Ch. 3 Biochemistry

Ch. 3-1 WATER

PolarityWater has chemical propertiesThese have to do with the structure of

water moleculesRecall: H2O is covalently bonded

Although they share the electrons, they DO NOT share them evenly The oxygen pulls the shared electron more strongly

towards itselfTherefore the electrical charge is unevenly distributed:

this is POLARITYOxygen has a slightly more negative charge &

hydrogens have a slightly more positive charge

OH H+ +

-

Hydrogen Bonding The polar nature of water cause H2O molecules to

be attracted to one another This attraction is what holds two water molecules

together is called: Hydrogen bonding Caused by positive region of one water molecule

attracted to negative region of another water molecule

Very weak bonds BUT still attractive enough to cause water molecules to cling to each other

Cohesion and Adhesion Cohesion: attractive force between

particles of the same kind Ex. Water molecules attracted to one

another This allows for surface tension of water

Adhesion: attractive force between unlike substances

Example:

Cohesion

Capillary Action .

Due to adhesion, the ability of water to move upward through narrow tubes against the force of gravity = Capillarity

Temperature Moderation In order for the temperature of water to change,

it must gain or lose a large amount of energy When water it heated, the majority of the thermal

energy (heat) is used to break the hydrogen bonds between the molecules

Why is this important to living things? Living things contain a lot of water

This water needs to remain at a relatively constant temperature in order to maintain HOMEOSTASIS!

Review Questions Describe the structure of a water molecule. How do molecules of a polar compound differ

from those of a nonpolar compound? What happens when ionic compounds are mixed

with water? What are two properties of water that result

from water’s tendency to form hydrogen bonds? What is capillarity? Most automobiles have water-cooled engines.

What must be true about a solution that can replace water in the cooling system, such as antifreeze?

Review Questions: Answers Describe the structure of a water molecule: What is composed of

two hydrogen atoms covalently bonded to one oxygen atom. Water is polar, with the oxygen atom slightly positively charged and the hydrogen atoms slightly negatively charged.

How do molecules of a polar compound differ from those of a nonpolar compound? Polar molecules have slightly differing charges on different regions, while nonpolar molecules have a uniform charge.

What happens when ionic compounds are mixed with water? Ionic compounds dissociate when they are dissolved in water.

What are two properties of water that result from water’s tendency to form hydrogen bonds? Two properties of water that arise from hydrogen bonding are adhesion and cohesion, capillarity.

What is capillarity? It is the ability of water to move up the sides of a narrow tube as a result of water’s properties of adhesion and cohesion

Most automobiles have water-cooled engines. What must be true about a solution that can replace water in the cooling system, such as antifreeze? Solutions that can replace water as a coolant in automobile engines must have the ability to absorb large quantities of heat withou easily changing temperature.

CH. 3-2CARBON COMPOUNDS

Carbon Bonding Carbon has 4 electrons in outermost energy level:

it wants 8 electrons Because of this, carbon readily forms 4 covalent

bonds with other elements Carbon also readily forms bonds with other

carbon atoms forming: Straight chains Branched chains Rings

Carbon Chains

STRAIGHT CHAIN BRANCHED CHAIN RING

Covalent Bonds Single covalent bond: bond formed when

two atoms share a pair (2) electrons C C

Double covalent bond: bond formed when two atoms share two pairs (4) of electrons C C

Triple covalent bond: bond formed when two atoms share three pairs (6) of electrons C C

Functional Groups Clusters of atoms in organic compounds that

influence the properties of the molecules in which they are located

Functional groups determine the characteristics of the compound

Ex: hydroxyl group (-OH) Important to living things

Hydroxyl Group (-OH) Alcohol-organic compound-with

hydroxyl group attached to one of its carbon atoms

Some common alcohols: Ethanol

In alcoholic beverages Causes cell death in liver and brain

Methanol AKA Wood alcohol Causes blindness or death when consumed

Glycerol IMPORTANT FOR LIVING ORGANISMS Assembles certain molecules within the body

Alcohols

Large Carbon Molecules Monomers: simple molecules used to build large

carbon molecules This is done by bonding to each other to form complex

molecules: Polymers

MONOMER + MONOMER + MONOMER (etc) = POLYMER

Large polymers = Macromolecules

Macromolecules The process of building a polymer is

called Dehydration synthesis or Condensation Reaction This is the taking away of a water molecule in

order to bond monomers with each other forming a polymer

The process of breaking apart a polymer is called Hydrolysis This is the reversal of dehydration synthesis Hydrolysis is the addition of a water molecule

to a polymer which breaks it apart

Dehydration Synthesis

Hydrolysis Reaction

Building a Polymer

Breaking apart of Polymer

Energy CurrencyLife processes require constant supply of

energyAdenosine Triphosphate (ATP): compound that

contains a large amount of energy in the structure

Part of the structure of ATP is a phosphate group

Each phosphate is bonded to each other by a covalent bond

When a phosphate is taken away, this covalent bond is broken releasing a lot of energy

COVALENT BOND

•When one of the phosphate group bonds in broken, a large amount of energy is released.

