BIOCHEMISTRYBiology 1 Mr. Greene Unit 2

Bellringer

Look at the different substances and write down which substances you think are composed of elements and which are composed of compounds.

Key Ideas

What makes up matter?

Why do atoms form bonds?

What are some important interactions between substances in living things?

Atoms Every living and nonliving thing is

made of matter. Matter is anything that has mass and takes up space.

All matter is made of very small particles called atoms. An atom is the smallest unit of matter that cannot be broken down by chemical means.

100 million atoms would make a row about 1 cm long

these are represented by chemical symbols                        H - hydrogen           He -

helium       N – nitrogen      O -

oxygen    

Atoms The nucleus of an atom

is made up of: positively charged

protons uncharged neutrons.

Negatively charged electrons have very little mass and move around the nucleus in a large region called the electron cloud.

As a whole, atoms have no electrical charge.

Elements

Elements An element is a substance made up of

atoms that have the same number of protons.

For example, each atom of the element carbon has six protons.

Atoms of an element may have different numbers of neutrons. These atoms are called isotopes of elements.

Atomic Structure

6

CCarbon12.011

An Element in the Periodic Table

          atomic number - number of protons/ electrons too if neutral           mass number - number of protons and neutrons

Ions and Isotopes

ions atoms that have either lost or gained electrons.

if there are more protons than electrons = positive ions

if there are more electrons than protons = negative ions

  isotopes atoms of the same element that have different

numbers of neutrons they have the same chemical properties because the

have the same number of electrons

Nonradioactive carbon-12 Nonradioactive carbon-13 Radioactive carbon-14

6 electrons6 protons6 neutrons

6 electrons6 protons8 neutrons

6 electrons6 protons7 neutrons

Section 2-1

Isotopes of Carbon

Chemical Bonds

The electron cloud of an atom may have levels.

Electrons in the outermost level, or shell, are called valence electrons.

Atoms tend to combine with each other such that eight electrons will be in the valence shell.

When atoms combine, a force called a chemical bond holds them together.

Chemical Bonds Chemical bonds form between groups of

atoms because most atoms become stable when they have eight electrons in the valence shell.

When atoms of different elements combine, a compound forms. A compound is a substance made of the bonded atoms of two or more elements.

Chemical Bonds

Covalent Bonding One way that atoms bond is by sharing

valence electrons to form a covalent bond.

A molecule is a group of atoms held together by covalent bonds.

A water molecule, H2O, forms when an oxygen atom forms covalent bonds with two hydrogen atoms.

Covalent Bonding

Visual Concept: Covalent Bonding

Chemical Bonds

Ionic Bonding Atoms can achieve a stable valence level by

losing or gaining electrons, resulting in a positive or negative charge.

An ion is an atom or group of atoms that has an electric charge because it has gained or lost electrons.

The attractive force between oppositely charged ions is an ionic bond.

Visual Concept: Ion

Ionic Bonding in SaltClick to animate the image.

Energy Levels and Ionic Bonding

Polarity In some covalent bonds,

the shared electrons are attracted more strongly to one atom than to the other.

As a result, one end of the molecule has a partial negative charge, while the opposite end has a partial positive charge.

Molecules with partial charges on opposite ends are said to be polar.

Polarity

Solubility The partially charged ends of polar

molecules attract opposite charges.

Because of this behavior, polar molecules can dissolve other polar molecules and ionic compounds. For example, water can dissolve sugar and salt.

Nonpolar substances, such as oil, grease, and wax, do not dissolve well in water.

Ionic Compounds in Water

PolarityHydrogen Bonds When bonded to an oxygen,

nitrogen, or fluorine atom, a hydrogen atom has a partial charge nearly as great as a proton’s charge.

It attracts the negative pole of other nearby molecules. This attraction, called a hydrogen bond, is stronger than attractions between other molecules, but not as strong as covalent bonds.

Hydrogen bonding plays an important role in many of the molecules that make up living things.

Summary

All matter is made up of atoms. An atom has a positively charged nucleus surrounded by a negatively charged electron cloud.

Chemical bonds form between groups of atoms because most atoms became stable when they have eight electrons in the valence shell.

Polar attractions and hydrogen bonds are forces that play an important role in many of the molecules that make up living things.

