BM

Week 3

Organic Chemistry: the study of naturally occurring and synthetic carbon-containing compounds

Carbon atoms are most likely to form covalent bonds with other atoms.

Hydrocarbons are linear chain of covalent carbon bonds

Biochemistry: the study of chemistry of living systems. Carbon is most important Atom in Biological molecules

Carbon: The Tetravalent nature of carbon will allow it to form 4 covalent bonds. Very stable under Octet Rule (8 electrons)

Bond Energy: a molecule’s stability is related to its electron configuration. The stability is expressed as Bond Energy (E). The amount of energy required to break a specific bond in 1 mole (6X10²³), not the energy store in the bond.

  • expressed in kilocalories/mole (kcal/mol) amount of energy needed to raise temp of 1 gram of water by 1*C

  • A kcal is equal to 1000 calories

Most non-covalent bonds in biologically important molecules have low bond energies.

The high E of covalent bonds prevent them from being broken by energy carried in the sunlight. UV is filtered out by the ozone layer, but can break covalent bonds.

Functional Groups: The nature of a hydrocarbon can be changed by removing a hydrogen and adding one or more functional groups.

  • Simplest example is -OH (Hydroxyl group). By replacing one Hydrogen (H) with OH group to ethane (CH3CH3), we get Ethanol (CH3CH2OH)

Water: indispensable for life. Accounts for 75-85% of cell’s weight.

  • Critical properties- cohesiveness, temp-stabilizing capacity, solvent properties

  • Water’s polity results from uneven sharing of electrons. Electrons spend more time around oxygen than hydrogen. Also a hydrogen bond

Hydrogen bonds: account for the high cohesiveness, high boiling point, high specific heat capacity (amount of energy needed to take from 0*C to 100*C-boiling), and high heat vaporization (amount of energy needed to take from boiling point to gas) for water.

Thanks to water, we can regulate our body temp. The heat is absorbed by water and goes into the hydrogen bonds without raising the temp.

Vaporization of water acts as a coolant

Water acts as a universal solvent by dissolving polar molecules

Solutes that dissolve readily in water are called Hydrophilic. (Polar)

Solutes not very soluble are called Hydrophobic

Water will form electrostatic bonds with results ions from dissociated molecules, forming Spheres of Hydration

Polymerization: long chains of repeating units (monomers)-proteins, nucleic acids, polysaccharides

Lipids are not polymers

Stepwise Polymerization of Monomers: synthesizing macromolecules-activation of monomer by bonding with a carrier molecule using energy (ATP), condensation reaction by removing water and one carrier molecule, polymerization.

Directionality: both ends o the polymer chain have their own ways

ATP=energy

Self-Assembly: the spontaneous folding of macromolecules. DNA can do this

When we deal with Proteins, Shape is Everything. If it isn’t shaped correctly it will not work.

Macromolecules of the Cell

Macromolecules: large organic molecules such as Carbohydrates, Proteins, Lipids, Nucleic Acids.

Carbs and fats are essential for cellular function.

3 main parts of cell:

  • Plasma Membrane: the boundary between the maternal and external environment

  • Nucleus: contains DNA

  • Cytoplasm: organelles

Proteins: important macromolecules found in all organisms and everywhere in the cell. Fall into 9 different classes:

  • enzymes- catalysts

  • Structural proteins- shape of cell and physical support

  • Motility proteins - muscle movement

  • Regulatory proteins-control

  • Transport proteins- move substances

  • Hormonal proteins- communication

  • Receptor proteins- enables cells to respond to chemical stimuli from the environment

  • Defensive proteins- protect again disease

  • Storage proteins- reservoirs of amino acids

Only 20 kinds of amino acids are used in protein synthesis

Proteins re polymers made of amino acids

No 2 different proteins have the same amino acid sequence

Every amino acid has the same basic structure.

All amino acids scepter glycine have an asymmetric carbon atom that bonded to a carboxyl and amine group

Stereoisomers:molecules tat ave the same molecular formula and sequence of bonded atoms, turns they differ in 3D orientation

Enantiomers: stereoisomers that are mirror images of one another

A peptide is two or more amino acids joined together by peptide bonds

Polypeptide: a chain of many amino acids joined by peptide bonds

A proteins contain one of more polypeptides.

Protein synthesis: elongation a chain of amino acids

Immediate product of amino acids polymerization is a polypeptide, not a protein

A polypeptide does not become a protein until it is folded in a way that it has a specific function

Proteins can be monomeric or multimeric.

Native conformation: stable 3D structure of a particular polypeptide

Proteins divided into 3 categories:

  • Fibrous- extensive regions of secondary structure and repetitive. Form filamentous and sheet-like structures. Found in connective tissue, tendons bones, muscles. keratin, collagen, elastin

  • Globular- rounded, each type has its own tertiary structure. A-helix and b sheet mix. Most enzymes

  • Membrane - interact with parts of the cell membranes. Fall into several broad categories depending on their location.

Nucleic acids: linear, polymers of Nucleotides. Peptide Bonds. Store, transmit, and express genetic info. DNA, RNA

  • DNA serves as the repository of genetic info

  • RNA plays several roles in expressing genetic info.

Nucleic acids all have a sugar, phosphate group, and Nitrogenous base

DNA is missing the Oxygen in the sugar group

Purines: adenine, Guanine. 6-ring and 5 ring together

Pyrimidines: Thymine, Uracil, Cytosine. Just a 6-ring

DNA backbone is the phosphate and the sugar

If there is sugar it’s out phosphate it is called a Nucleoside

Watson and Crick- 1953

Franklin’s do Wilkens proved double helix with X-ray diffraction image

DNA→ mRNA(transcription) -> leaves nucleus into the cytoplasm where ribosome bonds to it, creating a polypeptide with amino acids (translation).

Adenosine-derived molecules: Adenosine Triphosphate (ATP)= Nitrogenous base (adenine), ribose, triphosphate.

Outer phosphoanhydride bond is High energy. It’s the one we will break

Carbohydrates: Polysaccharide is the most abundant carb found in food. Long chains of monosaccharides bound o get her by Glycosidic linkages

Polysaccharides contain more than 10 monosaccharides.

General formula of monosaccharides is CH2O6. Have between 3-7 carbons

Most common monosaccharide is Aldohexose D-glucose (C6H12O6)

Chair confirmation of Glucose is most stable because there is less strain on the C-C bonds

Two ring forms of D-glucose: OH points down in Alpha (repeating units of starch and glycogen) and up in Beta (repeating unit of cellulose)

Alpha glycosidic bond is straight, Beta Glycosidic bond is at an angle

Lactose is a Beta glycosidic bond. Requires a different enzyme to break the bond.

Anaerobic process means there is no oxygen. Large colon is anaerobic

Most familiar storage polysaccharides are starch in plant cells and glycogen in animal cells and bacteria. How cells store energy

Starch and glycogen consist of a-D-glucose units linked by a-glycosidic bonds

Main chain is a-1,4 glycosidic bond. Branched spot is a1,6 glycosidic bond

Glycogen: branches every 8-10 and 8-12 long

Starch: branches 12-25. And 20-25 long

Glycogen stored mainly in the liver.

Mammals do not possess an enzyme capable of hyrolyzing the bond in cellulose. Repeating monomer is B-D-glucose linked by B-1,4 glycosidic bond. Cows have a bacteria in their gut that breaks it down