Organic Compounds

Importance of MacromoleculesImportance of Macromolecules

• Molecules and atoms from the environment are necessary to build new molecules within the cells of living things– Carbon moves from the environment to

organisms where it is used to create macromolecules that are used in storage compounds and the formation of new cells

4 MAJOR MACROMOLECULES4 MAJOR MACROMOLECULES

•Carbohydrates•Lipids•Proteins•Nucleic acids

POLYMERSPOLYMERS

Large molecule made by linking smaller subunits together– Monomers (small subunits)– Covalent bonds– The structure and function of

macromolecules are determined by the way monomers are assembled

Image by Riedell

SEE ANANIMATION

SEE ANANIMATION

CARBOHYDRATESCARBOHYDRATES

http://www.graphic-design.com/Type/sugar/index.html http://www.ifr.ac.uk/SPM/images/Starch%20products.jpg

MONOSACCHARIDESMONOSACCHARIDESSimple sugar moleculesSimple sugar molecules

C6H12O6

http://www.cybercolloids.net/library/sugars/glyceraldehyde.gifhttp://www.estrellamountain.edu/faculty/farabee/biobk/BioBookCHEM2.htmlhttp://217.60.75.10/llt/biokemi/images/galactose.jpghttp://217.60.75.10/llt/biokemi/images/galactose.jpghttp://www.estrellamountain.edu/faculty/farabee/biobk/BioBookCHEM2.html

C5H10O5

D-glyceraldehyde

C3H6O3

Composed of C,H,O (CH2O)n

3-7 carbonsName often ends in –ose

CARBOHYDRATES SUPPLY ENERGYCARBOHYDRATES SUPPLY ENERGY

Images from: http://www.miranda.com/library.en/Images/Pictures/girls-runners.jpg http://www.estrellamountain.edu/faculty/farabee/biobk/BioBookCHEM2.html

Cells burn glucose and store the energy released as ATP

Disaccharides • Use dehydration synthesis to join

TWO sugar molecules

• covalent bond between 2 monosaccharides = GLYCOSIDIC linkage

EX: Sucrose (table sugar) • most common disaccharidehttp://faculty.clintoncc.suny.edu/faculty/michael.gregory/files/Bio%20101/Bio%20101%20Lectures/Biochemistry/bioche1.gif

http://www.biotech.iastate.edu/lab_protocols/HSSB-TLC_images/sucrose.gif

DISACCHARIDESDISACCHARIDES

Glucose + Fructose → Sucrose + H20

Glucose + Glucose → Maltose + H20

Glucose + Galactose → Lactose + H20

POLYSACCHARIDES~ “many POLYSACCHARIDES~ “many sugars” sugars”

Ex: STARCH Ex: STARCH • polymer glucose

Function: Energy storage in PLANTSMost animals have the enzymes to hydrolyze starch, too

http://www.langara.bc.ca/biology/mario/Assets/Amylopectin.jpg

http://www.district87.org/biology87/apbio/biochem/Activity6_notes.pdf

POLYSACCHARIDES~ “many POLYSACCHARIDES~ “many sugars” sugars”

EX: GLYCOGENEX: GLYCOGEN

FUNCTION:FUNCTION: Energy storage in ANIMALS Energy storage in ANIMALS

Stored in liver and muscle tissue

http://www.abcbodybuilding.com/magazine04/scientific.htm

POLYSACCHARIDES~ “many POLYSACCHARIDES~ “many sugars” sugars” FUNCTION: StructuralFUNCTION: Structural

PLANTS ~ CELLULOSEPLANTS ~ CELLULOSEMajor component in cell wallsMajor component in cell wallsMost abundant organic compound on Most abundant organic compound on

EarthEarth

• Enzymes that digest starch by hydrolyzing alpha linkages can’t hydrolyze beta linkages in cellulose• Cellulose in human food passes through the digestive tract as insoluble fiber• Some microbes use enzymes to digest cellulose• Many herbivores, from cows to termites, have symbiotic relationships with these microbes

POLYSACCHARIDESPOLYSACCHARIDESFUNCTION: StructuralFUNCTION: Structural

EX: CHITINEX: CHITINMajor component of:Major component of: Exoskeletons in Arthropods Exoskeletons in Arthropods Cell walls in Fungi Cell walls in Fungi Dissolvable surgical thread Dissolvable surgical thread

FATTY ACIDS USED CAN :FATTY ACIDS USED CAN :• Be same or different in one molecule• Vary in length• Vary in number/location of double

bonds• Saturated (single bonds)

vs. unsaturated fats (double bonds)

Kink in chain wherever a cis double bondoccurs

FATSFATS

LONG HC chain• NON-POLAR• HYDROPHOBIC

FUNCTION:•Energy storage very rich

2X energy in carbos•Cushions organs•Insulates body

Think whale blubber!