Bellringer

Write what you think an acid and a base are and why. Guess if the following substances are acids or bases, and give a reason for your choice:

lemon juice, water, household ammonia, blood, soda pop, milk, antacid, shampoo

Can you find any similar characteristics between acids and bases?

Key Ideas

What makes water a unique substance?

How does the presence of substances dissolved in water affect the properties of water?

Properties of Water Water has many unique properties that make it an

important substance for life.

Most of the unique properties of water result because water molecules form hydrogen bonds with each other.

Water heats more slowly than most other substances

It also retains its temperature longer than other substances

When water freezes, the crystal structure formed due to hydrogen bonding makes ice less dense than liquid water.

Properties of Water

Water can absorb a large amount of heat without changing temperature. This property can help organisms maintain a constant internal temperature.

The attraction of particles of the same substance, such as water, is called cohesion. Cohesion keep water from evaporating easily; thus, water is a liquid at ordinary temperatures.

Water molecules also stick to other polar molecules. This attraction between particles of different substances is called adhesion.

Visual Concept: Comparing Cohesion and Adhesion

Solutions A solution is a mixture in which ions or

molecules of one or more substances are evenly distributed in another substance. solute – the substance that is dissolved solvent – substance in which the solute is dissolved

Many substances are transported throughout living things as solutions of water. Dissolved substances can move more easily within and between cells.

Water dissolves many ionic and polar substances but does not dissolve nonpolar substances.

solution

Solutions

Acids and Bases Some water molecules break apart to form

hydronium and hydroxide ions.

In pure water, hydronium and hydroxide ions are present in equal numbers.

Acids and bases are compounds that change the balance of these ions.

Solutions

Solutions

Acids and Bases Acids are compounds that form extra

hydronium ions when dissolved in water.

Bases are compounds that form extra hydroxide ions when dissolved in water.

When acids and bases are mixed, the extra hydronium and hydroxide ions react to form water.

Visual Concept: Acids

Visual Concept: Bases

Solutions

pH and Buffers pH is a measure of how acidic or basic a

solution is.

Each one-point increase in pH represents a 10-fold decrease in hydronium ion concentration.

Pure water has a pH of 7. Acidic solutions have a pH below 7, and basic solutions have a pH above 7.

Oven cleaner

Bleach

Ammonia

SoapSea water

Human bloodPure waterMilkRain

Acid rainTomato juiceLemon juice

Stomach acid

Neutral

Incr

easi

ngly

Basi

cIn

creasi

ngly

Aci

dic

Section 2-2

pH Scale

Visual Concept: pH

Solutions

pH and Buffers The pH of solutions in living things must

be stable.

For a stable pH to be maintained, the solutions in living things contain buffers.

A buffer is a substance that reacts to prevent pH changes in a solution.

Summary

The hydrogen bonding between water molecules explains many of the unique properties that make water an important substance for life.

Acids and bases change the concentration of hydronium ions in aqueous solutions. The pH of solutions in living things must be stable.

Bellringer

Look at all the different foods that are shown. Write down what you think all of these substances have in common.

Key Ideas

What are the chemicals of life made from?

What is the role of carbohydrates in cells?

What do lipids do?

What determines the function of proteins?

What do nucleic acids do?

Compounds in Living OrganismsTwo Main Categories of Compounds in Living

Organisms 1) Inorganic

don't contain carbon (except carbon dioxide) can't be produced by organisms except water, carbon dioxide, and oxygen

2) Organic

always contain carbon carbon - element most closely associated to life has four electrons in the outermost shell likes to bond to elements in a variety of ways

molecules with C-C bonds are called organic

molecules (i.e. the backbone) can be made biologically and synthetically

Building Blocks of Cells The parts of a cell are made up of large, complex

molecules, often called biomolecules.

Large, complex biomolecules are built from a few smaller, simpler, repeating units arranged in an extremely precise way.

The basic unit of most

biomolecules contain atoms

of carbon. Carbon atoms can

form covalent bonds with as

many as four other atoms.

Carbon Bonding

Carbohydrates

Carbohydrates are molecules made of sugars.

A sugar contains carbon, hydrogen, and oxygen in a ratio of 1:2:1.

Compounds with the basic formula, CH2O they can be a multiple of

the formula (C6H12O6)glucose

Glucose is a common sugar found in grape juice.

