Ch. 2 - The Chemistry of Biology

Matter

all materials that occupy space and have mass

What is matter composed of?

atoms

Atom

simplest form of matter not divisible into simpler substances

Protons

(+) subatomic particles

Neutrons

neutral subatomic particles

Electrons

(-) subatomic particles

4 Fundamental Forces

1. Gravity
2. Electromagnetism
3. Strong nuclear force
4. Weak Force

Electromagnetism

like charges repel, unlike attract

Strong nuclear force

Holds nucleus together

Weak force

Radioactivity (neutron)

What do all atoms share?

The same fundamental structure

Element

pure substances w/ a characteristic number of protons, neutrons, and electrons and predictable chemical behaviors

Atomic number

number of protons

Atomic mass

number of protons **and** neutrons

Isotopes

variant forms of the same element that differ in the number of neutrons

Atomic weight

average mass numbers of all isotopic forms

Electron orbitals

volumes of space surrounding the atomic nucleus where electrons are likely to be found

Molecule

a chemical substance that results from the combination of two or more **atoms**

Compounds

molecules that are combinations of two or more different **elements**

Formula/Mass Weight

sum of all of the atomic masses of the atoms a molecule contains

Chemical bonds

when 2 or more atoms share, donate, or accept electrons to form molecules and compounds

What are the three different types of chemical bonds?

1. Covalent bonds
2. Ionic bonds
3. Hydrogen bonds

Covalent bonds

* electrons are shared among atoms
* strongest

Polar covalent bonds

* unequal sharing (negative and positive pole)

Nonpolar covalent bonds

equal sharing

Ionic bonds

* one or more electrons from one atom are removed and attached to another atom which forms **positively charge cations** and **negatively charged anions**
* least important

Hydrogen bonds

**weak** bonds between hydrogen and other atoms

* electrons are not shared, lost, or gained

Organic chemicals

compounds containing carbon bonded to hydrogens

Ionization

aqueous dissociation of an electrolyte into ions

Functional group

a particular molecular combination that reacts in predictable ways and confers particular properties on a compound

What can functional groups help define?

The chemical class of certain groups of organic compounds

C Hopkins Cafe Mg NaCl

* Carbon
* Hydrogen
* Oxygen
* Phosphate
* Potassium
* Iodine
* Nitrogen
* Sulfer
* Calcium
* Iron
* Magnesium
* Sodium
* Chlorine

Functional Groups of Organic Compounds

* accessory molecules that bind to organic compounds
* confer unique reactive properties on the whole molecule

Hydroxyl Formula

R-OH

Where can hydroxyl be found?

Alcohols and carbohydrates

Carboxyl formula

R−COOH

Where can carboxyl be found?

Fatty acids, proteins, organic acids

Amino formula

R-CH(NH2)-COOH

Where can amino be found?

Proteins, nucleic acids

Ester formula

R-COO-R

Where can ester be found?

Lipids

Phosphate formula

Where can phosphate be found?

DNA, RNA, ATP

Carbohydrate

A compound containing primarily carbon, hydrogen, and oxygen in a 1:2:1 ratio

What is the general formula for Carbohydrates?

(CH2O)n

Dehydration synthesis

loss of water in a polymerization reaction

What is the function of carbohydrates?

polysaccharides provide cell structure, adhesion and metabolism

How does cellulose affect cell walls?

Cellulose provides the strength and rigidity of the cell wall

Chitin

* Polysaccharide similar to cellulose in chemical structure
* Major compound in the cell walls of fungi and the exoskeletons of insects

Peptidoglycan

* When polysaccharides are linked to peptide fragments
* Provides the main source of structural support to the bacterial cell wall

Gram-negative bacteria’s cell wall contains what?

Lipopolysaccharide

Lipopolysaccharide

LPS of gram-negative bacteria is an endotoxin w/ generalized pathologic effects such as fever

Glycocalyx

* attachment to other cells
* site for receptors
* carbohydrate-rich molecule

Glycosidic bonds

link of subunits of disaccharides and polysaccharides

Peptide

Molecule composed of short chains of amino acids, such as a dipeptide, tripeptide, and a tetrapeptide

Phosphodiester bond

Forms when **two hydroxyl groups** **in phosphoric acid** react w/ a **hydroxyl group** on other molecules, forming **ester bonds**

Disulfide bonds

Occurs between sulfur atoms on the amino acid cysteine

Lipids (what are they? created by? classification?)

* long hydrophobic, C-H chains attached to a glycerol molecule
* created by **dehydration synthesis**
* triglycerides, phospholipids, steroids and waxes

Triglycerides

* 3 fatty acids bound to glycerol
* Saturated/unsaturated
* Energy storage

Saturated fatty acid

has all carbons in the chain bonded to hydrogen w/ single bonds

Unsaturated fatty acids

Has at least one carbon-carbon double bond

Give an example of a more saturated fat?

Solid fats (butter)

Example of unsaturated fats

Oils (liquid fats)

Name some bad things **saturated fats** can do to you

* Raise your cholesterol levels
* Increase risk of heart disease
* low density lipoproteins

Name good things **unsaturated fats** can do to you

* Lower cholesterol levels

Structure of phospholipids

* Glycerol w/ 2 fatty acids + a phosphate group
* Bilayers of phospholipids form membranes

What does the structure of phospholipids provide?

Impenetrable barrier that accounts for the selective permeability and transport of molecules

How are amino acids attached in order to form proteins?

Through peptide bonds

Functions of proteins

support, enzymes, defense, transport, movement

Primary structure of a protein

* Series of amino acids bound in a chain
* Amino acids display small charged functional groups

Secondary structure of a protein

* Develops when CO- and NH- groups on adjacent amino acids form **hydrogen bonds**
* then folds the chain forming an alpha helix and beta pleated sheet

Tertiary structure of a protein

* forms when parts of the secondary structure interact by forming **covalent disulfide bonds** and other interactions


* creates a 3-D mass

Quartenary structure of a protein

* exists only in proteins that consist of more than 1 polypeptide chain
* typical of antibodies and some enzymes that act in cell synthesis

Structure of DNA

* adenine & thymine, cytosine & guanine
* Double Helix
* formed by **2 very long polynucleotide strands** linked along their length by **hydrogen bonds** between the **nitrogenous bases**

Structure of RNA

* polynucleotide that consists of a long chain of nucleotides
* **single strand** that contains **ribose sugar** instead of **deoxyribose**
* **uracil** instead of thymine

Three types of RNA

mRNA: messenger RNA

tRNA: transfer RNA

rRNA: ribosomal RNA

Purines

* two rings
* 2 types: adenine & guanine

Pyrimidines

* one ring
* 3 types: thymine, cytosine, and uracil

ATP

* adenosine triphosphate
* nucleotide: adenine, ribose, 3 phosphates

Function of ATP

transfer and storage of energy