The Make-Up of Life

Biology 392 Chapter 2

Mrs. Gallagher

Tree of Life by Gustav Klimt

2-1 The Nature of Matter

What is everything made of?• Anything that has mass and takes of

space is called MATTER.Is there anything that is not

matter?

• The smallest unit that an element can be broken down to and still have the properties of that element is called an ATOM.

Organization of Matter

• Atoms usually do not occur alone, but exist with other atoms as:

–Elements (all of the same atoms)–Molecules or Compounds• Same or different atoms bonded

MATTER: anything that has mass & takes up space

ProtonsNeutronsElectrons

Does not contain C-C bonds

LIFE!

Organic

Molecules orCompounds

Inorganic

C-C, C-H bond

ATOMSElements: Shown in

Periodic Tablepure

bonded

Atomic Number# of protons

(and also # of electrons)

Chemical symbol

Name of Element

Atomic MassThe weight Of carbon

atom oraverage

weight of all isotopes

6

CCarbon12.011

Elements

• A substance which cannot be split into simpler substances by a chemical reaction

• A grouping of the same type of atoms– ORDER MATTERS!

• More than 100 elements exist (shown in the periodic table)

• Carbon Elements:

Elements found in Living Organisms

About 97% of the compounds present in organisms contain only six elements: CHNOPS

PINK: CHNOPS! BLUE: lesser elementsGREEN: trace elements

Source: Dept. of Chemistry, University of Florida

BONDING

• Atoms need to bond together to make molecules or compounds– “Molecule”is often used to refer to an

individual grouping. “singular”– “Compound”- larger conglomerate of

bonded molecules. • Molecules and compounds are

written out in a chemical formula: example- C6H12O6

Why do atoms bond?• An atom wants to have a complete

outer shell (called valence level) of electrons.

To do this, it can…• Share electrons with another atom• Give away its electron(s) in this level• Receive electrons from another atom

*Remember: an atom is when its outer orbital is filled

TYPES OF BONDS1. IONIC - One atom (very unstable) gives 1, 2 or 3 electrons

away to another atom. The atom that loses electrons becomes positively charged. The atom that gains the electrons becomes negatively charged. The opposite charges cause the atoms to “bond” together (opposites attract).

2. COVALENT- atoms share a pair of electrons (sometimes share 2 (double bond) or 3 (triple bond) pairs)

3. VAN DER WAALS-Attraction between oppositely charged areas of adjacent molecules

4. HYDROGEN- (will be discussed in detail in next section)

Na (sodium) is very unstable because it only has one e- in its outer orbital. Cl’s (chlorine) outer orbital is

almost filled. Na gives its lonely e- to Cl.

Na become Na+ Cl becomes Cl-

Their opposite charges cause them to be attracted to one another- This is an ionic bond.

Example of Ionic Bonding-NaCl

Electrolytes• A solution that conducts electricity.• Term for salts, specifically ions. • Main electrolytes in the body: Na+, K+, Ca2+, Mg2+ , Cl−

• Why are they important in your body?

– Role in regulating hydration of the body as well as blood pH

– Critical for nerve and muscle function

Example of a Covalent Bond

Example of Covalent Bonding- Water

Van der Waals forces• Attraction between oppositely

charged areas of adjacent molecules

*weaker than covalent bonds and ionic bonds

Learning Checkpoint• What is an ion?• Why is it important that atoms bond?• What causes atoms to bond?• Explain the difference between an

ionic bond and a covalent bond.• What are Van der Waals forces?

2-2 Properties of Water

Water!• What is the chemical formula for

water?• How much water covers the

Earth?• How much of your body is

water?• Is there water in food?• How long could you live without

water?

• H2O• 75% • 60-

70%• Yes!• 3 days

Properties of Water• Phases: Solid, Liquid, Gas• Polarity• Hydrogen bonds– Adhesion– Cohesion

• Making Mixtures– Solutions– Suspensions

• Making Acids and Bases

Water Density

• Ice is less dense than liquid water• When water freezes it forms a rigid

structure that makes the cube spread- it becomes larger and less dense

• Benefits:– Fish and plant life can survive in liquid

layers of water under ice

PHASE CHANGES: the closeness and speed of the compounds

Polarity

• Water is polar

• Although the compound is neutral overall there is a shift of charge within the compound

The much larger atom, Oxygen, pulls more on the shared e-

This end of the compound becomes slightlymore negative.