•ATP ADP

•adenosine TRIphosphate adenosine DIphosphate

Review Questions What is an organic compound? What property allows carbon compounds to exist

in a number of forms? Define functional group and give an example: How does a polymer form? How does a polymer break down? Scientists can determine the age of a substance

using a method that compares the amounts of different forms of carbon atoms present in the substance. Is this method more useful for organic substances or inorganic substances?

Review Questions: Answers What is an organic compound? With few exceptions,

organic compounds contain carbon covalently bonded to itself and other atoms (carbon backbone)

What property allows carbon compounds to exist in a number of forms? Carbon can form four covalent bonds with any number of atoms, including other carbon atoms. This allows it to form molecules of different shapes.

Define functional group and give an example: Functional groups are clusters of atoms that influence the properties of the molecules they compose. For example, the hydroxyl group is a functional group.

How does a polymer form? How does a polymer break down? Scientists can determine the age of a substance using a

method that compares the amounts of different forms of carbon atoms present in the substance. Is this method more useful for organic substances or inorganic substances?

Ch. 3-3 MOLECULES OF LIFE

Carbohydrates Organic compounds composed of:

Carbon, Hydrogen, Oxygen In ratio of 2:1 (2 hydrogen: 1 oxygen) Number of carbon atoms varies Carbohydrates exist as:

Monosaccharides Disaccharides Polysaccharides

Carbohydrates: MonosaccharidesA monomer of a carbohydrateMonosaccharide = simple sugarCarbon: Hydrogen: Oxygen

1 : 2 : 1Common monosaccharides:

Glucose, fructose, galactose Glucose = main source of energy for cells Fructose = found in fruits; sweetest of all

monosaccharides Galactose = found in milk Glucose, fructose, galactose are all isomers:

Compounds with a single chemical formula but different forms All have chemical formula = C6H12O6

Isomers

Carbohydrates: Disaccharides Disaccharide = double sugar Disaccharide is made up of

monosaccharide + monosaccharide This process is also through the

dehydration synthesis AKA condensation reaction

Carbohydrates: Polysaccharides Complex molecules composed of three

or more monosaccharides Ex: Glycogen

Consists of hundreds of glucose molecules strung together

Glycogen is “stored sugar” and located in liver and muscles

Ready to be used for quick energy

Carbohydrates

Proteins Organic compounds made of:

Carbon, hydrogen, oxygen, nitrogen Formed from linkage of monomers Catalysts are made of proteins Muscle and skin made of proteins

Proteins: Amino Acids 20 different amino acids (AA) AA are monomer building blocks of proteins All share basic structure: 4 main parts

Hydrogen atom Carboxyl group (-COOH) Amino group (-NH2) R group

Differences btwn AA located in R group Difference causes each protein to be a different shape Different shapes allow proteins to perform many different roles/functions

Amino Acid

CN C OH

OH

R

H

H

AMINO GROUP

CARBOXYL GROUP

R GROUP

HYDROGEN

Proteins: PeptidesPeptide bond: two amino acids bonded by

a covalent bondDipeptide: two amino acids bonded

This bonding results from Dehydration reaction (condensation reaction)

Polypeptide: many amino acids bonded together forming a long chain of AA Proteins are made of one or more polypeptides Some proteins are very large molecules

These are bent and folded upon themselves due to: Hydrogen bonding Temperature

Example: cooking an egg: this heat changes the shape of the proteins in the egg went from clear, runny liquid to a solid white solid

Proteins: Enzymes Act as catalysts Essential for cell functioning Enzyme reactions depend on physical fit between

enzyme & substrate: reactant being catalyzed “Lock & Key” mechanism The linkage of enzyme & substrate changes the

enzyme’s shape slightly Conforms to substrate’s shape Weakens bonds in substrate which lowers activation

energy

***AFTER REACTION, ENZYME RELEASES PRODUCTS & ENZYME ITSELF IS UNCHANGED THEREFORE CAN BE USED AGAIN!

Enzymes in Action

What do enzymes have to do with homeostasis?Enzymes may fail to work in the wrong

conditionsFor example

Change in temperature Change in pH

These can change the shape of the enzyme causing it not to work properly it will not fit into the substrate therefore the reaction it would have catalyzed will not happen!

