ch. 1 the chemistry of life general chemistry atoms molecules and compounds the structure of atoms...

Ch. 1 The Chemistry of Life General Chemistry

Atoms Molecules and Compounds

The Structure of Atoms Reactions in Living Cells

Reactions in Living Cells Chemical Bonds Ions and Living Cells

Biochemistry Organic Compounds and Life Carbohydrates Lipids Proteins Nucleic Acids

Genetic Coding in the Cells The Double Helix The Functions of DNA

The Chemistry of Life Is water a chemical?

All organisms are composed of chemicals.

An understanding of life requires an understanding of chemistry.

Atoms, Molecules and CompoundsWhy is water important

to living things?

A molecule of water would be the smallest unit that would have the essential properties of water.

An element is a substance that cannot be broken down into simpler substances. (ex: Hydrogen and Oxygen)

Atoms, Molecules and CompoundsWhat is the smallest

unit of an element?

John Dalton’s experiments showed elements were composed of minute particles.

Atoms are the smallest unit of an element that still has the property of that element.

Atoms, Molecules and CompoundsWhat happens when atoms

combine?

Molecules are made from atoms – can be more than one type (O2 or CO2).

Chemists have given elements a symbol – H : hydrogen, C : carbon etc…

About 97% of the compounds in organisms are composed of C, H, O, N, P and S

Atoms, Molecules and CompoundsThe number of atoms

of each element in a molecule is shown by the subscript.

Carbon Dioxide : CO2

Ammonia : NH3

The Structure of an AtomWhat are atoms made

of?

Atoms are built of smaller subatomic particles:Electrons (-)Protons (+)Neutrons (0)

Protons and neutrons remain in the center, or nucleus, of the atom.

The Structure of an AtomHow are electrons situated

in an atom?

Electrons move in electron shells around the nucleus.

Shells are separated by energy levels - closer the shell, tighter the hold.

The first shell can hold 2 electrons, the second shell, 8 and the third, 8

H : 1 e-, C: 6 e-, O: 8 e-, etc…

The Structure of an AtomAtoms have an equal

number of protons and electrons – thus no charge.

Atoms with unfilled shells want to lose or gain electrons - basis for chemical reactions.

Atoms of the same element that differ in their number of neutrons are called isotopes.Oxygen-16, Oxygen-17,

Oxygen-18

Chemical ReactionsWhen atoms share or

transfer electrons from their outermost shell – chemical bonds form.

Chemical reactions involve the making and breaking of these bonds.

2 H2O 2 H2 + O2

The equation is written to balance the number of atoms on both sides of the arrow (Law of the Conservation of Matter)

Chemical ReactionsThe arrow in a chemical

reaction points from reactants to products.

Activation energy is the amount of energy needed to get a chemical reaction started.

Energy may need to be supplied from an outside source.

Chemical BondsWhat is an ion?

When electrons move from one atom to another atom – an ion will form.

Ex: Na – Cl

An ionic bond is the attraction between oppositely charged ions: NaCl

Chemical BondsHow can atoms fill

their outer most shells with electrons?

In a covalent bond, two atoms share one or more pairs of electrons.

Ex: H2

Ex: H2O

Chemical BondsHow do electrons move

around a water molecule?

In water, the oxygen end is slightly negative and the hydrogen end slightly positive – polar molecule.

Hydrogen bonds are weak bonds between polar molecules.

Structural FormulasWhat is a structural

formula?

Structural formulas show the number and arrangement of atoms in a molecule.

If atoms share two electrons a double bond forms, three, a triple bond.

H-H, O=C=O

Ions and Living CellsHow does salt dissolve

in water?

Na+ is attracted to the negative end of water and Cl- is attracted to the positive end of water.

Ions are important for maintaining water balance in living organisms.

Ions and Living CellsHow does the ionization of

water affect living organisms?

When a nonionic compound like water is converted to ions, the process is called ionization.

The result is a positively charged hydrogen ion (H+) and a negatively charged hydroxide ion (OH-)

Ions and Living CellsIn ionization – a

hydrogen ion will combine with a water to form hydronium ion (H3O+) … we refer to the H+ number.

Ionization is rare 1 in 500 million water molecules.

Living cells need specific levels of H+ and OH-

Ions and Living CellsHow do we measure H+

and OH- ions?

pH Scale. (potential hydrogen)

Scale 0 – 14 (logarithmic – pH of 3 is 10x pH of 4)

pH of 7 has the same amount of H+ and OH- ions and is neutral (pure water).

Ions and Living CellsWhat is the difference

between an acid and a base?

A solution with more H+ ions is acidic and has a pH less than 7.

A solution with more OH- ions is basic (alkaline) and has a pH greater than 7.

Ions and Living CellsHow does pH affect

the body?

The pH of a cell’s interior helps to maintain the cell’s chemical reactions – a very specific pH is often required .

Blood at 7.4; 6.8 or 8.0 means death.

Ions and Living CellsHow do living organisms

cope with changes in pH?

Buffers help to prevent changes in pH caused by the addition of an acid or a base.

A buffer works by accepting H+ ions when their levels rise and donating H+ ions when their levels fall.

Organic CompoundsWhat are organic

compounds?

Organic compounds are composed of carbon, hydrogen usually oxygen and frequently nitrogen, sulfur, or phosphorus.

CO2, CO and H2CO3 are not organic.

Organic CompoundsWhat does the term

macro-molecule mean?

Carbon atoms combine in long chains to form complex macromolecules.

Other atoms attach to the carbon skeleton giving the macromolecule a specific structure and function.

Organic MoleculesWhat does a chain of macromolecules look

like?

