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Biochemistry of Cells

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Uses of Organic MoleculesAmericans consume an average of 140 pounds of sugar per person per yearCellulose, found in plant cell walls, is the most abundant organic compound on Earth

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Uses of Organic MoleculesA typical cell in

your body has about 2 meters of DNA

A typical cow produces over 200 pounds of methane gas each year

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WaterAbout 60-90 percent of an organism is water

Water is used in most reactions in the bodyWater is called the universal solvent

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Water Properties

Polarity

CohesivenessAdhesivene

ss

Surface Tension

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Carbon-based MoleculesAlthough a cell is mostly water, the rest of the cell consists mostly of carbon-based molecules

Organic chemistry is the study of carbon compounds

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Carbon is a Versatile Atom

It has four electrons in an outer shell that holds eight

Carbon can share its electrons with other atoms to form up to four covalent bonds

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Hydrocarbons

The simplest carbon compounds …

Contain only carbon & hydrogen atoms

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Carbon can use its bonds to::

Attach to other carbons

Form an endless diversity of carbon skeletons

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Large Hydrocarbons:

Are the main molecules in the gasoline we burn in our cars

The hydrocarbons of

fat molecules provide energy for our bodies

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Shape of Organic Molecules

Each type of organic molecule has a unique

three-dimensional shape

The shape determines its function in an

organism

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Functional Groups are:

Groups of atoms that give properties to the compounds to which they attach

Gained Electrons Lost Electrons

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Common Functional Groups

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Giant Molecules - PolymersLarge molecules are called polymers

Polymers are built from smaller molecules called monomersBiologists call them macromolecules

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Examples of Polymers

Proteins

Lipids

Carbohydrates

Nucleic Acids

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Most Macromolecules are Polymers

Polymers are made by stringing together many smaller molecules called monomers

Nucleic Acid

Monomer

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Linking Monomers

Cells link monomers by a process called dehydration

synthesis (removing a molecule of water)

This process joins two sugar monomers to make a double

sugar

Remove H

Remove OH

H2O Forms

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Breaking Down PolymersCells break

down macromolecules by a process called hydrolysis (adding a molecule of water)

Water added to split a double sugar

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Macromolecules in Organisms

There are four categories of large molecules in cells:

Carbohydrates

Lipids

Proteins

Nucleic Acids

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Carbohydrates

Carbohydrates include: Small sugar molecules

in soft drinksLong starch molecules in pasta and potatoes

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CarbohydratesCarbohydratesSmall sugar moleculesSmall sugar molecules to large large

sugar moleculessugar molecules.

Examples:Examples:A.A. monosaccharidemonosaccharideB.B. disaccharidedisaccharideC.C. polysaccharidepolysaccharide

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CarbohydratesCarbohydrates

Monosaccharide: one sugar unitMonosaccharide: one sugar unit

Examples:Examples: glucose (glucose (C6H12O6)

deoxyribosedeoxyribose

riboseribose

FructoseFructose

GalactoseGalactose

glucoseglucose

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Monosaccharides:

Called simple sugars

Include glucose, fructose, & galactoseHave the same chemical, but different structural formulas

C6H12O6

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Monosaccharides

Glucose is found in sports drinks

Fructose is found in fruitsHoney contains both glucose & fructoseGalactose is called “milk sugar”

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Isomers

Glucose & fructose are isomers because they’re structures are different, but their chemical formulas are the same

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Rings

In aqueous (watery) solutions, monosaccharides form ring

structures

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Cellular Fuel

Monosaccharides are the main fuel that cells use for cellular work

ATP

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Disaccharides

A disaccharide is a double sugar

They’re made by joining two monosaccharides

Involves removing a water molecule (dehydration)

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Disaccharides

Common disaccharides include:

Sucrose (table sugar)

Lactose (Milk Sugar)

Maltose (Grain sugar)

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Disaccharides

Sucrose is composed of glucose + fructose

Maltose is composed of 2 glucose moleculesLactose is made of galactose + glucose

GLUCOSE

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CarbohydratesCarbohydrates

Disaccharide: two sugar unitDisaccharide: two sugar unit

Examples: Examples: Sucrose (glucose+fructose)Sucrose (glucose+fructose)

Lactose (glucose+galactose)Lactose (glucose+galactose)

