Unit 2: Molecular Biology

Active Site

A region on the surface of an enzyme to which substrates bind and which catalyzes the reaction.

Adhesion

Particles of different substances sticking together; in the case of water, it occurs as a result of the polarity of a water molecule and its ability to form hydrogen bonds.

Advantages of Immobilized Enzymes

They can easily separate from the product, retrieved enzymes can be reused, increases stability, and can be exposed to higher enzyme concentrations.

Amino Acids

Carbon atom bonds to 4 different things: amine group, carboxyl group, a hydrogen atom, an R group which is just represented by an R.

Amylopectin

A form of branched starch.

Amylose

A form of unbranched starch.

Anabolism

Reactions that create larger molecules from smaller ones, require energy supplied in the form of ATP.

Anions

Ions with a negative net charge.

Aqueous Solution

Water is the solvent in this type of solution.

Body Mass Index (BMI)

A screening tool used to identify potential health problems though other factors such as diet, physical activity, and family history also need to be assessed.

Body Mass Index Formula (BMI)

Mass in kilograms/(height in metres)^2.

Bohr-Rutherford Diagram

An atomic model which shows the number of electrons in each shell of an atom as well as the number of protons and neutrons.

Carbohydrates

Composed of carbon, oxygen, and hydrogen; hydrogen and oxygen are usually found in a ratio of 2:1; can be a monosaccharide, disaccharide, or polysaccharide .

Carbon

A nonmetal with 6 protons, 6, neutrons, and 6 electrons in its naturally found neutral state; important in organic compounds.

Catabolism

Larger molecules are broken down into smaller molecules, can release energy, which can be captured in the form of ATP.

Cations

Ions with a positive net charge.

Cellulose

Cellulose forms the plant cell wall, unbranched chains of β-glucose, hydrogen bonds link the molecules together, link molecules form bundles called cellulose microfibrils, very high tensile strength.

Chemical Enzyme Specificity

Substrates that are not chemically attracted to the active site won't be able to react.

Chitin

Made of β-glucose with an -NH2 group attached and is found on the exoskeleton of insects.

Cis Isomer

Hydrogen atoms are on the same side of the double bond in this case, and it causes a bend in the fatty acid chain.

Cohesion

Particles of the same substance sticking together; in the case of water, hydrogen bonds cause water molecules to stay close together.

Collision

The coming together of a substrate and active site.

Commercial Uses of Enzymes

Detergent, biofuels, brewing, medicine, bioengineering.

Condensation Reaction

When two monosaccharides are joined together to form a disaccharide with the release of a water molecule, hence its name.

Covalent Bonding

A bond that forms when two nonmetals share a pair electrons.

Denaturation

The process in which the protein unravels and loses its native shape, it becomes inactive and interactions between R groups are interrupted, and it can be caused by heat or changes in pH.

Dependant Variables (Enzymes)

Gas production, digestion of a solid, digestion of a liquid, colour change.

Dipole

The charge difference across the molecule.

Disaccharide

Consists of two monosaccharides joined by a covalent bond, linked by a condensation reaction, creates water.

Double Bond

Two pairs of shared electrons.

Enzyme-Substrate Specificity

The fact that enzymes only catalyze one biochemical reaction and thousands of reactions take place in cells, nearly all of which need to be catalyzed.

Enzymes

A globular protein which acts as a catalyst for biochemical reactions.

Examples of Disaccharides

Maltose (2 α-glucose), sucrose (α-glucose and β-fructose), lactose (β-galactose and β-glucose), cellobiose (2 β-glucose).

Examples of Water Insoluble Substances

Are mostly nonpolar; fat molecules, cholesterol.

Examples of Water Soluble Substances

Are mostly polar; sodium chloride, amino acids, glucose, oxygen.

Fibrous Proteins

These are long and narrow proteins, they are structural, generally insoluble in water, have a repetitive amino acid sequence, and are less sensitive to changes in heat and pH.

