Chem 6b 17-20

3. Describe the structure and nomenclature of a disaccharide.

Disaccharides consist of two monosaccharide units, linked together with glycosidic bonds in the α or β orientation. The most important of them are sucrose, lactose, and maltose.

Define an enzyme

A biological catalyst that carries out metabolic reactions in living organisms

3. Describe the structure of peptides and proteins.

Both peptides and proteins are made up of strings of the body's basic building blocks - amino acids - and held together by peptide bonds. In basic terms, the difference is that peptides are made up of smaller chains of amino acids than proteins.

1. Define lipids

any of a class of organic compounds that are fatty acids or their derivatives and are insoluble in water but soluble in organic solvents. They include many natural oils, waxes, and steroids.

Differentiate between cellulose and chitin in terms of sugar composition.

chitin is a polymer of N-acetyl-D-glucosamine whereas the cellulose is a polymer of D-glucose.

Define and differentiate between denaturation and digestion of proteins.

denaturation only involves the unfolding of a protein, where quaternary, tertiary and secondary structures are disrupted but primary structure remains intact.J

Differentiate between a monosaccharide, a disaccharide and a polysaccharide.

monosaccharides are monomers of sugars and disaccharides are composed of two monomers whereas polysaccharides are composed of a large number of monomers

2. Describe the structure and nomenclature of monosaccharides.

monosaccharides have the formula as (CH2O) n. Here, the two hydrogen atoms and one oxygen atom associate itself to the central carbon molecule

Differentiate between trioses, tetroses, pentoses and hexoses and between aldoses and ketoses.

trioses have 3-C atoms, tetroses have 4-C atoms, pentoses have 5-C atoms, and hexoses have 6-C atoms.

Given the condensed structural formula of a molecule, identify which carbons are chiral and calculate the number of potential stereoisomers for that compound.

2^n=total possible sterioisomers n=chiral carbons

Define the active site

A region on an enzyme which binds to the substrate during a reaction

Recognize the structure of a wax.

A long-chain fatty acid linked through an ester oxygen to a long-chain alcohol.

Differentiate the reducing end from the nonreducing end of a di- or polysaccharide.

A nonreducing end of a sugar is one that contains an acetal group, whereas a reducing sugar end is either an aldehyde or a hemiacetal group

Describe the role of allosteric regulation in feedback inhibition of metabolic pathways.

Allosteric activators induce a conformational change that changes the shape of the active site and increases the affinity of the enzyme's active site for its substrate.

2. Describe the reactivity of amino acids

Amino acids react with each other in a typical acid-base neutralization reaction to form a salt. The reaction is simply the transfer of the -H (positive ion) from the acid to the amine and the attraction of the positive and negative charges.

Differentiate between amylose, amylopectin and glycogen and cellulose in terms of types of linkages between glucose units, frequency of branching and biological role.

Amylose is an unbranched, coiled chain and amylopectin is a long branched chain, of which some are coiled. Cellulose: Cellulose is a straight, long, unbranched chain, which forms H-bonds with adjacent chains. Glycogen: Glycogen is a short, many branched chains of which some chains are coiled.

Define transition state

An activated form of a molecule in which the molecule has undergone a partial chemical reaction; the highest point on the reaction coordinate.

3. Describe the utility of artificial inhibitors of enzymes, including an example of a commercial inhibitor, and differentiate between irreversible and reversible inhibition.

Artificial enzyme inhibitors block acetylcholinesterase, an enzyme which breaks down acetylcholine, and are used as nerve agents in chemical warfare. Examples of enzyme-inhibiting agents are cimetidine, erythromycin, ciprofloxacin, and isoniazid. An irreversible inhibitor inactivates an enzyme by bonding covalently to a particular group at the active site. A reversible inhibitor inactivates an enzyme through noncovalent, reversible interactions. A competitive inhibitor competes with the substrate for binding at the active site of the enzyme.

Describe temperature and pH effects on enzymes and why they have the effect they do.

At low temperatures, an increase in temperature increases the rate of an enzyme-catalyzed reaction. At higher temperatures, the protein is denatured, and the rate of the reaction dramatically decreases. An enzyme has an optimum pH range in which it exhibits maximum activity

Define a carbohydrate (CH2O, polyhydroxy aldehyde or ketone).

Carbohydrates are bio molecules which are polyhydroxy aldehydes or ketones made up of Carbon C, Hydrogen H and Oxygen O in the ratio (1:2:1)

5. Describe the structure and properties of biological membranes. a. Describe how and why form bilayers. b. Describe the structure and major components of a biological membrane

Cell membranes are thin enclosures that form closed boundaries. (2) Cell membranes are made up of lipids, proteins and carbohydrates. (3) Cell membranes consists of a phospholipid bilayer. (4) Cell membranes are held together by non-covalent interactions (5) Membranes are fluid-like structure.

Define coenzymes and cofactors, and describe the types of molecules that serve as coenzymes and cofactors.

Coenzymes and cofactors are molecules that help an enzyme or protein to function appropriately. Coenzymes are organic molecules and quite often bind loosely to the active site of an enzyme and aid in substrate recruitment, whereas cofactors do not bind the enzyme.

