Chapter 2: The Molecules of Cells

Matter: Anything that takes up space and has weight – can be solid, liquid or gas

Atoms: the building blocks of matter

Element: Substance that cannot be broken down into substances with different properties; composed of only 1 type of atom

•Only 92 naturally occurring elements (others are man-made)

•98% of body weight of organisms made up of only 6 elements: carbon, hydrogen, nitrogen, oxygen, phosphorous, and sulfur

Parts of an atom: •Protons (+) •Electrons (-)•Neutrons (0)

•Protons and neutrons are found in the nucleus•Electrons orbit shells around the nucleus

•Outer energy shell holds eight electrons

•Inner energy shell holds two electrons

•The number of electrons in the outer energy shell determines the chemical properties of the atom.

•Atom is most stable when the outer shell is filled

•Ex: Helium – 2 electrons in 1st shell Neon – 8 electrons in 2nd shell

•Elements in last column of periodic table have filled outer shells – Noble gases

•To become stable, atoms form bonds with other atoms

Using the periodic table:

•Atomic number = # of protons

•Atomic mass = # of protons + neutrons

•If number of protons = number of electrons, atom is electrically neutral

•Elements are arranged horizontally in order of increasing atomic number

•Elements are arranged vertically according to the number of electrons in the outer shell (valence electrons)

•Isotopes: atoms that differ in their number of neutrons

•Carbon has 3 isotopes:

•Carbon 12 (most abundant)

•Carbon 13

•Carbon 14 (radioactive - unstable)

•Molecules: Formed when atoms bond with other atoms; atoms can be same or different

•Ex: O2 or CO2

•Compound: Formed when atoms of different elements bond

•Ex: CO2 or C6H12O6

Chemical/molecular formula: shows kind and proportion of atoms of element/molecule

Ex: 5HCl 8C14Fe 6H2O C6H12O6 3CO2

Na+ 2N2

6O2 Cl-

Structural formula: Shows the arrangement of atoms within the molecule

The three-dimensional shape of molecules can be represented in two ways:

•Space-filling model closer to actual shape of molecule.•Shapes of molecules determine how they function in organisms.

•Ex: HIV binds to certain blood cells Enzymes fit with substrate to

help digest food

Types of bonds: ionic bonds, covalent bonds & hydrogen bonds

•In ionic bonds, atoms give up or accept electrons, resulting in ions.

•Ions with opposite charges (- or +) are attracted to each other and form an ionic bond.

Ionic Bonds

Animation

•In covalent bonds, atoms share electrons

Animation: forward to 0:50

Other ways to represent covalent bonds:

Single, double, triple covalent bonds:

Single:

Double:

Triple: :N:::N: NN N2 Nitrogen

Animation

• Within some molecules, the nuclei of the atoms within do not attract electrons equally, resulting in slightly positive and negative charges within the molecule

• Adjacent molecules with these positive and negative regions may be attracted and held together• These attractions are called van der

Waals forces• These are not as strong as covalent and

ionic bonds

• Hydrogen bonds (a strong type of van der Waals force) form when a covalently-bonded H+ is attracted to a negatively-charged atom in a neighboring molecule (such as oxygen in neighboring water molecule, or chlorine

in NaCl).

• Hydrogen bonds are relatively weak bonds.

• Without hydrogen bonding between water molecules, our body fluids would be gaseous.

•Oxidation is the loss of electrons; hydrogen atoms are removed from glucose.•Reduction is the gain of electrons; oxygen atoms gain electrons.•Remember OIL RIG (oxidation is loss, reduction is gain)

Acids and Bases

Water dissociates and releases hydrogen ions (H+) and hydroxide ions (OH-).

Acids are molecules that release hydrogen ions in solution.

HCl H+ + Cl-

**What your book doesn’t tell you…

When those H+ are released, they bond to water molecules, forming H3O+ (hydronium ions).

If the number of hydronium ions is greater than hydroxide ions, the solution is acidic.

Bases are molecules that either take up hydrogen ions or give off hydroxide ions in solution (also called alkaline).

NaOH Na+ + OH-

pH in moles/liter:1 x 10-6 [H+] = pH 61 x 10-7 [H+] = pH 71 x 10-8 [H+] = pH 8

Pure water contains 10-7 moles per liter of both hydrogen ions and hydroxide ions, so it is neutralGreater the quantity of H+, the more acidic the solution (greater quantity – smaller exponent).

•Buffers: substances that help to resist change in pH – do so by taking up excess H+ or OH- ions.

•Help maintain pH in blood, stomach acid, urine, and intestinal fluid – example of how your body maintains homeostasis!!!

Example of how buffers work:•Blood contains combination of bicarbonate ions and carbonic acid (which can dissociate as seen below)

•When H+ are added to blood, they combine with bicarbonate ions•When OH- are added to blood, it produces bicarbonate ions and water•The above 2 reactions keep pH in blood steady

Properties of Water Water makes up between 60 and 70% of

organisms’ bodies

Characteristics of water:

1. Liquid at room temperature

2. Universal solvent for polar molecules

3. Water molecules are cohesive

4. Temperature of water changes slowly

5. High heat of vaporization

6. Frozen water is less dense so ice floats

Some of these properties are due to water’s polarity

•Polarity Oxygen atoms are larger than hydrogen, so

electrons spend more time near oxygen, giving it a slight negative charge, and hydrogen a slight positive charge.

Why is polarity important?Makes water a universal solvent“Like dissolves like” – polar substances are good at dissolving other polar substances and substances that are ionic - hydrophilicPolar substances DO NOT dissolve substances that are non-polar (without charged ends) – hydrophobicPolarity helps chemical reactions to take place.