Functions Carried Out by Proteins

Catalysis (enzymes), muscle contraction (actin myosin), cytoskeleton, cell adhesion, membrane transport (Na/K pumps), immunity, tensile strengthening, blood clotting, transport of nutrients and gases, receptors, hormones, and packing of DNA (histone).

Gene (Biochemistry)

An unit of inheritance consisting of a specific DNA sequence and information for the amino acid sequence of a polypeptide is stored in a DNA sequence.

Globular Proteins

These are rounded or spherical proteins, they are functional, generally soluble in water, have an irregular amino acid sequence, and are more sensitive to changes in heat and pH.

Glucose

C6H12O6, 6 numbered ring with 1 side chain, ring contains five carbon atoms and one oxygen atom, one carbon atom form side chains, carbon atoms are numbered, hydroxyl (OH-) groups on carbon atoms one, two, and four points down, and up on three; is the primary biomolecule of cellular respiration.

Glycogen

Similar to amylopectin, made of α-glucose, but more branching, made by animals and some fungi, stored in the liver and some muscles in humans, glucose molecules are evenly added or removed, functions to store energy in the form of glucose.

Heat Capacity

The amount of heat needed for 1 g of a substance to change temperature by 1 degree Celsius; in the case of water, water has a high heat capacity as a lot of heat must be absorbed to break hydrogen bonds.

Hydrolysis Reaction

When a disaccharide is split and a water molecule is used as a source of hydrogen and a hydroxyl group.

Identifying a Carbohydrate, Lipid, or Amino Acid

Carbohydrates do not contain nitrogen, carbohydrates contain hydrogen and oxygen in a 2:1, lipids contain relatively less oxygen than carbohydrates.

Immobilized Enzymes

Enzymes that are attached to a material so their movement is restricted.

Independent Variables (Enzymes)

Temperature, pH, substrate concentration, presence of inhibitor(s).

Induced-Fit Model (Enzymes)

A model that theorizes that as the substrate approaches the enzyme, it induces a conformational change in the active and it changes shape to fit the substrate.

Ionic Bonding

A bond that forms between a metal and nonmetal through electrostatic attraction.

Isomers

Molecules with the same number and type of atoms, but with a different arrangement of those atoms.

Lactase

An enzyme produced by the human body that helps break lactose down into β-galactose and β-glucose; it is also an enzyme produced in humans that uses anaerobic production, too much can make your body sore.

Lactose-Intolerance

A condition where someone is not able to fully digest the sugar, lactose, as their body does not produce lactase.

Lipids

Insoluble in water enter composed of amino acids, contains carbon, hydrogen, oxygen, sulphur; two contain sulphur.

Lock and Key Model (Enzymes)

A model that says that a substrate is like a key, it has to fit into the enzyme, the lock, for it to be able to work and "open the door" or react in this case.

Metabolism (Enzymes)

The web of all the enzyme catalyzed reactions in a cell or organism.

Molecular Biology

A branch of biology focused on structures and functions at the molecular level.

Molecular Formula

A formula that expresses the number of atoms in a molecule but does not convey its structure.

Molecular Model

A model that conveys the structure of the molecule.

Monosaccharide

A single sugar units, simplest form of carbohydrate.

Monounsaturated Fats

There is only one double bond between the carbon atoms in this fat.

Neutral Fats

These are composed of a glycerol molecule attached to one (monoglyceride), two (diglyceride), or many (polyglyceride) fatty acids.

Nonogram

This is an alternative to calculating BMI, a ruler is used to draw a line from the body mass to height and where the line intersects is the BMI.

Nonpolar

This means that the electrons in the bond are shared equally, and there is no change of charge.

Nucleic Acids

DNA and RNA; carbon, hydrogen, oxygen, nitrogen, phosphorus.

Optical Isomer

These isomers are identical in every way except they are mirror images of each other.

Organic Compounds

Compounds that make up living things.