Hydrogen ends become slightly

positive

Hydrogen Bonding• Due to polarity, water compounds

attract to one another• Slightly negative oxygen attracts

slightly positive hydrogen from another compound

• This attraction among water is COHESION.

• Water is also attracted to other materials. This is ADHESION.

COHESION

Water compounds attractTo glass molecules

And form a meniscus

Water compounds attract To one another-

causes water to “bead”

ADHESION

Capillary Action!• Water “climbs” up plant veins by attracting

to the sides (adhesion) and attracting to each other (cohesion)

The greatest solvent on Earth!

• Water’s polarity allows it to break ionic bonds of other compounds…creating free ions.

Mixtures Two or more elements physically mixed

together but not chemically combined (not bonded)

1. SOLUTIONS- a solute is dissolved into a solvent – Distributes evenly– “Like dissolves Like”– Ex: Koolaid, salt water

2. SUSPENSIONS- added substance does not dissolve but breaks into small enough pieces that it remains suspended in the water and does not settle out.- Ex: blood

Learning Checkpoint

• Why does ice float on a lake?• Explain the polarity of water – how

are the charges distributed?• What is the difference between

adhesion and cohesion?• Explain the difference between a

solution and a suspension.

Water DissociationWater can break apart on its own into 2

charged ions

Acids and Bases

Water can react to form individual ions:

H2O H+ + OH-

• In pure water this occurs naturally but the amount of H+ is always = to the amount of OH- so water remains neutral

pH scale: “the power of Hydrogen”

• Some solutions made with water become acidic or basic. This is determined by the amount of H+ (hydrogen ions) in the solution

• pH = - log [H+]

• Because it’s logarithmic, each pH unit represents a tenfold difference in concentration of H+ ions. This means something with a pH of 4 is 10 times more acidic than something with a pH of 5.

ACID: Any compound that forms H+ ions in solution

BASE: Any compound that forms 0H- ions in solution

pH and Living Things• pH values in living cells are usually

kept between 6.5 and 7.5– Optimal pH for chemical reactions to

take place in the body– Any switch in pH could cause

serious/fatal problems

2-3 Carbon Compounds• Why Carbon?– Carbon can from 4 covalent bonds (can create

many different compounds)– Carbons can bond to one another forming

large chains or rings• Linking of carbons can form very large

molecules called Macromolecules• Each individual unit is called a monomer.

When they are linked together they are called a polymer.

• 4 macromolecules necessary for life: carbohydrates, lipids, protein, nucleic acids

Nucleic Acid

• Contain hydrogen, oxygen, nitrogen, carbon and phosphorus

• Monomer- nucleotide• Polymer- DNA or RNA• Store or transmit genetic information*Nucleic Acids will be studied in greater

detail when we study genetics

Carbohydrates

• Made of carbon, hydrogen and oxygen (ratio of 1:2:1)

• Monomer- monosaccharides (simple sugars): glucose, galactose and fructose– Disaccharides- 2 sugars linked together:

sucrose, maltose, lactose

• Polymer- polysaccharides: glycogen (animals), starch and cellulose (plants)

• Main source of energy

Lipids

• Made mostly of carbon and hydrogen and some oxygen

• Not soluble in water: fats, oils and waxes• Monomer: all lipids have an end called

glycerol in which fatty acid chains attach• Polymer- lipid• Used to store energy, also for membrane

structure

Saturated vs. unsaturated fats

Saturated- no double bondsbetween carbons, all possible hydrogens

Unsaturated- at least one double bond,

less hydrogen, can bend

Saturated vs. Unsaturated • All single bonds

connect C• Solid at room temp• Ex: butter, lard• “Straight, stackable”

• Contain double bonds

• Liquid at room temp

• Ex: olive oil, corn oil

• Typically plant-based

What are trans-fats?

• “Trans” double bonds are not naturally found in biological systems

• When unsat. fats are “hydrogenated” to become sat. fat (easier to store, ship, use), the H’s can rearrange and ‘straighten out’ the molecule

• Trans fat is bad (?) b/c it is not recognized by our body’s enzymes (?)

