Chapter 6 Chemistry in Biology - Wikispacesoverlinscience.wikispaces.com/file/view/Bio+Ch+6.pdf · Click on a lesson name to select. Chapter 6 Chemistry in Biology Section 1: Atoms,

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Chapter 6 Chemistry in Biology

Section 1: Atoms, Elements, and Compounds

Section 2: Chemical Reactions

Section 3: Water and Solutions

Section 4: The Building Blocks of Life

Atoms

Chemistry is the study of matter.

6.1 Atoms, Elements, and Compounds

Atoms are the building blocks of matter.


Neutrons and protons are located at the center of the atom.

Protons are positively charged particles.

Neutrons are particles that have no charge.

Electrons are negatively charged particles that are located outside the nucleus.

Chemistry in Biology

6.1 Atoms, Elements, and CompoundsChapter 6

Elements


An element is a pure substance that cannot be broken down into other substances by physical or chemical means.

There are over 100 known elements, 92 of which occur naturally.

Each element has a unique name and symbol.


The Periodic Table of Elements


Horizontal rows are called periods. Vertical columns are called groups.


Isotopes


Atoms of the same element that have the same number of protons and electrons but have a different number of neutrons


Radioactive Isotopes


When a nucleus breaks apart, it gives off radiation that can be detected and used for many applications.


Uses in Biology…

• determine the age of rocks and fossils

• irradiation of food to kill bacteria

• radiation treatment for cancer

• tracers and labels to detect disorders

Compounds


A pure substance formed when two or more different elements combine

Compounds are always formed from a specific combination of elements in a fixed ratio.

Compounds cannot be broken down into simpler compounds or elements by physical means.


Example

• Example: carbohydrates C1:H2:O1 (glucose is C6H12O6)

Chemical Bonds


Covalent bondsChemical bond that

forms when electrons are shared

A molecule is acompound in which the atoms are held together by covalent bonds.


Ionic Bonds


Electrical attraction between two oppositely charged atoms or groups of atoms



The elements identified as metals tend to donate electrons.

The elements identified as nonmetals tend to accept electrons.


Some atoms tend to donate or accept electrons more easily than other atoms.

Most ionic compounds are crystalline at room temperature and have higher melting points than molecular compounds formed by covalent bonds.




van der Waals Forces

When molecules come close together, the attractive forces between slightly positive and negative regions pull on the molecules and hold them together.

The strength of the attraction depends on the size of the molecule, its shape, and its ability to attract electrons.


This is because atoms of different elements do not have the same ability to attract electrons (ELECTRONEGATIVITY).

• some atoms have a stronger attraction for electrons than others.

• therefore, the sharing of electrons between two atoms in a covalent bond is not always equal.

Reactants and Products A chemical reaction is the

process by which atoms or groups of atoms in substances are reorganized into different substances.

6.2 Chemical Reactions

Clues that a chemical reaction has taken place include the production of heat or light, and formation of a gas, liquid, or solid.


Chemical reaction

Physical reaction

Chapter 6

Chemical Equations


Chemical formulas describe the substances in the reaction and arrows indicate the process of change.

Reactants are the starting substances, on the left side of the arrow.

Products are the substances formed during the reaction, on the right side of the arrow.

6.2 Chemical ReactionsChapter 6

• the reaction ALWAYS involves BREAKING bonds in reactants and FORMING new bonds in products resulting in a rearrangement of atoms.

Glucose and oxygen react to form carbon dioxide and water.




Balanced Equations The law of conservation of mass states matter

cannot be created or destroyed.

The number of atoms of each element on the reactant side must equal the number of atoms of the same element on the product side.



The activation energy is the minimum amount of energy needed for reactants to form products in a chemical reaction.

Energy of Reactions


• Endothermic (enter): reactions which absorb energy and do not occur without energy input

• Exothermic (exit): reactions which release energy and occur spontaneously (without the additional input of energy).


This reaction is exothermic and released heat energy.

The energy of the product is lower than the energy of the reactants.



This reaction is endothermic and absorbed heat energy.

The energy of the products is higher than the energy of the reactants.


• Many biochemical reactions take place so slowly or have such high activation energies that they would not occur in a timely manner without “help”.


A catalyst is a substance that lowers the activation energy needed to start a chemical reaction.

Enzymes are biological catalysts.

It does not increase howmuch product is made and it does not get used up in the reaction.

Enzymes


• ENZYMES are proteins that act as biological catalysts.

• Enzymes end with –ase and are named after the molecule they act upon (Ex. Lipase – lipids).