Maltose (glucose+glucose)Maltose (glucose+glucose)

glucoseglucoseglucoseglucose

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Polysaccharides

Complex carbohydrates

Composed of many sugar monomers linked togetherPolymers of monosaccharide chains

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Examples of Polysaccharides

Starch

Glycogen

Cellulose

Glucose Monomer

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Starch

Starch is an example of a polysaccharide in plants

Plant cells store starch for energy

Potatoes and grains are major sources of starch in the human diet

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Glycogen

Glycogen is an example of a polysaccharide in animals

Animals store excess sugar in the form of glycogen

(in muscles and liver)Glycogen is similar in structure to starch

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Cellulose

Cellulose is the most abundant organic compound on Earth

It forms cable-like fibrils in the tough walls that enclose plants

It is a major component of wood

It is also known as dietary fiber

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Cellulose

SUGARS

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Dietary Cellulose

Most animals cannot derive nutrition from fiber

They have bacteria in their digestive tracts that can break down cellulose

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CarbohydratesCarbohydratesPolysaccharide: many sugar unitsPolysaccharide: many sugar units

Examples:Examples: starch (bread, starch (bread, potatoes)potatoes)

glycogen (beef glycogen (beef muscle)muscle)

cellulose (lettuce, cellulose (lettuce, corn)corn)

glucoseglucoseglucoseglucose

glucoseglucoseglucoseglucose

glucoseglucoseglucoseglucose

glucoseglucoseglucoseglucose

cellulosecellulose

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Sugars in Water

Simple sugars and double sugars dissolve readily in water

They are hydrophilic, or “water-loving”

WATER MOLECULE

SUGAR MOLECULE

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Lipids

Lipids are hydrophobic –”water fearing”

Includes fats, waxes, steroids, & oils

Do NOT mix with water

FAT MOLECULE

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Function of Lipids

Fats store energy, help to insulate the body, and cushion and protect organs

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Types of Fatty Acids

Unsaturated fatty acids have less than the maximum number of hydrogens bonded to the carbons (a double bond between carbons)

Saturated fatty acids have the maximum number of hydrogens bonded to the carbons (all single bonds between carbons)

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Types of Fatty Acids

Single Bonds in Carbon chain

Double bond in carbon chain

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Triglyceride

Monomer of lipids

Composed of Glycerol & 3 fatty acid chainsGlycerol forms the “backbone” of the fat Organic

Alcohol

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Triglyceride

Glycerol Fatty Acid Chains

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Fats in Organisms

Most animal fats have a high proportion of saturated fatty acids & exist as solids at room temperature (butter, margarine, shortening)

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Fats in Organisms

Most plant oils tend to be low in saturated fatty acids & exist as liquids at room temperature (oils)

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Fats

Dietary fat consists largely of the molecule triglyceride composed of glycerol and three fatty acid chains

Glycerol

Fatty Acid Chain

Dehydration links the fatty acids to Glycerol

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SteroidsThe carbon skeleton of steroids is bent to form 4 fused ringsCholesterol is the “base steroid” from which your body produces other steroids

Estrogen & testosterone are also steroids

Cholesterol

TestosteroneEstrogen

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Synthetic Anabolic SteroidsThey are variants of testosteroneSome athletes use them to build up their muscles quicklyThey can pose serious health risks

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LipidsLipidsGeneral term for compounds which are not not

soluble in watersoluble in water.Lipids are soluble in hydrophobic solventsare soluble in hydrophobic solvents.Remember:Remember: “stores the most energy”“stores the most energy”Examples:Examples: 1. Fats1. Fats

2. Phospholipids2. Phospholipids3. Oils3. Oils4. Waxes4. Waxes5. Steroid hormones5. Steroid hormones6. Triglycerides6. Triglycerides

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Proteins

Proteins are polymers made of monomers called amino acids

All proteins are made of 20 different amino acids linked in different orders

Proteins are used to build cells, act as hormones & enzymes, and do much of the work in a cell

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Four Types of Proteins

Structural

Contractile

Storage

Transport

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Proteins (Polypeptides)Proteins (Polypeptides)Amino acids (20 different kinds of aa) bonded

together by peptide bondspeptide bonds (polypeptidespolypeptides).

