BIOLOGICAL CHEMISTRY

Microbiology – Chapter 2

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What is an atom?

What is an element?

What is the name of the table that keeps track of all the elements?

Why do biologists study chemistry??

Chemical changes in matter are essential to all life processes

All living things are made of the same kinds of matter that make up non-living things

If you learn how changes in matter occur you will understand the life processes of organisms

Elements

Elements – pure substances that cannot be broken down chemically into simpler kinds of matter

Of more than 100 elements fewer than 30 are important to livings

More than 90% of the mass of living things is composed of combinations of just: O, C, H and N

Elements

Chemical Symbol – usually part of the element’s name or the Latin word for the element

Organized into the periodic table of elements There are 118 elements, 94 are naturally occurring,

the rest are synthetic (made in particle accelerators) Elements listed by increasing atomic number Columns – groups of elements with similar properties

because of the number of electrons in their outer shell Rows - periods

Atoms – basic units of matter

-Atoms are the simplest particles of an element that retain all the properties of that element

-Atoms are so small that their true structure has not been observed

-Models of the atom help us understand their structure enough to predict how they will act in nature

Atoms

Structure – net electrical charge of zero a. Protons (charge +) 1 AWU b. neutron (charge 0) 1 AWU c. electrons (charge -) .008 AWU

AWU – atomic weight unit

Nucleus – central mass of an atom, contains protons and neutrons

Atoms

Electrons – high energy particles that move about the nucleus at high speeds in one of several different energy levels- Electrons in outer energy levels have more energy than those in inner energy levels

- Each energy level can only hold a certain number of electrons- 1st energy level can hold 2 electrons-2nd energy level can hold 8 electrons

- In most elements, the outer energy level is not filled

Atom

Number of Protons?

Atom

animation of an atom

Atomic number – the number of protons in the nucleus of the atom

Atomic mass – the number of protons plus neutrons in the nucleus of the atom

Isotopes

Isotope – A different form of an element which has the same number of protons

and electrons, but has a different number of neutrons

Carbon (C):-atomic number is 6 - it has 6

protons-mass number is 12 – it has 6

protons and 6 neutrons-C14 – isotope that has 8 neutrons

Hydrogen Isotopes

Isotopes

Radioisotopes – radioactive element forms whose nuclei can undergo spontaneous change in which charged particles and radiant energy are released

Atoms Activity

Complete worksheet on atoms

Finish for homework if not completed in class

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What is the positively charged particle in an atom called?

What is the negatively charged particle in an atom called?

What is the neutral particle in an atom called?

What is an isotope?

Compound

1. A pure substance made up of two or more elements combined chemically

2. The properties of compound differ from the elements it is composed of – H2O vs. H and O

3. The proportion of each kind of element are fixed – Water always H2O

4. Elements combine and form compounds to become more stable

5. Elements are more stable when their outer electron shells are filled

Bonds

Chemical bonds – forces link two or more atoms

a. Covalent bonds – sharing of electrons (water H2O)

b. Ionic bonds – transfer of electrons (sodium chloride NaCl)

Chemical Bond Animation

Molecules

A molecule is the simplest part of a substance that retains all of the properties of that substance and that can exist in a free state

Hydrogen gas (H2) Water (H2O)

Matter Activity

Complete “Composition of Matter” worksheet.

Finish what you don’t complete for homework.

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What is a compound?

What is a covalent bond?

What is an ionic bond?

2. INORGANIC CHEMISTRY

STUDY OF COMPOUNDS THAT DO NOT CONTAIN THE THREE ELEMENTS C, H, & O AT THE SAME TIME.

CAN CONTAIN TWO OF THOSE THREE AND ANY OF OTHER ELEMENTS

ORGANIC CHEMISTRY

LIVING THINGS DIFFER GREATLY FROM NON-LIVING THINGS

THERE MUST BE A BIG DIFFERENCE IN HOW THEY ARE CONSTRUCTED

THEY ARE ACTUALLY CONSTRUCTED OF THE SAME MATERIALS

THE ONLY DIFFERENCE IS IN HOW THEY ARE ORGANIZED

ALL BIOLOGY HAS A CHEMICAL BASIS

3. ORGANIC CHEMISTRY

STUDY OF CARBON COMPOUNDS - CHEMICAL BASIS FOR LIVING CELLS ALWAYS C, H, & O SOMETIMES NITROGEN & PHOSPHORUS USUALLY SMALL AMOUNTS OF METALS

THERE ARE “FOUR” DIFFERENT CLASSES OF ORGANIC COMPOUNDS Carbohydrates Lipids Proteins Nucleic Acids

Carbohydrates

Organic compounds of C, H and O

Used as energy sources in cells

Also found in several cellular structures such as bacterial capsules

They are synthesized from water and carbon dioxide during photosynthesis

Carbohydrates

Monosaccharides are the simplest carbohydrates

They are the building blocks for the larger carbohydrates (polysaccharides)

Glucose, galactose and fructose are examples of isomers – they have the same chemical formula C6H12O6