Negative ends of water are attracted to Na+

Positive ends of water are attracted to Cl-

CohesionBecause of polarity and hydrogen bonding, water molecules “stick together.”

Causes water to form dropletsCohesive forces are strong enough to cause water to act as though it has a thin “skin” on its surface – surface tension.

Lizard video

Polarity affects density•As water cools, hydrogen bonding becomes more rigid but also more open – makes ice less dense than liquid water.•Water freezes at surface first – insulates life beneath to survive winter.•Hydrogen bonding makes water liquid at room temperature

Adhesion - the attraction between water and something else; forms hydrogen bonds between water and molecules on other surfaces.

Capillary action – adhesion of water molecules allows water to move upward through narrow tubes

Ex: water moving through a stem of a plant, helps blood flow in blood vessels

Temperature moderationBecause of hydrogen bonds, water can absorb large amounts of energy

Absorbs lot of heat before it boilsHelps keep cells at an even temperature despite changes in the environment – homeostasis again!!Allows large bodies of water to maintain a relatively constant temperature.

Organic Molecules

• Molecules of life: carbohydrates, lipids, proteins, nucleic acids

• Always contain carbon and hydrogen (often oxygen as well)

• Why carbon? Carbon has 4 electrons in outer shell – can form covalent bonds with up to 4 other atoms.

•Carbon can share electrons with other carbon atoms to form a hydrocarbon chain

•Hydrocarbon chain can turn back on itself to form ring compound

•Organic molecules (carbs, protein, lipid, nucleic acids) are macromolecules – molecules joined together.

•Monomers – smaller building block molecules

•Polymers – when same type of monomers join together repeatedly

Polymer Monomer carbohydrate monosaccharides protein amino acid nucleic acid nucleotide

Functional groups – can be attached to hydrocarbon chains and cause the macromolecule to behave in a certain way.

Ex: -COOH (carboxyl group)

CarbohydratesImportance:• Quick energy and short-term energy

storage• Structural role in plants, bacteria, and

insects• Help cells to recognize one another

•Monomers of carbohydrates are the monosaccharides (single sugar):

•glucose – blood sugar•fructose – found in fruit•galactose – found in milk

•Glucose, fructose, and galactose are all isomers of one another – same molecular formula, C6H12O6, but different structural formulas

Fructose Galactose

Glucose

•Below are 3 ways to represent glucose:

• Disaccharide - made from linking two monosaccharides together.

• Examples of disaccharides:• Maltose = glucose + glucose• Sucrose = glucose + fructose• Lactose = glucose + galactose

Sucrose

•When monomers join to form polymers, water is removed – condensation synthesis

•Also called dehydration synthesis******•When polymers are broken down, water is added - hydrolysis

Animation of condensation synthesis and hydrolysis

Animation

•Polysaccharides – long polymers that contain many glucose units

•Ex: Starch -can be up to 4000 glucose units

•Ex: Glycogen – after eating starchy foods, the body converts glucose in the blood into glycogen – stored in liver and released as needed

•Ex: Cellulose – found in plant cell walls. •Glucose units joined in such a way that we can’t digest it – passes through as roughage – may help prevent colon cancer

•Foods they can be found in:•Simple sugars – mono and disaccharides:

•Fruit, milk, sweets, sodas, juices

•Starches – polysaccharides:•Breads, pasta, rice, corn, wheat, cereal, leafy vegetables, carrots

Lipids

• Examples:

• Fats (triglycerides) - solid at room temp. – animal origin

• Oils - liquid at room temp. – plant origin

• Waxes – protective covering on plants & animals

• Lipids do not dissolve in water - nonpolar

Importance:

•Long-term energy reserves

•Form membranes in cells

•Hormones such as testosterone and estrogen

•Insulation, nerve impulses

•Repel water – duck feathers

•Structure – 1 glycerol plus 3 fatty acid molecules

•Fatty acids are long chains of hydrocarbons ending in - COOH

• Saturated vs. unsaturated fatty acids:

• Saturated – no double covalent bonds between carbon atoms – makes butter and lard solids

• Unsaturated – have double bonds between carbon atoms

• Polyunsaturated – more than 2 double bonds – makes cooking oil liquid

• Unsaturated and polyunsaturated are better for you than saturated fats

Phospholipids - form cell membranes

Steroids -

Examples include cholesterol, and the sex hormones estrogen and testosterone.

•Foods they can be found in:•Butter, foods fried in oil, bacon, red meat, cheese

Proteins

Importance:

• Build living tissue - keratin makes up hair and nails, collagen supports tendons and ligaments, hemoglobin to transport oxygen in blood

• Act as enzymes to speed reactions

• Serve as transport carriers

• Act as antibodies

• Allow materials to cross cell membranes

Proteins are polymers of amino acids – central carbon atom bonded to a hydrogen atom, and amino group (-NH2), a carboxyl group (-COOH), and an R group – which differs between amino acids

Amino acids are joined by peptide bonds to form polypeptides.

Levels of organization:

• Shape of protein is related to its function.• When exposed to extremes in heat or pH,

proteins change their shape – undergo denaturation – normal bonding between R groups is disturbed.

• Change cannot be reversed – protein no longer works.

•Foods they can be found in:•Meat, eggs, cheese, beans, nuts, soy

Nucleic Acids

• Examples: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)

• Importance: molecules of inheritance – needed for cell reproduction and activities, and making proteins

•Structure – polymers of nucleotides.

DNA is double-stranded, with complementary base pairing – A and T, C and G always pair.