplasm

Predict phenotypes in genetic screens involving single and double mutants in metabolic pathways.

single mutants reveal where the pathway is disrupted

double mutants clarify gene order and interactions

predict phenotypes by analyzing where substrate accumulation or product loss occurs, considering upstream-downstream relationships and compensatory mechanisms

Promotors

DNA sequences located upstream of a gene that signal where RNA polymerase should begin transcription (before the 1+ region)

the TATA box

RNA polymerase

an enzyme that synthesizes RNA by reading the DNA template strand

binds to the promotor region with the help of sigma protein, unwinds the DNA helix

Transcription factors

proteins that assist in the initiation and regulation of transcription bny interacting with DNA and RNA polymerase

help RNA polymerase recognize and bind to the promotor

Predict how amino acid changes alter protein folding and function.

alter protein folding by disrupting stabilizing interactions (e.g. hydrophobic interactions, hydrogen bonds)

affect function by modifying active sites, ligand-binding pockets or allosteric regulation. The severity of the impact depends on the nature of the substitute (how similar it is to the original), its location, and the protein’s structural and functional context