LG 3 Presentation OutlineMolecules of Cells

Carbon3 Carbon Bonding

Functional Groups in BiologicalMolecules2 Hydroxyl Groups –2 Carbonyl Groups –2 Carboxyl Groups –2 Amino Groups –3 Phosphate Groups –2 Sulfhydryl Groups –

Biological Molecules14 Carbohydrates –10 Lipids –10 Nucleotides

Proteins5 Amino Acids –

Levels of Structure2 Primary Structure –2 Secondary Structure –2 Tertiary Structure –2 Quaternary Structure –

Role of Enzymes6 Enzymes –

Enzyme Activity4 Activation Energy –4 Enzyme Specificity –2 Cofactors –2 Coenzymes –5 Transition State –6 Factors Affecting Enzyme Activity –

Effect of Enzyme Inhibitors2 Competitive Inhibition –2 Noncompetitive Inhibition –4 Allosteric Regulation –

Unit IV

Learning Goal 3

Analyze the molecules that make up cells.

Carbon

Carbon BondingCarbon atoms form 4 covalent bonds to fill their outer electron shells. This allows them to form a variety of chain and ring structures that form the backbone of all biological molecules.

• These are known as organic molecules.

• Molecules consisting of carbon and hydrogen are called hydrocarbons.

Functional Groups in Biological Molecules

• Hydroxyl GroupsConsist of an oxygen atom linked to a hydrogen (--OH).They give the molecule they are attached to a polar nature.Key component of alcohols.

• Carbonyl Groups

A carbon atom linked to an oxygen atom by a double bond (C=O).

Important molecules for cellular energy.

• Carboxyl GroupsA combination of a carbonyl group and a hydroxyl group. (--COOH).Characteristic functional group of organic acids because it releases hydrogen in water solutions.Examples are citric and acetic acid.

• Amino Groups

Contain a nitrogen atom bonded to two hydrogen atoms

(--NH2).

Functional group of amino acids which are the building blocks of proteins.

• Phosphate GroupsConsists of a central phosphorus bound to oxygen atoms and hydroxyl groups (--OPO3

2-).Form chemical bridges between organic molecules.Added or removed to release energy.Control chemical activity of many proteins.

• Sulfhydryl Groups

A sulfur atom is linked on one side to a hydrogen atom and on the other to a carbon chain (-SH).

Act a molecular fastener holding protein molecules in their folded form or linking protein subunits into larger structures.

Biological Molecules

CarbohydratesMonosaccharidesSmallest carbohydrate molecules.Consist of 3, 5, or 6 carbon atoms bonded to hydrogen.Can be linear or ring forms.Many exist as isomers, meaning same chemical formula but different molecular structures causing them to react differently.

• DisaccharidesConsist of two monosaccharides linked together by a dehydration synthesis reaction.Sucrose (fructose + glucose) is the sugar transported in plants and crystalized to form table suger.Lactose (glucose+galactose) is sugar found in milk.

• PolysaccharidesLong chains of monosaccharides linked to form macromolecules.Result from the polymerization of monosaccharide monomers into larger polymers.

• Plant Starches

Storage form of carbohydrates in plants.

Long chains of glucose molecules that are digestible by humans.

• Glycogen

Storage form of carbohydrates in animal livers.

Highly branched chains of glucose molecules.

• CelluloseMost abundant carbohydrate in nature.Primary structure of plant cell walls .Can be digested by herbivores, but not by humans. Still important fiber for healthy digestive functions.

• ChitinTough carbohydrate chains with nitrogen-containing groups.Main component of the shells of arthropods such as insects and crabs.Also cell walls of fungi such as mushrooms.

Lipids

• Neutral LipidsLipids are a group of water-insoluble, nonpolar molecules made up mostly of hydrocarbons.Neutral lipids have no charged groups at cellular pH.Consist of fats, oils, and waxes made from a glycerol backbone and 3 fatty acid side chains.

• Fatty Acids

Single hydrocarbon chains with a carboxyl group at one end.

If it contains the maximum number of hydrogen atoms is considered saturated.

Main component of fats which are semisolid.

If one or more double bonds link the carbon atoms it is considered unsaturated.These are the main component of oils which are liquid a biological temperatures.Unsaturated lipids are considered healthier in the human diet than saturated.

• PhospholipidsFormed from a glycerol backbone attached to two fatty acid side chains and a polar phosphate group.In a polar environment (such as water) phospholipids assume arrangements in which only their polar ends are exposed to water. This is the reason cell membranes form a lipid bilayer.

• SteroidsGroup of lipids with structures based on four carbon rings.Most abundant are the sterols which have a single –OH group linked to one end of the ring framework and a complex, nonpolar hydrocarbon chain at the other end.

Nucleotides and Nucleic Acids

• NucleotidesA nucleotide consists of three parts linked together by covalent bonds:1. a nitrogenous base (either a purine or a pyrimidine)2. a five-carbon, ring-shaped sugar (either ribose or deoxyribose)3. one to three phosphate groups

• Nucleotide Functions

Important molecules such as ATP (adenosine triphosphate) and GTP (guanosine triphosphate) are the primary molecules that transport chemical energy in cells.