DENATURATION

Lipids Large, non-polar organic molecules that

DO NOT dissolve in water Store energy efficiently Have many hydrogen-carbon bonds

which store more energy than carbon-oxygen bonds common in other organic compounds

Made up of fatty-acids

Lipids: Fatty AcidsFatty acids: un-branched carbon chains

that make up most lipidsContain long, straight carbon chain with a

carboxyl group –COOH attached at one end

Each end of a fatty acid has very different properties Carboxyl group end:

Polar-attracted to water molecules Hydrophilic: “water-loving”

Hydrocarbon end: Nonpolar-not attracted to water molecules

Hydrophobic: “water-fearing”

Fatty acids are made up of two parts:

1) Carboxyl End: -COOH

2) Hydrocarbon Chain: made of only hydrogen & carbons!

Fatty Acid Structure

Fatty Acids: two main types

SATURATED: all carbon atoms are single-bonded to hydrogen atoms

UNSATURATED: some carbon atoms have formed double-covalent bonds to each other

Complex Lipids Lipids are divided into categories according to

their structure Three classes are:

1) Triglycerides Composed of 3 molecules of fatty acid joined to 1

molecule of glycerol Can be saturated or unsaturated Saturated Triglycerides: solid at room temp., high

melting points, EX. Shortening & animal fats Unsaturated Triglycerides: liquid at room temp., EX.

Plant seeds & fruits

Complex Lipids Cont.2) Phospholipids: composed of 2 fatty

acids joined to 1 molecule of glycerolCell membrane is composed of two layers

of phospholipids = phospholipid bilayerLipids do not dissolve in water which is

important for the cell because it forms a barrier between the inside and outside of the cell

Complex Lipids Cont. 3) Waxes: consists of long fatty-acid

chain joined to a long alcohol chain Highly waterproof Plants have protective coating on outer

surfaces made of wax We have ear wax for prevention of

microorganisms from entering

Lipids: Steroids NOT composed of fatty acids Composed of four fused carbon rings with

functional groups attached to them Many hormones are steroid compounds Most familiar in humans: Cholesterol

Nucleic AcidsVery large and complex organic

molecules that store important information

Use system of four compounds to store hereditary information in cells

Deoxyribonucleic acid (DNA): contains information essential for all cell activities

Ribonucleic acid (RNA): stores & transfers info essential for making proteins

Both DNA & RNA are composed of monomers called nucleotides

Nucleotides Each made of three main components:

Phosphate group Five-carbon sugar backbone Ring-shaped nitrogen base- there are 4

different bases

Review QuestionsDefine monosaccharide, disaccharide, and polysaccharide

Describe the structure of amino acids and proteins

Explain the relationship between an enzyme and its substrate

How do the two ends of a fatty acid differ?Name the two types of nucleic acids, and

describe their functions.High temperatures can weaken bonds

between different parts of a protein molecule, thus changing its shape. How might this change alter the effectiveness of an enzyme?

Review Questions: Answers Define monosaccharide, disaccharide, and

polysaccharide: A monosaccharide is a simple sugar that contains carbon, hydrogen, and oxygen in the ratio of 1:2:1. A disaccharide is composed of two monosaccharides. A polysaccharide is a complex carbohydrate composed of three or more monosaccharides.

Describe the structure of amino acids and proteins: An amino acid consists of a central carbon atom bonded to a hydrogen atom, an amino group, a carboxyl group, and a variable R group. Proteins are polymers of amino acids.

Explain the relationship between an enzyme and its substrate: An enzyme attaches physically to the substrate and catalyzes the reaction. The enzyme molecule then releases the resulting products and can be used again.

How do the two ends of a fatty acid differ? The carboxyl end is polar and therefore hydrophilic. The hydrocarbon end is nonpolar and therefore hydrophobic.

Review Questions: AnswersName the two types of nucleic acids, and

describe their functions: DNA stores information essential for almost all cellular activities. RNA stores and transfers information essential for the manufacture of proteins.

High temperatures can weaken bonds between different parts of a protein molecule, thus changing its shape. How might this change alter the effectiveness of an enzyme? Changing the shape of an enzyme may affect its ability to function because the enzyme may no longer physically interact appropriately with its substrate.