Carbohydrates Glucose is a

monosaccharide, or “single sugar.”

Two sugars can be linked to make a disaccharide.

Many sugars can be linked to make a polysaccharide.

Monosaccharides and disaccharides are considered simple carbohydrates. Polysaccharides are considered complex carbohydrates.

Visual Concept: Carbohydrates

Carbohydrates

Cells use carbohydrates for sources of energy, structural materials, and cellular identification.

Carbohydrates are a major source of energy for many organisms, including humans.

Carbohydrates

Chitin and cellulose are complex carbohydrates that provide support. Chitin is found in the shells of insects

and the cell walls of mushrooms. Cellulose is found in the cell walls of

plants.

In a complex organism, cells recognize neighboring cells by the short, branched chains of varying sugar units on their outer surface.

Lipids Lipids are another class of biomolecules,

which includes fats, phospholipids, steroids, and waxes.

Lipids consist of chains of carbon atoms bonded to each other and to hydrogen atoms. This structure makes lipids repel water.

The main functions of lipids include storing energy and controlling water molecules.

Lipids The main purpose of fats is to store energy.

Fats can store energy even more efficiently than carbohydrates.

The cell’s boundary is made of phospholipids. The structure of cell membranes depends on how this molecule interacts with water.

Waxes, found on the surfaces of plants and aquatic bird feathers, help prevent evaporation of water from the cells of the organism.

Steroid hormones such as testosterone and pigments (retinal in eyes and chlorophyll in plants) are made of lipids.

Lipids

Types of Fats saturated - most

carbons are bonded to 2 hydrogens

unsaturated - there are some C=C

  Lipids surround taste

buds and the food mixes with them to give the taste. 

Visual Concept: Types of Lipids

Proteins

Proteins are chains of amino acids that twist and fold into certain shapes that determine what the proteins do.

There are many types of proteins that perform many types of functions.

Proteins may be involved in structure, support, movement, communication, transportation, and carrying out chemical reactions.

ProteinsAmino Acids A protein is a molecule made up of amino

acids, building blocks that link to form proteins.

Every amino acid has an amino group and a carboxyl group. Units of amino acids can form links called peptide bonds.

The side group gives an amino acid its unique properties. Twenty different amino acids are found in proteins. The human body only makes 12, we must get the other 8 through dietary intake.

General structure Alanine Serine

Amino Acids

Amino

groupCarboxyl group

Visual Concept: Proteins

Visual Concept: Amino Acid

Uses of Proteins structure – cartilage, skin, ligaments,

and tendons ---> collagen horns of rhinoceros and hair ---> keratin

enzymes a catalyst that increases rate of

chemical reactions fight infection - antibodies

Nucleic Acids A nucleic acid is a long chain of nucleotide

units.

A nucleotide is a molecule made up of three parts: a sugar, a base, and a phosphate group.

Nucleotides of deoxyribonucleic acid, or DNA, contain the sugar deoxyribose.

Nucleotides of ribonucleic acid, or RNA, contain the sugar ribose.

A phosphate group nitrogen-containing molecule,called a base

deoxyribose (sugar)

Nucleic Acids

DNA - deoxyribonucleic acid two interlocking, coil-shaped strands

(a spiral staircase/double helix)

unicellular ---> long strands multicellular ---> compact bundles called

chromosomes

 

RNA - ribonucleic acid variety of shapes depending upon function three types - messenger, transfer, ribosomal

Visual Concept: Nucleic Acid

Nucleic Acids

Energy Carriers Some single nucleotides have other important

roles.

Adenosine triphosphate, or ATP, is a nucleotide that has three phosphate groups and supplies energy to cells.

Energy is released in the reaction that breaks off the third phosphate group.

Other single nucleotides transfer electrons or hydrogen atoms for other life processes.

CarbonCompounds

include

that consist of

which contain

that consist of that consist of that consist of

which contain which contain which contain

Organic Compounds

Carbohydrates Lipids Nucleic acids Proteins

Sugars and starches

Fats and oils Nucleotides Amino Acids

Carbon,hydrogen,

oxygen

Carbon,hydrogen,

oxygen

Carbon,hydrogen,

oxygen, nitrogen,phosphorus

Carbon,hydrogen,oxygen, nitrogen,

Summary

Large, complex biomolecules are built from a few smaller, simpler, repeating units arranged in an extremely precise way.

