Ch. 2: Molecular Interactions

Ligand

Any molecule or ion that binds to another molecule (Ex: protein signal molecules and protein transcription factors.

Buffer

Any substance that moderates changes in pH

Functional group

Atoms that move from molecule to molecule as a single unit; occur repeatedly in biological molecules.

Decrease

Bases __________ the H+ concentration in a solution

R group

Because of the ___ ______ each amino acid reacts with other molecules in a unique way.

HCO3-

Bicarbonate ion

Lipids

Biomolecules made mostly of carbon and hydrogen

Nucleotides

Biomolecules that play an important role in energy and information transfer. ADP, ATP, cAMP.

Covalent bonds

Bonds created by sharing electrons with other atoms.

Van der waals interactions

Bonds that are weak, nonspecific interactions between atoms

Hydrogen bonds

Bonds that form between a hydrogen atom and a nearby oxygen, nitrogen, or flourine atom.

Ionic bonds

Bonds that have an electrostatic attraction between ions. (NaCl)

Amino acids

Building block molecules within proteins

Ca2+

Calcium ion

Disaccharides

Carbohydrate that consists of two rings and are made up of glucose plus another monosaccharide; Sucrose, maltose, lactose.

Cl-

Chloride ion

Important anions of the body

Chloride, Bicarbonate, Phosphate, and Sulfate

Form and function

Determined by the molecular interactions

Kinks

Double bonds cause ______ in fatty acids.

High-energy electrons

Electrons in certain atoms can capture energy from their environment and transfer it to other atoms (Bioluminescence)

Saturated fatty acids

Fatty acids that have no double bonds between carbons, so they are completely overwhelmed with hydrogens. The more "overwhelmed" a fatty acid is, the more likely it is to be solid at room temperature.

Monounsaturated fatty acids

Fatty acids that have one double bond between two of the carbons in the chain. For each double bond, the molecule has two fewer hydrogen atoms attached to the carbon chain.

Polyunsaturated fatty acids

Fatty acids that have two or more double bonds between carbons in the chain.

Hydrogen bonding and van der waals interactions

Free H+ in a solution can participate inn what two types of interactions

Polysaccharides

Glucose polymers. All living cells store glucose for energy in this form. Glycogen and Chitin in animals Cellulose and starch in plants

Triglyceride

Glycerol plus three fatty acids More than 90% of lipids are in this form

Low pH

High acidity is measured with a _____ _____.

H+

Hydrogen ion

Adhesive

Interactions between different molecules

Cohesive

Interactions between molecules of the same type

Substrates

Ligands that bind to enzymes and membrane transporters

Phospholipids

Lipid related molecule that is an important component of animal cell membranes.

Steroids

Lipid related molecule that is cholesterol based. (Ex: Cortisol)

Nonpolar

Lipids are ________ and therefore are not very soluble in water.

Carbohydrates, lipids, proteins, and nucleotides

List the four type of biomolecules.

Monosaccharides, disaccharides, and polysaccharides

List the three categories of carbohydrates.

Eicosanoids, steroids, and phospholipids

List the three types of lipid related molecules

Fatty acids

Long chains of carbon atoms bound to hydrogens, with a carboxyl or "acid" group at one end of the chain

High pH

Low acidity levels is measured with a _______ ______.

Mg2+

Magnesium ion

Glycosylated molecules

Molecules that a carbohydrate is attached to Example: glycoproteins, glycolipids, etc.

Biomolecules

Molecules that contain carbon, hydrogen, and oxygen

Hydrophilic

Molecules that have an affinity to water and are soluble in water

Nonpolar molecules

Molecules that have an even distribution of electrons

Polar molecules

Molecules that have regions of partial charge.

Hydrophobic

Molecules that repel from water and do not dissolve well in water

Glycerol and fatty acids

Most lipids have a backbone of _____ and 1-3 _______ ______

Reversibly

Noncovalent interactions allow proteins to associate __________ with other molelcules, creating functional pairings such as enzymes and substrates, or signal receptors and molecules.