• They are very specific and will only catalyze one reaction.


The reactants that bind to the enzyme are called substrates.

The specific location where a substrate binds on an enzyme is called the active site.



Factors such as pH, temperature, and other substances affect enzyme activity.


The active site changes shape and forms the enzyme-substrate complex, which helps chemical bonds in the reactants to be broken and new bonds to form.

Water’s Polarity

6.3 Water and SolutionsChemistry in Biology

Molecules that have an unequal distribution of charges are called polar molecules.

Polarity is the property of having two opposite poles.

A hydrogen bond is a weak interaction involving a hydrogen atom and a fluorine, oxygen, or nitrogen atom.

Chapter 6


6.3 Water and SolutionsChapter 6

Enzyme-Controlled Reactions

Properties of Water

1) Water is a POLAR MOLECULE: the H end is (+) and the O end is (-) because O is more electronegative than H.

1)Because water is polar it forms HYDROGEN BONDS with oppositely charged parts of other molecules. Each water molecule can form 4 of these bonds.

* These two properties give rise to the other properties of water

1)COHESION – the attraction of water molecules to EACH OTHER.

2)ADHESION – the attraction of water molecules to OTHER SUBSTANCES. *Importance to living organisms: 3 & 4 explain how water travels against gravity from roots to shoots in tall plants such as trees (CAPILLARY ACTION)

1)Water has a high SPECIFIC HEAT – the amount of energy it takes to raise or lower the temperature of water 1 C. The value is high because of hydrogen bonding.

Importance to living organisms:• Keeps Earth’s temperature suitable for life.• Coastal regions have more moderate

temperatures than inland regions. • Keeps the temperature of the oceans stable.

1.Water has a high HEAT OF VAPORIZATION – the amount of energy needed to convert liquid water into a gas. The value is high due to hydrogen bonding.

Importance to living organisms:• EVAPORATIVE COOLING – cools surfaces

as it evaporates (sweating) • Keeps plants and animals from overheating • Moderates the Earth’s climate • Stabilizes aquatic environments

1)Water EXPANDS when it freezes and becomes LESS dense. * Water is MOST dense at 4° C, yet it freezes at O° C. * As bonds FORM, heat is RELEASED, as bonds BREAK heat is ABSORBED (requires energy)

Importance to living things:

• Seasonal changes are less abrupt

• Deep bodies of water don’t freeze solid and freeze from the top down.

1)Water is a versatile SOLVENT (due to polarity).

*Because of its polarity water can dissolve SOLUTES (other polar molecules) into SOLUTION.

• HYDROPHILLIC – water LOVING, polar molecules

• HYDROPHOBIC – water FEARING, non polar molecules.

• SUSPENSION – mixture of water and undissolved substances (Ex. Blood)


Homogenous Mixtures

A mixture that has a uniform composition throughout

A solvent is a substance in which another substance is dissolved.

A solute is the substance that is dissolved in the solvent. Food coloring dissolved in

water forms a homogenous mixture.



Heterogeneous Mixtures

In a heterogeneous mixture, the components remain distinct.

A salad is a heterogeneous mixture.



Substances that release hydrogen ions (H+) when dissolved in water are called acids.

Substances that release hydroxide ions (OH–) when dissolved in water are called bases.

Acids and Bases



The measure of concentration of H+ in a solution is called pH.

Acidic solutions have pH values lower than 7. Basic solutions have pH values higher than 7.

pH and Buffers


pH

*most bodily functions require a pH of between 6 and 8 (6.5 – 7.5)


Buffers are mixtures that can react with acids or bases to keep the pH within a particular range.


Organic Chemistry

The element carbon is a component of almost all biological molecules.

6.4 The Building Blocks of LifeChemistry in BiologyChapter 6

• As the name suggests, these molecules all contain the element Carbon (C).

6

CCarbon12.011

Carbon has four electrons in its outermost energy level.

One carbon atom can form four covalent bonds with other atoms.


Carbon compounds can be in the shape of straight chains, branched chains, and rings.

6.4 The Building Blocks of LifeChapter 6

Macromolecules


Carbon atoms can be joined to form carbon molecules.

Macromolecules are large molecules formed by joining smaller organic molecules together.

Polymers are molecules made from repeating units of identical or nearly identical compounds linked together by a series of covalent bonds.


* POLYMERS are formed by a condensation reaction, also called dehydration synthesis. Remove a water, make a bond.

