BMB 401 MSU Exam 1 Flashcards

A collection of vocabulary flashcards covering the fundamental concepts of biochemistry, thermodynamics, cellular biology, and protein structure from BMB 401 MSU Exam 1 notes.

Biochemistry

The chemistry dealing with chemical compounds and processes in living plants and animals.

Homeostasis

A tendency to maintain a balanced or constant internal state.

Catabolic reactions

Reactions that break down large chemicals; they are oxidative and release energy.

Anabolic reactions (anabolism)

Reactions that build-up larger molecules; they are reductive and require energy.

Bacteria

Unicellular organisms lacking membrane-bound organelles with single circular DNA molecules.

Archea

Prokaryotic organisms that live in extreme environments, often without oxygen, and obtain energy from inorganic molecules and light.

Covalent bond

The inter-atomic linkage that results from the sharing of an electron pair between two atoms.

Resonance structures

Lewis structures that have the same arrangement of atoms in a molecule but differ in the distribution of electrons; these structures tend to have lower energy states.

Electronegativity

A measure of the ability of an atom in a chemical compound to attract electrons, a concept developed by Linus Pauling.

Ionic bonds

Bonds formed when a great electronegative difference causes one atom to gain an electron and the other to lose one, held together by electrostatic attraction.

Non-covalent interactions

Types of interactions including van der waals, hydrogen bonds, ionic bonds, and hydrophobic interactions.

Coulomb's Law equation

$$\text{E (or F)} = \frac{k q_1 q_2}{r^2}$$

Dielectric constant

A quantity measuring the ability of a substance to store electrical energy in an electric field.

Dipole-Dipole Interactions

Attractive forces between the positive end of one polar molecule and the negative end of another polar molecule.

Hydrogen Bond

A primarily electrostatic force of attraction between a hydrogen atom covalently bound to a more electronegative atom and another electronegative atom bearing a lone pair of electrons.

Van der Waals forces (London Dispersion)

Forces of attraction between instantaneous dipoles, most often found in non polar molecules.

Triglycerides

Lipids used as fuel and stored in fat cells.

Phospholipids

Lipids that spontaneously arrange to form membrane-like structures.

Nucleic acids

Molecules that encode genetic information into DNA and RNA.

Reducing end

The end of a carbohydrate chain with a free anomeric carbon where the ring can open.

Enthalpy

A thermodynamic quantity equivalent to the total heat content of a system, equal to the internal energy plus the product of pressure and volume.

Entropy

A thermodynamic quantity representing the degree of disorder or randomness in a system.

Hydrophobic effect

The observed tendency of nonpolar substances to aggregate in an aqueous solution and exclude water molecules.

Amphoteric

The characteristic of being able to react both as a base and as an acid, as seen in water.

Ka

The acid dissociation constant, expressed as $\frac{[H^+][A^-]}{[HA]}$.

Henderson-Hasselbalch equation

$$pH = pK_a + \log\frac{[A^-]}{[HA]}$$

Open system

A material system in which mass or energy can be lost to or gained from the environment.

First law of thermodynamics

The total energy of a system is constant; energy can neither be created nor destroyed.

Second law of thermodynamics

Every energy transfer or transformation increases the entropy of the universe.

Gibbs free energy equation

You know

Central Dogma of Molecular Biology

Proposed by Watson and Crick, it describes the flow of information: DNA -> RNA -> Protein.

Transcription

The synthesis of an RNA molecule from a DNA template.

Translation

The process by which mRNA is decoded and a protein is produced.

Nucleoside

A chemical unit consisting of a nitrogenous base and a sugar (ribose or deoxyribose) but no phosphate group.

Purines

Bases with a double-ring structure, including Adenine and Guanine.

Pyrimidines

Bases with a single six-membered ring, including Cytosine, Thymine (DNA), and Uracil (RNA).

A-form DNA

A condensed form of DNA with a deeper major groove and shallower minor groove that spirals to the right.

Z-form DNA

A left-handed helical form of DNA.

Hairpin

A secondary structure in RNA consisting of a stable loop formed by hydrogen bonding between bases on the same strand.

Polycistronic mRNA

mRNA that codes for more than one protein, found in prokaryotes.

Glycine

The only achiral amino acid because its alpha carbon is attached to two hydrogen atoms.

Stereoisomers

Two molecules that vary in configuration at one stereo center.

Fischer Projection

A simple 2D drawing of stereoisomers where horizontal lines are wedges and vertical lines are dashes.

Zwitterions

Bipolar molecules, such as free amino acids, that carry both a plus and a minus charge.

pI (Isoelectric point)

The pH at which an amino acid is neutral in charge.

Essential amino acids

Nutrients like Histidine, Leucine, and Tryptophan that must be obtained from the diet because the body cannot synthesize them.

Primary Protein Structure

The ordered sequence of amino acids and the peptide bonds that link them together.

Secondary structure

Local folded structures (alpha helix and beta pleated sheet) that form within a polypeptide due to interactions in the backbone.

Ramachandran diagram

A plot of the $\phi$ and $\psi$ angles that defines the secondary structure of a protein.

Motif (supersecondary structure)

Combinations of secondary structure present in many proteins that frequently exhibit similar functions.

Tertiary Structures

The overall shape of a protein molecule resulting from interactions of amino acid side chains.

Quaternary structure

The level of protein structure resulting from the association of two or more polypeptide subunits.

Denaturation

The loss of the native state and function of a protein due to the disruption of tertiary structure.

Chaotropic Agents

Substances like Sodium Dodecyl Sulfate (SDS) that disturb non-covalent interactions in proteins by increasing the entropy of water.

Chaperones

Proteins that limit regions available for intermolecular interaction to ensure proper folding occurs.

Ubiquitin

A molecule that binds to lysine residues of misfolded proteins to target them for destruction.

Proteasome

A complex that hydrolyzes proteins bound to ubiquitin.

Amyloid

A deposition of protein aggregates that exposes proteins normally hidden, typically formed from protein that is primarily beta-sheet.

Homologs

Proteins with sufficient similarity that they are thought to arise from a common ancestor.

Orthologs

Homologous proteins in different species that often share similar or identical functions.

Paralogs

Homologous proteins that arise from gene duplication within the same species.

Hemoglobin

A tetrameric protein in red blood cells whose primary function is to transport oxygen.

Heme

An iron-containing prosthetic group consisting of protoporphyrin IX and a central iron ion.

Tense (T) State

The quaternary structure of deoxyhemoglobin which is constrained by salt bridges and has lower oxygen affinity.

Relaxed (R) State

The quaternary structure of oxyhemoglobin where oxygen-binding sites are free of strain and have higher affinity.

2,3-Bisphosphoglycerate

A molecule that decreases hemoglobin affinity for oxygen to improve delivery to tissues by stabilizing the tense state.

The Bohr effect

The regulation of oxygen binding by hydrogen ions and carbon dioxide.

Sickle cell anemia

A genetic disorder caused by Valine replacing Glutamate, leading to hydrophobic packing and fiber formation.

Thalassemia

A blood disorder where normal tetramers of hemoglobin cannot form, often resulting from truncated beta-globin chains.