A polymer is a long chain of single building blocks called monomers.

Organic CompoundsHow does water aid in the

building and breaking down of long chains of macromolecules?

Two monomers may attach by dehydration synthesis in which a water molecule is removed.

Two monomers may break apart by hydrolysis in which a water molecule is added.

CarbohydratesWhat are carbohydrates?

Carbohydrates are sugars composed of C, H and O in a 1:2:1 ratio.

The simplest are monosaccharides,

Glucose, galactose and fructose are monosaccharides which provide energy.

CarbohydratesWhat is a ring form?

In solution, glucose and other sugars, exist in their ring forms.

Carbons at the corners with an O.

CarbohydratesHow do we combine two

monosaccharides?

A disaccharide consists of two monosaccharides linked by dehydration synthesis.

Glucose – Glucose: Maltose

Glucose – Fructose: Sucrose

Glucose – Galactose: Lactose

CarbohydratesWhere do we find

long chains of glucose molecules?

Several glucose molecules bond to form polysaccharides.

Plants store glucose in long chains called starch

Animals store glucose as chains called glycogen in the liver and muscles

CarbohydratesWhy can’t I eat wood

if it’s made from glucose?

The polysaccharide cellulose builds the tough cell walls.

Made of B-glucose which is not easily hydrolyzed.

wood/cotton; insoluble fiber, cows/ termites – prokaryotes

LipidsWhat are lipids?

Lipids consist of fats and oils.

Composed of C, H and O.

The main role of a lipid is in long term energy storage and building structures.

LipidsWhy doesn’t oil and

water mix?

Lipids will not dissolve in water because they are nonpolar.

The building blocks of lipids are fatty acids and glycerol.

Three fatty acids and one glycerol make a simple fat or triglyceride.

LipidsHow do the fatty acid

chains determine how healthy a lipid is for you?

If a single bond connects the carbons, it is a saturated fat (solids).

If a double bond connects some of the carbons, it is an unsaturated fat (oils).

LipidsHow do lipids help build

our cell membrane?

Phospholipids forms when a molecule of glycerol combines with two fatty acids and a phosphate group.

Cholesterol is part of the membrane structure of animals – we make steroids etc. from cholesterol.

LipidsWhat is wax?

A wax is a simple lipid w/ a long-chain alcohol and fatty acid.

Coats leaves and stems to prevent water loss.

Carnuba wax is found on the leaves of Brazilian palm trees; used in floor and auto waxes.

Nucleic AcidsWhat are nucleic

acids? What are they made of? What is their job?

Nucleic Acids are macromolecules that determine the structure and function of proteins.

Source of genetic information in chromosomes and a link to generations past.

Nucleic AcidsWhat are the subunits of

a nucleic acid? What are the parts of the subunit?

Nucleic acids are composed of simple units called nucleotides.

3 parts:5-carbon sugar (ribose

or deoxyribose)Nitrogen basePhosphate group

Nucleic AcidsWhat are the two major

types of nucleic acids?

Ribose containing are called ribonucleic acids or RNA.

Deoxyribose containing are called deoxyribonucleic acids or DNA.

RNA is single stranded where as DNA is double stranded.

Nucleic AcidsHow do nucleotides

differ?

DNA may contain 1 of 4 bases: adenine, thymine, guanine and cytosine.

In RNA the base uracil replaces the bases thymine.

Three types of RNA produce proteins (mRNA, tRNA, rRNA).

ProteinsWhat are proteins? What

are they made of? What are they used for?

Proteins are organic compounds used in building structures, defense, communication etc..

C, H, O and N

Proteins are built from monomers called amino acids.

ProteinsWhat does an amino acid look

like?

Amino acids are composed of C, H, O, and N (two contain S)

Carbon atom attached to: Hydrogen atom (-H)amino group (-NH2)acid or carboxyl group (-

COOH)variable group (R)

R may be one of 20 groups (polar/ nonpolar resulting in hydrophillic/ hydrophobic aa’s)

ProteinsHow do amino acids

combine to form long chains?

The carboxyl group of one molecule bonds with the amino group of another (dehydration).

These peptide bonds result in a long chain or polypeptide (50-3000 aa’s).

ProteinsWhat makes hair

different than muscle? (they’re both proteins..)

The type, number and sequence of aa’s determine the proteins’ structure and function.

ProteinsDescribe the structures of

a protein.

primary structure (sequence)

secondary structure (Folds)

tertiary structure (spherical).

quartenary structure (Multiple chains).

ProteinsHow does having

hydrophobic or hydrophilic amino acids affect a proteins shape?

Hydrophobicity is determined by the varying polarities of the R-groups.

Which of these three shapes is this protein most likely to adopt in water?

Genetic Coding in CellsThe four nucleotides in

DNA differ only in their nitrogen bases.

Single ring pyrimidines:Thymine (T)Cytosine (C)

Double ring purines:Adenine (A)Guanine (G)

Genetic Coding in CellsNucleotides are

joined when the sugar of one nucleotide connects to the phosphate group of another.

This forms a sugar-phosphate backbone.

Genetic Coding in CellsScientists Franklin,

Watson and Crick discovered that DNA exists as a double helix.

A double helix is like a twisting ladder.

Genetic Coding in CellsThe pairing of bases are

due to their size and ability to form hydrogen bonds.

Adenine (A) always pairs with Thymine (T) and Guanine (G) always pairs with Cytosine (C).

If we know one strand, we can figure out the complimentary strand.

Genetic Coding in CellsGenes are units of

genetic information passed from parent to offspring.

DNA stores information in three base pair codes called codons.

Each codon represents an amino acid.