Polypeptide

Peptide with 10-100 amino acids. Also serve as signalling proteins

Oligopeptide

Peptide with 2-9 amino acids

HPO42-

Phosphate ion

Peptides

Polymers of amino acids

Proteins

Polymers of amino acids

K+

Potassium ion

Cholesterol

Primary source of steroids in the human body.

Conjugated proteins

Protein molecules combined with another kind of biomolecule Example: lipoproteins

Secondary structure

Protein structure that contains covalent bond angle between amino acids. Contains a-helix and b-pleated sheets

Primary structure

Protein structure that is a sequence of amino acids in a peptide chain

Quaternary structure

Protein structure with multiple sub-units that are combined with noncovalent bonds Hemoglobin is bad up of four globular protein sub-units

Tertiary structure

Protein structure with three dimensional shape; Fibrous proteins (Collagen) and Globular proteins

Fibrous

Proteins that are made up of either long chains of a-helices or b-sheets; usually insoluble inn water and form important structural components of cells and tissues.

Globular

Proteins that have amino acid chains that fold back on themselves to create a complex tertiary structure containing pockets, channels, and protruding knobs.

Eicosanoids

Signalling molecules that act as regulators of physiological function. (Ex: prostaglandins)

Glycerol

Simple 3-carbon molecule that makes up the backbone of most lipids.

Monosaccharides

Simple one ring carbohydrates, simple sugars; Fructose, glucose, and galactose.

Na+

Sodium ion

Important cations of the body

Sodium, Potassium, Calcium, Hydrogen, and Magnesium

Covalent bonds

Strong chemical bond that requires energy to make and break it

SO42-

Sulfate ion

Solubility

The ability of a molecule to dissolve in water

Specificity

The ability of a protein to bind to a certain ligand or a group of related ligands

Proteolytic activation

The activation of an enzyme by peptide cleavage

Induced-fit model

The concept that substrate binding to an active site of an enzyme improves the fit between the two molecules.

Affinity

The degree to which a protein is attracted to a ligand

Carbohydrates

The most abundant biomolecule

Dissociation constant

The reciprocal of the equilibrium constant

Four

There are ______ types of biomolecules

Secondary

To be functional, a protein has to be at least a ___________ structure.

True

True or false: protein binding is reversible

Noncovalent bond

Type of bonds that include ionic bonds, hydrogen bonds, and van der waals interactions.

Free radicals

Unstable, reactive molecules with an unpaired electron. They are damaging to cells

Equilibrium

When the rate of protein ligand binding is the same as the rate of protein ligand dissociation.

Twenty

__________ different amino acids commonly occur in natural proteins.

Physiological classification of soluble proteins

1. Enzymes (metabolism) 2. Membrane transporters 3. Signal molecules (hormones & neurotransmitters) 4. Receptors (signalling) 5. Binding proteins (effect solubility) 6. Immunoglobulins 7. Regulatory proteins (transcription factors)

Cofactor

An ion or small organic functional group

Diglyceride

A glycerol plus two fatty acids

Ions

A molecule that gains or loses one or more electrons

Amphipathic

A molecule that has both hydrophilic and hydrophobic parts. (Phospholipid bilayer)

cAMP

A molecules important in the transfer of signals between cells.

Protein

A peptide with more than 100 amino acids.

b-pleated sheets

A secondary structure that is very stable and occurs in many proteins destined for structural uses.

pH

Acidity is measured in terms of_______

Increase

Acids __________ the H+ concentration in a solution

Nucleic acids

Also called nucleoide polymers (RNA and DNA), they store and transmit genetic information

Peptide bond

A bond where the amino group of one amino acids joins with the carboxyl group of the other, with the loss of water.

Oils

A category of lipids that are liquid at room temperature and make up most plant lipids

Fats

A category of lipids that are solid at room temperature and are mostly derived from animal sources

Disulfide bonds

A covalent bond that plays an important role in the shape of many globular proteins.

Modulator

A factor that influences either protein binding or protein activity.

Monoglyceride

A glycerol plus one fatty acid