Lecture Notes: Molecular Biology Concepts (Elements to Facilitated Diffusion)

A comprehensive set of Q&A flashcards covering basic chemistry (elements, bonds, acids/bases, pH), nucleic acids, proteins, carbohydrates, lipids, cell biology, and experimental design concepts from the provided notes.

An element is a distinct type of substance; its atoms have a unique number of protons in the nucleus.

What is an element and what unique feature do its atoms have?

Atom.

What is the fundamental unit of an element composed of protons, neutrons, and electrons?

An atom or molecule that carries a full charge; positive if it has more protons than electrons, negative if it has more electrons than protons.

What is an ion and when is it positive or negative?

A structure made of two or more atoms held together by covalent bonds.

What is a molecule?

An attraction between two atoms based on shared electrons.

What is a covalent bond?

The tendency for an atom's nucleus to attract the shared electrons in a covalent bond.

What is electronegativity?

An asymmetry in the sharing of electrons due to differences in electronegativity, creating partial charges.

What causes a polar covalent bond?

When electrons are shared equally due to equal or roughly equal electronegativities.

When is a covalent bond nonpolar?

An attraction between a partial positive charge on a hydrogen atom and a partial negative charge on another atom.

What is a hydrogen bond?

A molecule that can readily interact with the partial charges on water.

What is a hydrophilic molecule?

A molecule that contains mostly nonpolar covalent bonds and cannot readily interact with water.

What is a hydrophobic molecule?

An ion or molecule that releases a proton.

What is an acid?

An ion or molecule that acquires a proton.

What is a base?

The concentration of protons in a solution; the negative base-10 logarithm of [H+].

What does the pH scale express?

A molecule made up of a phosphate group and a nitrogenous base bonded to a 5-carbon sugar.

What is a nucleotide?

A molecule made up of nucleotides linked to form a chain or strand.

What is a nucleic acid?

Covalent bonds between the phosphate group on the 5' carbon of one nucleotide and the hydroxyl group on the 3' carbon of a second nucleotide.

What is a phosphodiester bond?

Hydrogen bonding between A-T (or A-U in RNA) and G-C pairs in a nucleic acid.

What is complementary base pairing?

The sequence of nucleotides in a nucleic acid, read 5' to 3'.

What is the primary structure of nucleic acids?

Formation of a double helix in DNA or a stem-and-loop structure in RNA based on base pairing.

What is the secondary structure of nucleic acids?

The backbone of nucleic acids consisting of 5-carbon sugars and phosphate groups; bases project from it.

What is the sugar-phosphate backbone?

DNA or RNA strands that align in opposite 5' to 3' orientations.

What are antiparallel strands?

A small subunit that can be linked covalently to form a polymer.

What is a monomer?

A large molecule made up of covalently bonded monomers.

What is a polymer?

A proposed explanation for observations.

What is a hypothesis?

A statement of an outcome that should occur if the hypothesis is correct.

What is a prediction?

The 'not' or 'no effect' contrast to the hypothesis being tested.

What is a null hypothesis?

A group that experiences experimental conditions aligned with the proposed mechanism.

What is a treatment (experimental) group?

A comparison group representing the normal or no-treatment condition.

What is a control group?

Aspects of the design used in both control and experimental groups to reduce bias and confounding.

What are controlled conditions in experiments?

The variable that is measured to assess the effect of the treatment; relevant to the hypothesis.

What is an outcome variable?

Building blocks that connect via covalent bonds to form proteins.

What are amino acids?

Amino group: NH2; can pick up a proton to form NH3+.

What is the amino group?

Carboxyl group: COOH; can lose a proton to form COO-.

What is the carboxyl group?

A highly variable group of atoms bonded to the central carbon of an amino acid.

What is an R-group?

The covalent bond that forms between the carboxyl group of one amino acid and the amino group of another.

What is a peptide bond?

The sequence of amino acids, linked via peptide bonds.

What is protein primary structure?

Formation of alpha helices and beta-pleated sheets; stabilized by hydrogen bonds between backbone atoms.

What is protein secondary structure?

Folding into a 3-D shape stabilized by hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions.

What is protein tertiary structure?

An interaction between a positively charged ion and a negatively charged ion.

What is an ionic bond?

Interactions that stabilize hydrophobic regions by minimizing contact with water.

What are hydrophobic interactions?

Assembly of multipart proteins from folded subunits, stabilized by hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions.

What is protein quaternary structure?

Unfolding or loss of 3-D structure (secondary, tertiary, quaternary) often due to heat or pH changes.

What does denaturing mean in proteins?

An organic molecule with a carbon chain, a C=O group, and C-OH groups; can be linear or ring; also called a simple sugar.

What is a monosaccharide?

A covalent bond that links monosaccharides together to form polymers.

What is a glycosidic linkage?

A polymer made up of many monosaccharides joined by glycosidic linkages; synonymous with polysaccharide.

What is a glycan?

A family of molecules that includes both monosaccharides and glycans.

What are carbohydrates?

A molecule that does not dissolve in water.

What is a lipid?

Contains only single bonds.

What characterizes a saturated hydrocarbon chain?

Contains one or more double bonds.

What characterizes an unsaturated hydrocarbon chain?

A lipid comprised of three fatty acids attached to glycerol.

What is fat?

A lipid with a four-fused-ring structure.

What is a steroid?

A lipid with a hydrophilic head (phosphate group and another polar group) and a hydrophobic tail.

What is a phospholipid?

A molecule with both a hydrophobic region and a hydrophilic region.

What does amphipathic mean?

The ability to conduct metabolism and reproduce.

What is life in biological terms?

Chemical reactions and processes enabling organisms to take in resources and process them for growth and reproduction.

What is metabolism?

A living being.

What is an organism?

A membrane-bound volume with metabolic processes inside; the smallest unit of life.

What is a cell?

A protein on the inner or outer surface of a cell membrane.

What is a peripheral membrane protein?

A protein that spans the lipid bilayer of a cell membrane.

What is a transmembrane protein?

The energy of motion.

What is kinetic energy?

Movement of ions or molecules from an area of higher concentration to an area of lower concentration.

What is diffusion?

The tendency of systems to move toward higher disorder or randomness.

What is entropy?

Movement of water across a cell membrane from higher water concentration to lower.

What is osmosis?

A difference in a substance's concentration in space, usually across a membrane.

What is a concentration gradient?

The energy of position.

What is potential energy?

The ability to do work.

What is energy in biological terms?

Diffusion of substances across cell membranes through integral membrane proteins.

What is facilitated diffusion?