BIOL4341 Lecture Notes Flashcards

Flashcards on Water, Amino Acids, and Proteins

Hydrogen Bond

Electrostatic attraction between the oxygen atom of one water molecule and the hydrogen of another.

Hydrophilic

Compounds that dissolve easily in water; generally charged or polar compounds.

Hydrophobic

Nonpolar molecules such as lipids and waxes.

Amphipathic

Molecules that contain both polar (or charged) and nonpolar regions.

Isotonic Solution

Osmolarity is equal to that of a cell’s cytosol.

Hypertonic Solution

Higher osmolarity than that of the cytosol.

Hypotonic Solution

Lower osmolarity than that of the cytosol.

Conjugate Acid-Base Pair

A proton donor and its corresponding proton acceptor.

Buffers

Aqueous systems that tend to resist changes in pH when small amounts of acid (H+) or base (OH–) are added.

Henderson-Hasselbalch Equation

Describes the shape of the titration curve of any weak acid.

Peptide Bond

Covalent bond formed through condensation and broken through hydrolysis.

Dipeptide

2 amino acids, 1 peptide bond.

Tripeptide

3 amino acids, 2 peptide bonds.

Polypeptide

Many amino acids, molecular weight < 10 kDa.

Protein

Thousands of amino acids, molecular weight > 10 kDa.

Multisubunit Protein

2+ polypeptides associated noncovalently.

Oligomeric Protein

At least 2 identical subunits.

Conjugated Proteins

Contain permanently associated chemical components.

Column Chromatography

First step is a buffered solution (mobile phase) that migrates through porous solid material (solid phase)

Electrophoresis

Visualize and characterize purified proteins using electric field.

Primary Structure

Covalent bonds linking amino acid residues in a polypeptide chain.

Secondary Structure

Recurring structural patterns.

Tertiary Structure

3D folding of polypeptide.

Quaternary Structure

2+ polypeptide subunits.

Mass Spectrometry

Measure molecular mass with high accuracy.

Native

Proteins in any functional, folded conformations.

Van der Waals Interactions

Dipole-dipole interactions over short distances.

Alpha Helix

Simplest arrangement, maximum number of hydrogen bonds.

Beta Conformation

Backbone extends into a zigzag.

Denaturation

Loss of three-dimensional structure sufficient to cause loss of function.

Renaturation (Refolding)

Process by which certain denatured globular proteins regain their native structure and biological activity.

Chaperone Proteins

Facilitate correct folding pathways or ideal microenvironments.

Globins

Widespread protein family with a highly conserved tertiary structure.

Association Constant

Provides a measure of the affinity of the ligand L for the protein.

Allosteric Protein

Binding of a ligand to one site affects the binding properties of another site on the same protein.

Heterotropic

Regulation in which the modulator is a molecule other than the substrate.

Antibodies

Bind bacteria, viruses, or large molecules identified as foreign and target them for destruction.

Enzyme inhibitors

Molecules that interfere with catalysis, slowing or halting enzymatic reactions.

Enzymes

Catalytic activity depends on the integrity of the native protein conformation.

Prosthetic Group

Metal ion or coenzyme that is very tightly or covalently bound to the enzyme protein.

Holoenzyme

Complete catalytically active enzyme together with its bound coenzyme and/or metal ions.

Apoenzyme or apoprotein

The protein part of a holoenzyme.

Induced Fit

The mechanism by which the enzyme itself undergoes a conformational change when the substrate binds, induced by multiple weak interactions with the substrate.

Enzyme Kinetics

The discipline focused on determining the rate of a reaction and how it changes in response to changes in experimental parameters.

Turnover Number

The number of substrate molecules converted to product in a given unit of time on a single enzyme molecule when the enzyme is saturated.

Enzyme Inhibitors

Molecules that interfere with catalysis, slowing or halting enzymatic reactions.

Competitive Inhibitor

Competes with the substrate for the active site of an enzyme

Uncompetitive Inhibitor

Binds at a site distinct from the substrate active site; binds only to the ES complex

Mixed Inhibitor

Binds at a site distinct from the substrate active site; binds to either E or the ES complex

Noncompetitive Inhibitor

Special case of mixed inhibition; affects the Vmax but not the Km

Regulatory Enzymes

Catalytic activity increases or decreases in response to certain signals.

Homotrophic Regulation

Regulation in which the substrate and modulator are identical.

Carbohydrates

Aldehydes or ketones with at least two hydroxyl groups, or substances that yield such compounds on hydrolysis.

Monosaccharides

Simple sugars, consist of a single polyhydroxy aldehyde or ketone unit.

Oligosaccharides

Short chains of monosaccharide units, or residues, joined by glycosidic bonds.

Disaccharides

Oligosaccharides with two monosaccharide units.

Polysaccharides

Sugar polymers with 10+ monosaccharide units.

Epimers

Two sugars that differ only in the configuration around one carbon atom.

Proteoglycans

Macromolecules of the cell surface or ECM consisting of 1+ sulfated glycosaminoglycan chain(s) joined covalently to a membrane protein or secreted protein.

Glycoproteins

Have one or several oligosaccharides joined covalently to a protein.

Glycomics

The systematic characterization of all carbohydrate components of a given cell or tissue

Glycoconjugate

Biologically active molecule consisting of an informational carbohydrate joined to a protein or lipid.