Chapter 2-Cell Chemistry and Bioenergetics

How to Read the Periodic Table

Covalent Bonds

- form when two atoms come in close contact and SHARE one or more of their outer-shell electrons

- atoms joined by two or more ________ cannot rotate freely around the bond axis

Weak Non-covalent Bonds

- have less than 1/20 the strength of a strong covalent bond

- have a cumulative strength effect

H Bonds

- strongest when the three atoms lie in a straight line

- form when an H atom is "sandwiched" between two electron-attracting atoms (usually O or N)

Hydrophilic

dissolve readily in water

Ionic

bond that generates two oppositely charged ions

Polar

molecules with uneven distribution of electron density, resulting in a partially positive and another partially negative end (dipole moment)

Hydrophobic

- nonpolar bonds are usually insoluble in water

- water molecules are not attracted to these molecules, therefore don't surround them

- repulse from water

Electrostatic Attractions

- occur between fully charged groups (ionic) and between partially charged groups (polar)

- weak in water

- inorganic ions also cluster around charged groups and further weaken these attractions

Acids

substances that release H ions (protons) into solutions

Weak Acids

do not completely dissociate, ie -COOH

Bases

substances that reduce the number of H ions in solution

- some combine directly with H ions, ie NH3 + H = NH4

- some reduce the number of H ions indirectly by producing OH ie NaOH = Na + OH-

Weak Bases

partially associated with H ions, ie -NH2

Condensation

- loss of water in a reaction

- energetically unfavorable

Hydrolysis

- gains water

- water breaks down larger molecules into smaller subunits

- energetically favorable

Sugars

are the small organic building blocks for polysaccharides, glycogen, and starch (in plants)

Fatty Acids

are the small organic building blocks for fats and membranes

Amino Acids

are the small organic building blocks for proteins

Nucleotides

are the small organic building blocks for nucleic acids

Monosaccharides

- A ___________ is a simple sugar and the most basic unit of carbohydrates

-he building blocks for more complex sugars

- general formula of (CH2O)n, where n can be 3, 4, 5, 6, 7, or 8 and have two or more hydroxyl groups

- contain either an aldehyde group and are called aldoses or a ketone group and are called ketoses

Sugar derivatives

Disaccharides

- the carbon that carries the aldehyde or ketone can react with any hydroxyl group on a second sugar molecule

- three common ________ - maltose (glucose + glucose), lactose (galactose + glucose), sucrose (glucose + fructose)

Oligosaccharides and Polysaccharides

simple repeated sugar subunits create large linear and branched molecules, short chains are _______________, longer chains are _________________

Nucleotide

consists of:

- an N-containing base (either pyrimidines or purines)

- a 5 C sugar (2 kinds of pentoses are used: B-D-ribose [used in ribonucleic acid (RNA)] and B-D-2-deoxyribose [used in deoxyribonucleic acid (DNA)]

- one or more phosphate groups (normally joined to the C5 hydroxyl or the deoxy/ribose sugar) and gives the nucleotide a negative charge

Pyrimidine

Purine

Nucleic Acids

nucleotides are joined together by PHOSPHODIESTER BONDS between the 5' and 3' C atoms of adjacent sugar rings

Nucleotides and the Functions of Their Derivatives

- di- and triphosphates carry chemical energy in their phosphoanhydride bonds, ie ATP

- combine with other groups to form coenzymes, ie CoA

- used as small intracellular signaling molecules in the cell, ie cAMP

Fatty Acids

- have a CARBOXYL GROUP at one end and a long hydrocarbon tail at the other

- unsaturated: one or more double bonds in their HC tail

- saturated: no double bonds

- stored in cells as an energy reserve through an ester linkage to GLYCEROL to for triacylglycerols

- have polar heads, hydrophobic tails

Carboxyl Groups

- if free, the ________ of a fatty acid will ionize

- most often are linked to other groups to form either esters or amides

Phospholipids

- major constituents of cell membranes

- two of the -OH groups in glycerol are linked to __________, third -OH group is linked to phosphoric acid

- phosphate linked to one of a variety of small polar groups, ie choline

Micelles and Liposomes

Nature of Soluble or Luminal Proteins vs Membrane Proteins?

soluble or luminal proteins are typically hydrophilic and exist in aqueous environments, while membrane proteins are largely hydrophobic

Triacylglycerols

form large, spherical fat droplets in the cell cytoplasm

Phospholipids and Glycolipids

form self-sealing lipid bilayers, which are the basis for all cell membranes

Lipids

water-insoluble molecules that are soluble in organic solvents, common lipids include steroids and polyisoprenoids, both made from isoprene units

Isoprene

Cholesterol

(steroid) found in many cell membranes

Testosterone

(steroid) male sex hormone

glycolipids

composed of two long HC tails and one or more sugars (no phosphate)

Catalysis and the Use of Energy By Cells

- ΔG determines whether a rxn occurs spontaneously

- enzymes do not affect free energy, only lower activation energy during a rxn

- the formation of an activated cell is due to an energetically unfavorable rxn

- ATP is the most widely used activated carrier molecule

- ATP joins two molecules together and drives anabolic rxns

Catabolic Pathways

- rxn that breaks down complex molecules into simpler ones, heat is lost

- exergonic

Anabolic Pathways

- process that synthesize complex molecules from simpler ones, they require energy, and it usually comes from ATP

- endergonic

Activation Energy

ATP Cycle

Molecular Interactions, Binding, Folding

- molecules are 3D via their folding and interactions

- molecular interations are driven by gibbs free energy

- molecules will interact, bind, and fold in order to reach their lowest state of free energy (lowest G)