Six functions of proteins:Six functions of proteins:1.1. Storage:Storage: albumin (egg white)albumin (egg white)2.2. Transport: Transport: hemoglobinhemoglobin3.3. Regulatory:Regulatory: hormoneshormones4.4. Movement:Movement: musclesmuscles5.5. Structural:Structural: membranes, hair, nailsmembranes, hair, nails6.6. Enzymes:Enzymes: cellular reactionscellular reactions

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20 Amino Acid Monomers

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Structure of Amino Acids

Amino acids have a central carbon with 4 things boded to it:Amino group -NH3Carboxyl group -

COOHHydrogen -H

Side group -R

Amino

group

Carboxylgroup

R group

Side groups

Leucine -hydrophobic

Serine-hydrophillic

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Linking Amino Acids

Cells link amino acids together to make proteinsThe process is called dehydration synthesisPeptide bonds form to hold the amino acids together

Carboxyl

Amino Side

Group

Dehydration Synthesis

Peptide Bond

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Proteins (Polypeptides)Proteins (Polypeptides)

Four levels of protein structure:Four levels of protein structure:

A.A. Primary StructurePrimary Structure

B.B. Secondary Structure Secondary Structure

C.C. Tertiary Structure Tertiary Structure

D.D. Quaternary Structure Quaternary Structure

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Primary Protein Structure

The primary structure is the specific sequence of amino acids in a protein

Amino Acid

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Protein Structures

Secondary protein structures occur when protein chains coil or fold

When protein chains called polypeptides join together, the tertiary structure forms

In the watery environment of a cell, proteins become globular in their quaternary structure

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Protein Structures

Hydrogen bond

Pleated sheet

Amino acid

(a) Primary structure

Hydrogen bond

Alpha helix

(b) Secondary structure

Polypeptide(single subunit)

(c) Tertiary structure

(d) Quaternary structure

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Denaturating Proteins

Changes in temperature & pH can denature (unfold) a protein so it

no longer worksCooking denatures protein in eggs

Milk protein separates into curds & whey when it denatures

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Changing Amino Acid Sequence

Substitution of one amino acid for another in hemoglobin causes

sickle-cell disease

(a) Normal red blood cell Normal hemoglobin

12 3

4 56

7. . . 146

(b) Sickled red blood cell Sickle-cell hemoglobin

2 314 5

67. . . 146

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Proteins as Enzymes

Many proteins act as biological catalysts or enzymes

Thousands of different enzymes exist in the body

Enzymes control the rate of chemical reactions by weakening bonds, thus lowering the amount of activation energy needed for the reaction

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Enzymes

Their folded conformation creates an area known as the active site.

Enzymes are globular proteins.

The nature and arrangement of amino acids in the active site make it specific for only one type of substrate.

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Enzyme + Substrate = Product

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How the Enzyme Works

Enzymes are reusable!!!

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EnzymesEnzymes

FreeEnergy

Progress of the reaction

Reactants

Products

Free energy of activationFree energy of activation

Without Enzyme

With Enzyme

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Nucleic Acids

Store hereditary information

Contain information for making all the body’s proteinsTwo types exist --- DNA & RNA

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Nucleic AcidsNitrogenous base

(A,G,C, or T)

Phosphategroup

Thymine (T)

Sugar(deoxyribose)

Phosphate

BaseSugar

Nucleic acids are polymers of nucleotides

Nucleotide

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Bases

Each DNA nucleotide has one of the following bases:

Thymine (T) Cytosine (C)

Adenine (A) Guanine (G)

–Adenine (A)

–Guanine (G)

–Thymine (T)

–Cytosine (C)

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Nucleotide Monomers

Form long chains called DNA

Backbone

Nucleotide

Bases

DNA strand

Nucleotides are joined by sugars & phosphates on the side

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DNA

Two strands of DNA join together to form a double helix

Basepair

Double helix

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DNA - double helixDNA - double helix

P

P

P

O

O

O

1

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4

5

5

3

3

5

P

P

PO

O

O

1

2 3

4

5

5

3

5

3

G C

T A

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RNA – Ribonucleic Acid

Ribose sugar has an extra –OH or hydroxyl groupIt has the base uracil (U) instead of thymine (T)

Nitrogenous base(A,G,C, or U)

Sugar (ribose)

Phosphategroup

Uracil

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Websites to Explore

http://www2.nl.edu/jste/biochem.htmMacromolecules of Life (animations)

http://faculty.ccbcmd.edu/biotutorials/energy/adpan.htmlHydrolysis of ATP molecule

http://www.okc.cc.ok.us/biologylabs/index.htmOKC Biology Labs Online: Organic Molecules

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Summary of Key Concepts

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Nucleic Acids

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Macromolecules

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Macromolecules

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End

http://www.bbc.co.uk/education/asguru/biology/02biologicalmolecules/index.shtml