Recognize the structure of a disulfide bond and describe its role in maintaining protein structure.

Disulfide bonds make proteins less susceptible to unfolding; typically, they will link -sheets, -helices, and loops, which means that they primarily maintain tertiary structure, not secondary, which refers to local conformations, and is maintained largely by hydrogen bonds.

1. Describe and identify the common features of the structure of amino acids

Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom.

Define activation energy

Energy needed to get a reaction started

1. Describe how enzymes control the rate of biochemical reactions.

Enzymes are biological catalysts. Catalysts lower the activation energy for reactions. The lower the activation energy for a reaction, the faster the rate. Thus enzymes speed up reactions by lowering activation energy

2. Describe how enzymes regulate metabolic pathways

Enzymes lower the activation energies of chemical reactions; in cells, they promote those reactions that are specific to the cell's function.

Define epimer, anomer, mutarotation.

Epimer: One of a pair of stereoisomers that differ in the absolute configuration of a single stereocenter Anomer: A pair of anomers is a pair of near-identical stereoisomers that differ at only the anomeric carbon, the carbon that bears the aldehyde or ketone functional group in the sugar's open-chain form. Mutarotation:

Differentiate between fibrous and globular proteins.

Fibrous proteins are structural in nature, which means they help maintain cell shape by providing a scaffolding or a framework. On the other hand, globular proteins are functional, which means they carry out a specific biological function in the body

Recognize both the Fisher projection and Haworth projection (cyclic structure) of D-glucose, D-galactose and D-fructose.

Fischer projections are used for sugars in their open-chain form, Haworth projections are often used to depict sugars in their cyclic forms

Given the Haworth projection of a disaccharide, identify whether the linkage is an - or -linkage.

If the 'OH' are placed on opposite side of each other, they are alpha, if they are on the same side, it is a beta link i.e 'OH' are pointed diagonally opposite = alpha i.e 'OH' are pointed on the same side = beta

Define zwitterion be able to draw the structure of an amino acid (like alanine) in its zwitterionic form

Ions that have both a permanent positive charge and a permanent negative charge, though the compound is neutral overall

Recognize the structure of maltose, lactose and sucrose.

Maltose is composed of two molecules of glucose while sucrose is made up of one molecule of glucose and Lactose is a disaccharide derived from the condensation of galactose and glucose,

Define substrate

Molecules on which an enzyme acts

Describe how enzymes are regulated by other small molecules.

Most enzymes are controlled by changes in their conformation, which in turn alter catalytic activity. In many cases such conformational changes result from the binding of small molecules, such as amino acids or nucleotides, that regulate enzyme activity.

From a Fisher projection differentiate between D- and L- sugars.

On a Fisher projection, a D- sugar has the OH on the right, where as a L- sugar has the OH on the left

Differentiate between a peptide and a protein.

Peptides are generally considered to be short chains of two or more amino acids. Meanwhile, proteins are long molecules made up of multiple peptide subunits, and are also known as polypeptides. Proteins can be digested by enzymes (other proteins) into short peptide fragments.

4. Describe the redox characteristics of carbohydrates

Some sugars readily oxidize (monosaccharides) and their known as reducing sugars while others can oxidize into reducing sugars

Given a Fisher projection of an amino acid, differentiate between L- and D- amino acids, and indicate whether standard biological amino acids are L- or D- amino acids

The difference between L- and D- amino acids is determined by the placement of the 'OH' whether its on the Left (L-) or Right (D-)

Describe how solutions of optical isomers affect plane-polarized light.

The enantiomer, which is a mirror image will rotate plane-polarized light in the opposite direction

Describe how activation energy controls the rate of a chemical reaction and how an enzyme accelerates the rate of a chemical reaction.

The lower the activation energy for a reaction, the faster the rate

5. Describe the structure, nomenclature and biological roles of polysaccharides

They are long chains of carbohydrate molecules, composed of several smaller monosaccharides. These complex bio-macromolecules functions as an important source of energy in animal cell and form a structural component of a plant cell.

1. Distinguish between a structural isomer, stereoisomers that are geometric (cis-trans) isomers, and stereoisomers that are optical isomers. a. Differentiate and define: i. Chiral Carbon ii. Enantiomers iii. Superimposable iv. Optical Isomers

i A carbon atom that is attached to 4 different types of atoms/group of atoms ii one of two stereoisomers that are mirror images of each other iii. The ability for an object to be placed over another object, usually in such a way that both will be visible iv two compounds that contain the same number and kinds of atoms and bonds (AKA enantiomer)

6. Describe common chemical tests used to characterize carbohydrates, i.e. identify what the following tests analyze for, and, given a carbohydrate structure, be able to predict whether it would give a positive test. a. Benedict Test b. Barfoed Test c. Seliwanoff Test d. Benedict Test e. Iodine Test

i to check for the presence of reducing sugars in a given analyte ii detecting the presence of monosaccharides iii distinguishes between aldose and ketose sugars iv the presence of starch.

Define catalyst

substance that speeds up the rate of a chemical reaction