But their structures and properties are different

A. CARBOHYDRATES

Glucose

Represents the basic supply of energy in the world

Half of the world’s carbon exists as glucose

GLUCOSE – UNIVERSAL ENERGY

Disaccharides

Double sugars – composed of two monosaccharides held together by covalent bonds

They are made from glucose molecules through dehydration synthesis – water is removed as the new bonds are formed

Examples are: maltose – found in barley and used to ferment beer lactose – found in milk and digested by bacteria to form

yogurt, sour cream Sucrose – table sugar and is the starting point in wine

fermentation and may be a cause of tooth decay

DISACCHARIDE – TWO MONOSACCHARIDES

Polysaccharides

Complex sugars

Large compounds formed by joining together 100’s or 1000’s of glucose molecules Starch – used by bacteria as an energy source Cellulose – a component of the cell walls of plants and

molds and also used as an energy source by microorganisms

Polysaccharide

Polysaccharide animation

Polysaccharides Activity

Complete polysaccharides color worksheet

Finish for homework if not completed in class

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What are the 4 classes of organic compounds?

What 3 elements are carbohydrates made up of?

What carbohydrate is considered a universal source of energy?

B. LIPIDS

Dissolve in organic solvents, but not in water

Like carbohydrates, they are composed of C, H, and O, but with much less O

The best known lipids are fats

Fats are important long-term energy sources for living things

Fats are also components of cell membranes

LIPIDS

cell membrane animation

LIPIDS

Fats consist of a 3 carbon glycerol molecule and up to 3 long-chain fatty acids

2 major types of fatty acids: Saturated – contain the maximum number of H

atoms Unsaturated – contain less than the maximum

number of H atoms Unsaturated fatty acids are good for us – they

lower the levels of cholesterol in the blood

Lipid molecules are sparingly to insoluble in water. Lipids are hydrophobic because the molecules consist of long, 18-22 carbon, hydrocarbon backbones with only a small amount of oxygen containing groups. Lipids serve many functions in organisms. They are the major components of waxes, pigments, steroid hormones, and cell membranes. Fats, steriods, and phospholipids are very important to the functioning of membranes in cells and will be the focus of this tutorial. Fats (triacylglycerols)

LIPIDS

Other types of lipids: Waxes – long chains of fatty acids

Bee’s wax Plant leaves

Phospholipids – contain a phosphate group Cell membranes

Steroids – composed of several rings of carbon atoms with side chains Cholesterol Estrogen Testosterone

C. PROTEINS

Most abundant organic compounds of living thingsThey can be:

Structural Enzymes – regulate the rate of chemical reactions

They are composed of chains of amino acids

Each amino acid contains Carbon atom Amino group (NH2) Carboxyl group (COOH) Another side group

Amino Acids – there are 20

Proteins

Amino acids are joined together by peptide bonds

The sequence of amino acids is extremely important

One mistake changes the protein (mutations)

Protein Structure: Primary – AA sequence Secondary – AA chain twists into a corkscrew pattern Tertiary – Protein folds back upon itself

Proteins

Protein structure animation

D. NUCLEIC ACIDS

Some of the largest molecules found in organisms DNA – genetic material of the chromosomes that carries

the genetic code RNA – cell messenger that functions in protein construction

Composed of nucleotides Carbohydrate molecule (ribose or deoxyribose) Phosphate group Nitrogenous base

DNA – adenine, guanine, cytosine, thymine RNA – adenine, guanine, cytosine, uracil

Nucleic Acids

DNA is located in the chromosomes of the cell

It passes on the genetic information and directs protein synthesis

DNA molecule consists of 2 single strands of DNA in opposite directions arranged in a double helix ladder

Nucleic acids can not be altered without disrupting or killing the organism – this can help us control microorganisms

DNA Structure Animation

Acids and Bases

Degree of acidity or alkalinity is very important to living systems

You may hear the term pH a lot

What does this mean?

Acids and Bases

Water can dissociate into:

Hydroxide Ions OH-

Hydronium Ions H3O+

Acids and Bases

- pH is a measure of a solution’s hydronium ion concentration

-pH is a scale of 0-14

- an acid = more hydronium ions (H3O+)

- a base = more hydroxide ions (OH-)

Acids and Bases

Acids : Have more hydronium ions Have a sour taste In concentrated forms can be very corrosive

Example:

Strong acid – HCl (hydrochloric acid) Weak acid – CH3COOH (vinegar)

Acid Rain

Acids and Bases

Bases : Have more hydroxide ions Have a bitter taste Tend to feel slippery because they react with the oil

on our skin to form soap

Example:

Strong base – NaOH (sodium hydroxide) Weak base – NH4 (ammonia)

Acids and Bases

pH scale ranges from 0 – 14:

Solution with a pH of 0 is very acidic Solution with a pH of 14 is very basic Solution with a pH of 7 is neutral pH can be measured with pH paper or strips

Acid Rain

Acid rain is a rain or any other form of precipitation that is unusually acidic (low pH)

It can have harmful effects on plants, aquatic animals, and infrastructure

Acid rain is caused by emissions of compounds of ammonium, carbon, nitrogen, and sulfur which react with the water molecules in the atmosphere to produce acids

Formation results from both natural sources (volcanoes, decaying vegetation) and man-made sources (fossil fuel combustion)

Activity

Complete Acids/Bases worksheet

Finish for homework if not completed in class