Molecules and Cells Flashcards

Flashcards covering vocabulary terms from the Molecules and Cells lecture notes.

Biological Molecules

Consist almost entirely of small atoms, mostly carbon, hydrogen, oxygen, nitrogen, and sulfur, resulting from the filling of the first or second energy level/shell.

Carbon in Biological Molecules

Carbon is central because it has four valence electrons, allowing it to form highly branched molecules through four possible covalent bonds.

Electronegativity

The ability of an atom to attract electrons to itself in a molecule; increases across the periodic table and to a maximum in the top right hand corner at fluorine, and is at a minimum at the bottom left hand corner at Cesium.

Nonpolar Covalent Bond

Electron density is spread equally over both atoms; EQUAL sharing.

Polar Covalent Bond

Electron density is greater over one of the atoms; UNEQUAL sharing, leading to partial charges on atoms.

Ionic Bond

Electron density is virtually entirely distributed to the more electronegative atom; TRANSFER instead of "sharing" electrons.

Hydrogen Bond

Forms when a d+ hydrogen atom interacts noncovalently with a more electronegative atom; depicted as dashed lines and are longer than covalent bonds.

Hydrophobic Effect

A nonpolar molecule cannot form H-bonds with water and disrupts its highly favorable lattice. Water "likes" its clique-y lattice and maximizes it, causing the non-polar molecules to coalesce.

Water Ionization

Water spontaneously dissociates into hydrogen cations (protons) and hydroxide anions. H2O

pH

pH = -log[H+]

Acid

A substance that, when added to water, gives up a proton, increasing the [H+], and therefore decreases the pH. E.g., HCl --> H+ and Cl-

Base

A substance that, when added to water, binds to a proton and decreases the [H+], and therefore increases the pH. E.g., NaOH --> Na+ and OH-

Buffer

A molecule (in two alternate forms, the acid and conjugate base) that protects against sharp changes in pH by absorbing excess protons or giving up protons when pH becomes low.

Isomers

Molecules that have the same chemical formula but different arrangements of atoms.

Monosaccharide

The simplest carbohydrate that is useful as fuel to make ATP.

Glycosidic Bonds

Polysaccharides are formed via condensation reactions that join monosaccharides through glycosidic bonds.

Lipids

A group of molecules that are functionally defined by their hydrophobicity due to their high hydrocarbon content.

Nucleotides

Molecules made up of a 5-C sugar portion, bound on one side to one or more phosphates and on the other to a nitrogenous (N-containing) base. Joined by phosphodiester bonds to form nucleic acids.

Central Dogma

DNA encodes genes, which are transcribed into messenger RNAs, which provide the instructions for translating into a protein.

DNA Structure

DNA is double-stranded, antiparallel, and stabilized by base-pairing. Convention: write nucleic acid sequences 5’ to 3’.

DNA Polymerase

Catalyzes replication, synthesizes DNA in the 5’ to 3’ direction and only adds a nucleotide to a pre-existing nucleic acid strand with a free 3’OH called a primer. Has proofreading activity.

Mutation

A change in DNA sequence. DNA damage only becomes a mutation when it is incorrectly replicated and unfixed/unfixable by the mismatch repair machinery.

Semi-conservative Replication

During replication, a complementary strand is synthesized from each pre-existing strand of the original DNA.

Telomeres

Chromosome ends that consist of many copies of a short repeat. Solved by an enzyme called telomerase.

Telomerase

An enzyme that brings its own RNA template, solves the end replication problem; binds to the template strand and elongates it.

Transcription

The synthesis of a single-stranded RNA in the 5’ to 3’ direction, complementary to a DNA template strand. Like DNA synthesis, can only occur in the 5’ to 3’ direction.

RNA Polymerase

Catalyzes transcription de novo (without a primer) adding nucleotides to the 3’ end as it moves along the template 3’à5’.