Cells use carbohydrates for sources of energy, structural materials, and cellular identification.

The main functions of lipids include storing energy and controlling water movement

Summary, continued

Proteins are chains of amino acids that twist and fold into shapes that determine what the protein does.

Nucleic acids store and transmit hereditary information.

Bellringer

Write down as many different kinds of energy that you can think of and give an example of each.

Key Ideas

Where do living things get energy?

How do chemical reactions occur?

Why are enzymes important to living things?

Changing Matter

Living things are made of matter, which consists of a substance with a form.

Changes constantly occur in living things.

A physical change occurs when only the form or shape of the matter changes.

A chemical change occurs when a substance changes into a different substance.

Changing Matter

Matter is neither created nor destroyed in any change. This observation is called the law of conservation of mass.

The ability to move or change matter is called energy.

Energy exists in many forms and can be converted from one form to another.

Every change in matter requires a change in energy.

Visual Concept: Energy

Changing Matter

Energy may change from one form to another, but the total amount of energy does not change. This observation is called the law of conservation of energy.

The total amount of usable energy decreases because some energy is given off to the surroundings as heat.

Living things use different chemical reactions to get the energy needed for life processes.

Chemical Reactions

Changing a substance requires a chemical reaction. During this process, bonds between atoms are broken, and new ones are formed.

A reactant is a substance that is changed in a chemical reaction

A product is a new substance that is formed.

Sometimes products can reform reactants.

Chemical Reactions

Activation Energy Chemical creacions can only occur under the

right conditions.

To form new bonds, the particles must collide fast enough to overcome the repulsion between their negatively charged electron clouds.

The activation energy of a reaction is the minimum kinetic energy required to start a chemical reaction.

Visual Concept: Activation Energy and Chemical Reactions

Chemical Reactions

Alignment Even if enough energy is available, the

product still may not form.

When the reactant particles, the correct atoms must be brought close together in the proper orientation.

Chemical reactions can only occur when the activation energy is available and the correct atoms are aligned.

Reaction Conditions

Biological Reactions

In living things, chemical reactions occur between large, complex biomolecules.

Many of these reactions require large activation energies.

Many of these reactions would not occur quickly enough to sustain life without the help of enzymes.

CO2 + H2O H2CO3

Biological Reactions

Enzymes An enzyme is a molecule that increases the

speed of biochemical reactions.

Enzymes hold molecules close together and in the correct orientation. An enzyme lowers the activation energy of a reaction.

By assisting in necessary biochemical reactions, enzymes help organisms maintain homeostasis.

Effect of Enzyme on Activation Energy

Biological Reactions, continuedEnzymes Each enzyme has an active site, the region

where the reaction takes place.

The shape of the active site determines which reactants, or substrates, will bind to it. Each different enzyme acts only on specific substrates.

Binding of the substrates causes the enzyme’s shape to change. This change causes some bonds in the substrates to break and new bonds to form.

Enzyme Action

Click to animate the image.

Biological Reactions

Enzymes Many enzymes are proteins. Changes in

temperature and pH can change a protein’s shape.

If an enzyme changes shape, it won’t work well.

Most enzymes need a certain range of temperatures, pH, and substrate concentration.

Reaction pathwaywithout enzyme Activation energy

without enzyme

Activationenergy

with enzymeReaction pathwaywith enzyme

Reactants

Products

Effect of Enzymes

Biological Reactions

Metabolism Cells get most of the energy needed for

metabolism by breaking down food molecules.

The release of energy from food molecules occurs in a series of reactions using many enzymes to capture energy in the form of ATP molecules.

The enzymes reduce the activation energy so much that only a little energy is needed to start the reactions. In this process, very little energy is lost as heat.

Other Necessary Terms

Coenzyme an organic molecule that assists an

enzyme

Inhibitor a molecule that slows down or stops the

action of an enzyme

Denaturation changing the shape of an enzyme due to

heat or extreme pH

Summary

Living things use different chemical reactions to get the energy needed for life processes.

An activation energy is needed to start a chemical reaction. The reactants must also be aligned to form the product.

By assisting in necessary biochemical reactions, enzymes help organisms maintain homeostasis.

Enzymatic Reactions