Biochemistry: Carbon and Macromolecules Notes

Chemisty Basics

• $Atom$- Smallest Unit of an element that maintains the chemical properties of the element

1. Protons
2. Neutrons
3. Electrons

• $Molecule$- Two or more atoms that are contently bonded together

1. E levels or shells
2. Valence shells
3. Valence electrons

Chemical Bonds

• Covalent Bonds

1. Polar molecules
2. Non-polar molecules
3. Electronegativity

• Ionic Bonds

1. Compounds held together by ionic bonds are called __salts__
2. $Cations$- Positive charges
3. $Anions$- Negatively Charges

• $Hydrogen Bonds$- Depicted by as dots in chemical diagrams
• Van der Waals interactions or London Dispersion Forces

Properties of Water

• $High specific heat$- Amount of heat needed to change the temperature of 1 gram of a substance by 1 degree
• Excellent solvent
• High heat of vaporization
• Water is cohesive and adhesive
• Water expands as it freezes
• $Ice$- Hydrogen Bonds are stable
• $Liquid Water$- Hydrogen bonds constantly, break and reform

Carbon Properties

• Organic Chemistry
• Science dealing with the element carbon
• __Carbon__ helps make the four major groups of macromolecules
• Original source of carbon is from the carbon dioxide
• $Organic molecule$- A molecule that contains carbon atoms (generally bonded to other carbon atoms as well as hydrogen atoms)

Organic Molecules

• $Polymers$- Large molecules that formed by bonding individual units together. “Chains” of monomers
• $Monomers$- Linked together by covalent bonds. Single subunits

Carbohydrates

• Monosaccharides (sugar)

1. Glucose
2. Fructose
3. Galactose

Polysaccharids

• Cellulose

1. Plant
2. B-glucose (subunit)
3. 1-4 (bonds)
4. No branches

• Starch (Amylose and Amylopectin)

1. Plant
2. A-glucose
3. 1-4, 1-4, 1-6
4. Amylose has no branches, Amylopectin has branches (per 20 subunits)

• Glycogen

1. Animal
2. A-glucose
3. 1-4, 1-6
4. Branches (per 10 subunits)

Steroid structures

• They are secreted by three “steroid glands”- the adrenal cortex, tests, and ovaries- and during pregnancy derived from cholesterol

Hydroxyl

• Structure= -OH or HO-
• Name of compounds- Alcohols (can end in -ol)
• Ethanol- The alcohol present in alcoholic beverages
• Functional properties

1. Is polar as a result of the electronegative oxygen atom drawing electrons towards itself
2. Attracts water molecules, helping dissolve organic compounds such as sugars

Carbonyl (Acetone, simpliest ketone)

• Name of Compounds

1. Ketons if the carbonyl group is within a carbon skeleton
2. Aldehydes if the carbonyl group is at the end of carbon skeleton

• Propanal, an aldehyde
• Functional Properties

1. A ketone and idehyde may be structures isomers with different properties, as in the case for acetone and propanal

Carboxyl (Acidic Acids)

• Name of Compounds

1. Carboxylic acids, or organic acids

• Functional properties

1. Has acidic properties because it is a source of hydrogen ions
2. The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly
3. In cells, found in the ionic form, which is called a carboxylate group

Amino (Glycine)

• Name of compounds

1. Amine

• Functional properties

1. Acts as a base; can pick up a proton from the surrounding solution
2. Ionized, with a charge of 1+, under cellular conditions

Sulfhydryl (Ethancthiol)

• Structure

1. -SH or HS-

• Name of compounds

1. Thiols

• Functional properties

1. Two sulfhydryl groups can interact to help stabilize protein structure

Phosphate (Gylcerol Phosphate)

• Name of compounds

1. Organic phosphate
2. Transfer energy between molecules

• Functional properties

1. Makes the molecule of which it is a part an anion

Primary Structure is IMPORTANT

• Normal red blood cells and the primary structure of normal hemoglobin
• Sickled red blood cells and the primary structure of sickle-cell hemoglobin

4 Levels of Protein Structure

• $Primary$- Sequence of Amino Acids
• $Secondary$- Interactions between adjacent amino acids
• $Tertiary$- 3D folding of the polypeptide
• $Quaternary$- Arrangement of multiple polypeptides

Nucleic Acids

• DNA
• RNA
• ATP (Nucleotide)
• cAMP
• NADH
• NADPH

DNA v.s. RNA Nucleotides

• DNA= Long Term (Double stranded)
• RNA= Temporary (Single Stranded)
• A-T, A-U, C-G, C-G

• $DNA will make proteins$
• Phosphorous comes from rocks

Macromolecules