Protein

• Contain nitrogen, carbon, hydrogen and oxygen (amino group and carboxyl group)

• Monomer- amino acid• Polymer- polypeptide or protein• Control reactions, regulate cell

processes, form bones and muscles, transport and help fight disease

Protein Structure

Hydrogen bonds and Van der Waals forces hold the protein shape together.

Why is protein structure so important?

2-4 Chemical reactions• Process that changes one set of chemicals

(reactants) into another set of chemicals (products) by making and/or breaking bonds

• Bonds are the storage place of energy in molecules / compounds

– Break a bond RELEASE energy

–Make a bond REQUIRES energy

Energy in Reactions• EXERGONIC (E exiting)• Chemical reactions that release energy • Often spontaneous (occur on their own)

– But often need a “push” to get started

• ENDERGONIC (E needing)• Chemical reactions that absorb energy • Need energy input to occur

• Activation energy-“The starting push” of chemical reactions-The minimal amount of energy required to get a

chemical reaction started

Types of Reactions• Hydrolysis

– Break apart monomers– by the addition of water. – An H is added to one monomer & an OH is added to

the other monomer.

• Dehydration Synthesis ( or Condensation)– Join monomers – One monomer loses a H+ and the other loses an OH-

– Water is removed– Covalent bond is formed

Dehydration Synthesis

Enzymes• Proteins that lower the activation energy required and

allow reactions to happen at the normal temperature of cells.

• Each enzyme is specific (only works on one particular reaction)

• Can be used over and over again for that reaction• The reactant that the enzyme helps is called the

substrate. The enzyme is usually named after the substrate with the ending –ase added to it.

• Coenzymes are non-protein helper molecules that sometimes assist enzymes with their job.

What can affect the rate of Enzymes function?

• Each enzyme will only do one specific reaction. Enzymes are never used up or changed in the reaction.

• Increasing the substrate concentration and/or enzyme concentration can speed up the rate of reaction.

• Enzymes are picky about the temperature, and pH. If either is not ideal the enzyme rate will slow and possibly stop. An enzyme will denature if temp. or pH are not right.

Learning Checkpoint

• What are the 4 carbon compounds necessary for life?

• What is the main function of carbohydrates?

• What are some of the functions of protein in the body?

• What is the easiest way to distinguish a lipid from a carbohydrate?

• What is a monomer and a polymer?

Practice Questions:

The diagram shows a reaction that forms a polymer from two monomers. What is this type of reaction called?a) Glycolysisb) Hydrolysisc) Photosynthesisd) Dehydration synthesis

Which statement best describes an effect of the low density of frozen water in a lake?

a)When water freezes, it contracts, decreasing the water level in a lake

b)Water in a lake freezes from the bottom up, killing most aquatic organisms

c)When water in a lake freezes, it floats, providing insulation for organisms below.

d)Water removes thermal energy from the land around a lake, causing the lake to freeze

Which statement correctly describes how carbon’s ability to form four bonds makes it uniquely suited to form macromolecules?

a)It forms short, simple carbon chainsb)It forms large, complex, diverse moleculesc)It forms covalent bonds with other carbon

atomsd)It forms covalent bonds that can exist in a

single plane

Carbohydrates and proteins are two types of macromolecules . which functional characteristic of proteins distinguishes them from carbohydrates?

a)Large amount of stored informationb)Ability to catalyze biochemical reactionsc)Efficient storage of usable chemical eergyd)Tendency to make cell membranes

hydrophobic

Substance A is converted to substance B in a metabolic reaction. Which statement best describes the role of an enzyme during this reaction?

a)It adjusts the pH of the reaction mediumb)It provides energy to carry out the reactionc)It dissolves substance A in the reaction mediumd)It speeds up the reaction without being consumed

 

A scientist observes that, when the pH of an environment surrounding an enzyme is changed, the rate the enzyme catalyzes a reaction greatly decreases. Which statement best describes how a change in pH can affect an enzyme?

a) A pH change can cause the enzyme to change its shape

b)A pH change can remove energy necessary to activate an enzyme

c) A pH change can add new molecules to the structure of an enzyme

d)A pH change can cause an enzyme to react to a different substrate