Chemistry in BiologyChapter 6

• During this process, a water molecule is lost and 2 smaller molecules (monomers) are bonded together.


• Polymers are usually broken down in a process called hydrolysis. This is the opposite of condensation. Add a water, break a bond.



Macromolecules• Carbohydrates• Lipids• Nucleic Acids• Proteins



Carbohydrates Compounds composed of carbon, hydrogen, and

oxygen in a ratio of one oxygen and two hydrogen atoms for each carbon atom—(CH2O)n


Their names almost always end in –ose. Example: fructose, sucrose, maltose, ribose.



Two monosaccharides joined together form a disaccharide.

Longer carbohydrate molecules are called polysaccharides.


Values of n ranging from three to seven are called simple sugars, or monosaccharides.



Functions of Carbohydrates:• Primary source of short-term energy (glucose,

sugars). Stored by animals as glycogen and by plants as starch.

• Structural support (plant cell walls are mostly cellulose, the exoskeletons of insects are composed of the carbohydrate chitin).


Lipids

Molecules made mostly of carbon and hydrogen

A triglyceride is a fat if it is solid at room temperature (butter) and an oil if it is liquid at room temperature (olive oil).


• Lipids are composed of 3 fatty acid tails and a glycerol molecule. Fats are hydrophobic (think salad dressing).



Lipids that have tail chains with only single bonds between the carbon atoms are called saturated fats.

Lipids that have at least one double bond between carbon atoms in the tail chain are called unsaturated fats.

Fats with more than one double bond in the tail are called polyunsaturated fats.



Functions of Lipids

• Long-term energy storage• Cell membranes (lipid bilayer)• Waterproof seal on aquatic animals• Cushioning to protect kidneys and other

organs. • Insulation for marine mammals like

whales.



Proteins

Made of monomers called amino acids which are held together by peptide bonds

Amino acids are small compounds that are made of carbon, nitrogen, oxygen, hydrogen, and sometimes sulfur.



Amino acids have a central carbon atom.

One of the four carbon bonds is with hydrogen.

The other three bonds are with an amino group (–NH2), a carboxyl group (–COOH), and a variable group (–R).



The number and the order in which the amino acids are joined define the protein’s primary structure.

After an amino acid chain is formed, it folds into a unique three-dimensional shape, which is the protein’s secondary structure, such as a helix or a pleat.


4 Levels

• Tertiary structure occurs with “contortions” of the secondary structure. Think gymnastics.


• Quaternary structure – when more than one protein molecule combine.


Functions of Proteins

• Some are enzymes which control the rate of chemical reactions and regulate cell processes

• Some serve as transport molecules to move substances into or out of cells


Functions of Proteins (continued)• Some act as parts of the immune system• Some help transport substances

throughout the body (hemoglobin carries oxygen)

• Some form bones and muscles



Nucleic acids are complex macromolecules that store and transmit genetic information.

Nucleic acids are made of monomers called nucleotides, composed of C, N, O, P and H.


1. A2. B3. C4. D

CDQ 1

A. electronB. isotopeC. neutronD. proton

Which of the following particles is negatively charged?


Chapter Diagnostic Questions

Chapter 6

1. A2. B3. C4. D

CDQ 2



Chapter 6

A. electronsB. neutronsC. protonsD. ions

Isotopes are created by a change in the number of what particle of an atom?

1. A2. B3. C4. D

CDQ 3



Chapter 6

A. substratesB. enzymesC. ionsD. reactants

Identify the proteins that speed up the rate of chemical reactions.

1. A2. B3. C

FQ 1


A. neutrons and electronsB. protons and electronsC. protons and neutrons

What particles are in an atom’s nucleus?

6.1 Formative Questions

1. A2. B3. C

FQ 2



A. an equal number of protons and neutrons

B. an equal number of protons and electrons

C. an equal number of neutrons and electrons

What causes the overall charge of an atom to be zero?

1. A2. B3. C4. D

FQ 3



A. a compoundB. an elementC. an isotopeD. a mixture

What type of substance is water?

1. A2. B3. C4. D

FQ 4



A. chemical bondsB. ionic compoundsC. radioactive isotopesD. van der Waals forces

What provides the energy for all living processes?

1. A2. B3. C4. D

FQ 5



A. a match burningB. salt dissolvingC. water boilingD. gasoline evaporating

Which is a chemical reaction?

1. A2. B

FQ 6



Which chemical reaction is endothermic?A.

A.

1. A2. B3. C4. D

FQ 7



A. It acts as a reactant.B. It reduces the amount

of heat produced.C. It increases the

amount of product.D. It lowers the activation

energy.