Sigma Factor

A general transcription factor required for transcription initiation in prokaryotes; recognizes and binds to the promoter, thereby recruiting RNA Polymerase to the gene.

Introns

Non-coding sequences that interrupt gene coding sequences (AKA exons).

Exons

Gene coding sequences (that are interrupted by non-coding intron sequences)

Translation

The process that follows the instructions in start codons (always AUG – Met) and stop codons to synthesize a protein from mRNA.

Codon

A set of three nucleotides that an mRNA is “read” in. Each codon specifies an amino acid, except for three STOP codons, UAA, UAG, and UGA, which indicate the end of a polypeptide.

Transfer RNA (tRNA)

An RNA that is the intermediary adapter bewteen mRNA and protein. Actually translates the mRNA because they directly couple nucleotide sequence to amino acid.

tRNA synthetases

Enzymes dedicated to a specific amino acid.

Wobble Hypothesis

Some tRNAs can “wobble” = work even with a mismatch in the 3rd position of a codon-anticodon pair.

Ribosomes

A macromolecular complex of ~50%/50% wt/wt RNA and protein.

Reading Frame

The set of the three bases that are read as a codon.

Peptide Bond

The bond that forms when the carboxyl group of one amino acid reacts with the amino group of another amino acid, and a molecule of water is released.

Homodimer

A protein that functions as by the interaction of two similar polypeptide chains (quaternary structure).

Heterodimer

A protein that functions as by the interaction of two different polypeptide chains (quaternary structure).

Protein Folding

Proteins fold into specific 3D structures, driven by various forces, including hydrophobic interactions, hydrogen bonds, van der Waals forces, and electrostatic interactions. These structures determine their function.

Chaperone Proteins

Assist other proteins to fold properly; bind to hydrophobic regions of nascent polypeptides and prevent aggregation. Some form isolation chambers to give a protein space to fold, isolated from disruptive factors.

Prions

Misfolded proteins that can transmit their misfolded shape to normal variants of the same protein. This can lead to diseases such as mad cow disease in cattle and Creutzfeldt-Jakob disease in humans.

Enzymes

Biological catalysts, typically proteins, that speed up chemical reactions by lowering the activation energy, E_a, without being consumed in the process.

Active Site

The region of an enzyme where the substrate binds and where catalysis occurs. Characterized by a specific shape and chemical microenvironment.

Cofactors

Non-protein chemical species required for enzyme activity; can be inorganic ions or organic molecules.

Coenzymes

Organic cofactors that are often derived from vitamins.

Competitive Inhibitors

Bind to the active site of an enzyme, preventing the substrate

Enzyme Regulation

Controlling enzyme activity through various mechanisms, including allosteric regulation, feedback inhibition, and covalent modification.

Allosteric Regulation

The regulation of an enzyme by binding an effector molecule at a site other than the enzyme's active site.

Feedback Inhibition

A process where the product of a metabolic pathway inhibits an enzyme earlier in the pathway, preventing overproduction.

Covalent Modification

Regulation of enzyme activity by adding or removing chemical groups (e.g., phosphorylation) to the enzyme.

Enzyme Kinetics

The study of the rates of enzyme-catalyzed reactions and the factors that affect them, such as substrate concentration, temperature, and pH.

Michaelis-Menten Kinetics

A model describing the kinetics of enzyme-catalyzed reactions, relating reaction rate to substrate concentration and enzyme properties.

Vmax

The maximum rate of an enzyme-catalyzed reaction when the enzyme is saturated with substrate.

Km

The Michaelis constant, representing the substrate concentration at which the reaction rate is half of Vmax; it is an indicator of the enzyme's affinity for its substrate.

Non-Competitive Inhibitors

Bind to an enzyme at a location away from the active site, altering its conformation and reducing its activity; Vmax decreases, but Km remains the same.

Uncompetitive Inhibitors

Bind only to the enzyme-substrate complex, preventing the reaction from occurring; both Vmax and Km decrease.