Other Elements that Bond With Carbon

Hydrogen, oxygen, nitrogen, phosphorus, sulphur.

pH (Enzymes)

As pH increases and H+ ions decrease, the rate of the reaction increases until the optimum rate is reached before the rate of the reaction decreases (pH still continues increasing).

Polar

This means that the electrons in the bond are not shared equally, one might have a partial negative charge and one might have a partial positive charge.

Polypeptide

Amino acids that are linked together in any sequence; contains between 4 and tens of thousands amino acids.

Polysaccharide

Consists of many monosaccharides units like together; starch, glycogen, cellulose.

Polyunsaturated Fats

There is more than one double bond between the carbon atoms in this fat.

Primary Protein Structure

Is basically an amino acid sequence and peptide bond, is read form the NH2 terminal to the COOH terminal.

Processes of Cells

Cell division, energy creation, energy utilization, energy specialization, cell communication.

Prosthetic Groups

Inorganic groups that bound to proteins.

Proteome

All the proteins produced by a cell, tissue, or organism and can vary by genome and environmental factors.

Quaternary Protein Structure

Is formed by a number of tertiary polypeptides joined together, an example of this is hemoglobin.

Ribose

C5H10O5, Ring is composed of four carbon atoms and one oxygen atom, and the side chain is formed of 1 carbon atom. carbon can be numbered, the hydroxyl group on carbon 1 points up, the hydroxyl groups on carbons 2 and 3 point down.

Saturated Fats

There is a maximum amount of hydrogens, so only single bonds between carbon atoms.

Saturated Fatty Acids

Carbon atoms form the unbranched chains, single bonds in saturated fatty acids, number of carbon atoms is between 14 and 20, one end is a carboxyl group (COOH), the other end is a carbon atom bonded to 3 hydrogen, other carbon atoms are bonded to 2 hydrogen atoms.

Secondary Protein Structure

Is a folding of the polypeptide backbone and stabilized by H-bonds, the three types include α-helix, β-pleated sheet, and open loops.

Single Bond

One pair of shared electrons.

Solute

The substance that is dissolved.

Solution

A liquid that is a homogeneous mixture of two or more substances.

Solvent

The dissolving agent.

Starch

Made by plants, used to store large amounts of glucose, energy storage, molecules can be added or removed, made of α-glucose.

Structural Enzyme Specificity

The 3D structure of the active site is specific to the substrate; substrates that don't fit won't react.

Structural Isomer

These isomers have the same chemical formula but a different chemical structure.

Substances Involved

Water, inorganic ions, (Na, Cl), polysaccharide, proteins, fatty acids, vitamins, nucleic acids (DNA, RNA).

Substrate

The reactant in a biochemical reaction.

Substrate Concentration (Enzymes)

As the concentration of substrate molecules increases, the rate of the reaction increases at decreasing rate, eventually becoming more and more constant.

Temperature (Enzymes)

As temperature increases, the rate of the reaction increases until the optimum temperature is reached before the increase of temperature decreases the rate of the reaction.

Tertiary Protein Structure

The three-dimensional form of a polypeptide where the amino acid chain links itself in places to form the unique twisted or folded shape of the protein, is stabilized by R group interactions, has a hydrophobic core and have functional properties.

Thermophile

Organisms that are able to withstand much higher temperatures before its enzymes denature.

Trans Isomer

Hydrogen atoms are on the opposite side of the double bond in this case, and it keeps the fatty acid chain straight.

Triglycerides

Formed by condensation from three fatty acids and one glycerol.

Triple Bond

Three pairs of share electrons.

Unsaturated Fats

There are one or more double bonds between carbon atoms.

Vitalism

Theory that the phenomena of life is due to a vital principle.

Water

An important molecule that is essential to life, it is made up of two slightly positive hydrogen atoms bonded together, and one slightly negative oxygen atom.

Ways to Immobilize Enzymes

Bonding enzymes together, attaching enzymes to surfaces, entrapping enzymes in gels.