How does an enzyme increase the rate of a chemical reaction?

1. A2. B3. C4. D

FQ 8



What occurs at the active site in the enzyme substrate complex?

A. An exothermic chemical reaction takes place.

B. Chemical bonds are broken and new bonds are formed.

C. The enzyme gets used up in the reaction.

D. The substrates provide energy for the enzyme.

1. A2. B3. C4. D

FQ 9



A. It acts as a catalyst.B. Its pH is neutral.C. It is a polar molecule.D. It is an ionic compound.

Why is water able to dissolve a wide variety of solutes?

1. A2. B3. C4. D

FQ 10



A. covalent bondsB. double bondsC. hydrogen bondsD. ionic bonds

What type of bonds attracts water molecules to each other and to other substances?

1. A2. B3. C4. D

FQ 11



A. Cl– B. OH–

C. H+

D. Na+

Which ion, when released in water, causes a solution to be basic?

1. A2. B3. C4. D

FQ 12



A. alkaliB. antacidC. bufferD. neutralizer

What is the name for a substance that keeps the pH in cells within the 6.5 to 7.5 pH range?

1. A2. B3. C4. D

FQ 13



A. carbonB. nitrogenC. phosphorusD. sodium

Which element do almost all biological molecules contain?

1. A2. B3. C4. D

FQ 14



A. 1B. 2C. 4D. 8

How many covalent bonds can carbon form with other atoms?

1. A2. B3. C4. D

FQ 15



A. hormoneB. nucleic acidC. proteinD. steroid

What type of biological molecule is an enzyme?

1. A2. B3. C4. D

FQ 16



A. lipidsB. nucleotidesC. polypeptidesD. sugars

What are fats, oils, and waxes composed of?

1. A2. B3. C4. D

FQ 17



A. amino acidsB. fatty acidsC. glycerolsD. nucleotides

What are the monomers that make up proteins?

1. A2. B3. C4. D

FQ 18


A. carbohydrateB. lipidC. nucleic acidD. protein

Which biological molecule transports substances between cells?


1. A2. B3. C4. D

CAQ 1


A. activation energyB. reactantsC. productsD. enzymes

Look at the following figure. Determine what the upward curve represents.

Chapter Assessment Questions

?

1. A2. B3. C4. D

CAQ 2



A. 2B. 4C. 6D. 8

Look at the energy levels in the atom. What is the maximum number of electrons energy level two can hold?

Explain why chemical equations must be balanced.


Answer: Chemical reactions require balanceof mass. Therefore, the number of atoms of each element on the reactant side must equal the number of atoms of the same element on the product side.


Chapter 6

CAQ 3

1. A2. B3. C4. D

STP 1


A. atoms sharing electrons

B. table salt dissolving in water

C. ionic compounds forming crystals

D. water molecules forming droplets

Which is a result of van der Waals forces?

Standardized Test Practice

1. A2. B3. C4. D

STP 2


What is true of this chemical reaction?

A. Energy is not needed to start the chemical reaction.

B. Heat and/or light energy are released in this reaction.

C. The activation energy is greater than the energy released.

D. The energy of the products and the reactants is the same.


1. A2. B3. C4. D

STP 3



A. tomatoesB. bananas

Which fruit contains a higher concentration of hydrogen ions?

1. A2. B3. C4. D

STP 4



What do cellulose and chitin have in common?

A. They are energy- storing polymers.

B. They are found in the cells of animals.

C. They are structural polysaccharides.

D. They are composed of repeating sucrose units.

1. A2. B3. C4. D

STP 5



A. glutenB. glycogenC. starchD. sucrolose

Which polysaccharide stores energy in muscle and liver tissue?

1. A2. B3. C4. D

STP 6



What is the function of this biological macromolecule?A. communicate signals

between cellsB. produce vitamins

and hormonesC. provide support

and protectionD. store and transmit

genetic information

1. A2. B3. C4. D

STP 7



Which is a characteristic of all lipids?

A. They are saturated triglycerides.

B. They do not dissolve in water.

C. They are liquid at room temperature.

D. They store less energy than carbohydrates.


Glencoe Biology TransparenciesChapter 6


Image BankChapter 6


Image BankChapter 6

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Chapter 6 Chemistry in Biology - Wikispacesoverlinscience.wikispaces.com/file/view/Bio+Ch+6.pdf · Click on a lesson name to select. Chapter 6 Chemistry in Biology Section 1: Atoms,