Nucleotides are the building blocks (subunits) of nucleic acids.

• Nucleic AcidsDNA (deoxyribose nucleic acid)Consists of two nucleotide chains wrapped around each other to form a double helix.Sugar (deoxyribose) and phosphate molecules make up the backbone and pairs of nitrogen bases make up the center.Nitrogen bases come in four varieties: adenine, guanine, cytosine, and thymine.

• RNA (ribonucleic acid)

Single stranded chain of nucleotides bound together by sugar (ribose) and phosphate bonds.

Nitrogen bases are the same as DNA except uracil replaces thymine.

Proteins

• Amino AcidsCells use 20 different amino acids to build proteins.Amino acids consist of a central carbon atom attached to an amino group, a carboxyl group, and a hydrogen atom.The remaining bond of the central carbon is linked to different side groups.

Amino acids are linked into protein molecules by peptide bonds.These are formed by a dehydration synthesis reaction between the –NH2 group of one amino acid and the –COOH group of a second.A chain of amino acids formed this way is called a polypeptide.

Levels of Structure

• Primary Structure

The sequence of amino acids makes up a proteins primary structure.

One amino acid out of place can alter the entire structure and function of a protein such as in the disease sickle-cell anemia.

• Secondary Structure

The folding of an amino acid chain into various arrangements.

They are alpha helix, beta strands, and random coils.

• Tertiary Structure

The content of alpha-helical, beta-strand, and random-coil segments, together with the number and position of disulfide linkages and hydrogen bonds, folds each protein into its tertiary structure. This is its overall three-dimensional shape.

• Quaternary Structure

When two or more amino acid chains combine to form a protein it is known as quaternary structure.

Role of Enzymes

Enzymes

Proteins that increase the speed of reactions millions to trillions of times.

Many reactions would proceed too slowly at cellular temperature.

Enzymes have names ending in –ase.

Example: Enzymes that break down proteins are called proteinases or proteases.

Substances with the ability to accelerate spontaneous reactions without being changed by the reactions are called catalysts.

Enzyme Activity

• Activation Energy

Enzymes accelerate reactions by reducing the activation energy of a reaction.

This is the initial input of energy required to start a reaction.

Reactions that take place in biological systems would normally require a large input of heat.

Enzyme Specificity

• Each type of enzyme catalyzes the reaction of only a single type of molecule or group of closely related molecules. This characteristic is known as enzyme specificity.

The reacting molecule is known as the substrate.

The region of an enzyme that recognizes and combines with a substrate molecule is the active site.

Cofactors

Many enzymes include a cofactor, an inorganic or organic nonprotein group that is necessary for catalysis to take place. Many are inorganic ions like iron, copper, magnesium, zinc, and potassium.

Coenzymes

Organic cofactors, also called coenzymes, are complex chemical groups of various kinds. Many are derived from vitamins.

Transition State

Enzymes reduce activation energy by forming an enzyme-substrate complex know as the transition state.

Three mechanisms contribute to the formation of the transition state:

• Bringing the reacting molecules into close proximity.

• Orienting the reactants in positions that favor the transition state.

• Exposing the reactant molecules to altered environments that promote their interaction.

Factors Affecting Enzyme Activity

• Temperature and pHEnzymes typically operate best in the range of about 0-40 degrees Celsius. Above 40 degrees, the increasing kinetic motion begins to unfold the enzyme, reducing the rate of enzyme activity.

Most enzymes have a pH optimum near the pH of the cellular contents, about pH 7.

Exceptions are enzymes of the digestive tract such as pepsin.

• Substrate Concentration

At very low concentrations, substrate molecules and enzyme collide less often.

As substrate concentration increases so does reaction rate to a point called saturation.

Effect of Enzyme Inhibitors

Competitive Inhibition

Enzyme inhibitors are substances that reduce enzyme activity by combining with enzyme molecules.Inhibitors that combine with the active site compete with the substrate. This is called competitive inhibition.

Noncompetitive Inhibition

Inhibitors that combine with enzymes at locations other than the active site often alter the conformation of the enzyme.

Because they don’t compete directly with the substrate this is called noncompetitive inhibition.

Allosteric Regulation

Occurs by the reversible combination of a regulatory molecule with the allosteric site, a location on the enzyme outside of the active site.

Frequently allosteric inhibitors are a product of the metabolic pathway that they regulate.This is called feedback inhibition because as the product builds up it inhibits the activity of the enzyme.

LG 3 and 4 Terms

1. Organic

2. Carbohydrate

3. Lipid

4. Nucleic Acid

5. Protein

6. Enzyme

7. Activation Energy

8. Feedback Inhibition

9. Allosteric Site

10. Competitive vs Noncompetitive Inhibition

1. Oxidative Phosphorylation

2. Glycolysis

3. Citric Acid Cycle

4. Electron Transfer System

5. Fermentation

6. CO2 Fixation

7. Chloroplast Structure

8. Photosystems

9. Calvin Cycle

10. C4 Cycle