Lipids, IILipids, II

PhospholipidsPhospholipidsHEAD (PHILIC) Glycerol Phosphate group-PO4

-

Negative charge

TAILS (PHOBIC)2 fatty acids

instead of 3

SEE AMOVIE !

PROTEINSPROTEINS

http://images.foodnetwork.com/webfood/images/gethealthy/nutritionalallstars/LeanProteins_header.jpg

PROTEINS ARE MADE FROM AMINO ACID SUBUITS

• Structure– Central carbon– Amino group– Carboxyl group– R group (side chain)

• Variable group• Confers unique chemical properties

•polar (hydrophilic), nonpolar (hydrophobic), acid or base

• Join via DEHYDRATION SYNTHESIS reactions by forming peptide bonds

Each kind of amino acid has a different R Each kind of amino acid has a different R groupgroup

20 different amino acids are used by cells to 20 different amino acids are used by cells to make proteins make proteins

(There are a few other aa’s, but rare)(There are a few other aa’s, but rare)

R GROUPS

See ananimation

POLYPEPTIDESPOLYPEPTIDES

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.htmlhttp://www.cherishedtimedesigns.com/images/BaliCharmBraceletGraduation500.jpg

• POLYMERS OF AMINO ACIDS ARE CALLED POLYPEPTIDES

•DNA determines the amino acid sequence

Image from:  http://www.tvdsb.on.ca/saunders/courses/online/SBI3C/Cells/Protein-Structure03.jpg

A functional PROTEIN is not just thepolypeptide chain.

A PROTEIN consists of one or more polypeptide chains twisted, folded, and coiled into aunique molecular shape

What determines the shape?

SEE AN ANIMATION

PROTEIN STRUCTURE & FUNCTIONPROTEIN STRUCTURE & FUNCTION

Function depends on structure• 4 levels of organization• result in 3-D structure

Primary StructurePrimary Structure

Amino acid substitution: in hemoglobin code

sickle-cell anemiaA

T

Secondary StructureSecondary Structurefolding along short sectionsfolding along short sections

• Due to: R group interactions (phobic/philic)

• Alpha Helix:coiling;

• ß Pleated Sheet:parallel;

• Hydrogen bondsbetween adjacentamino acidshold shape

Tertiary StructureTertiary Structureinteractions between side chainsinteractions between side chains

Conformation: irregular contortions from R group bonding

√ hydrophobic √ disulfide bridges √ hydrogen bonds

√ ionic bonds

Functional GroupsFunctional Groups• Sulfhydral Group

• Called: thiols•

http://www.mun.ca/biology/scarr/Disulfide_bridge.htm

DISULFIDE BRIDGESDISULFIDE BRIDGES

STABLIZE 3-D SHAPE

http://sandwalk.blogspot.com/2007/02/disulfide-bridges-stabilize-folded.html

BETWEEN nearbyCYSTEINE amino acids(Notice name change when bonded)

Quaternary StructureQuaternary Structure• Conformation:

2 or more polypeptide chains aggregated into one macromolecule

√ collagen (connective tissue)

√ hemoglobin

See ananimation

WHAT DO PROTEINS DO?WHAT DO PROTEINS DO?

* See page 78 in Campbell for other examples

ENZYMESENZYMEShttp://www.biologie.uni-hamburg.de/b-online/library/cat-removed/enzyme_.gif

Enzymes are protein catalysts that accelerate chemical reactions in living things

Enzymes reduce activation energy required for reaction

Enzymes are specific and fit substrate like a lock and key.

Enzymes are not changed by reaction and are reusable.

http://www.grand-illusions.com/images/articles/toyshop/trick_lock/mainimage.jpg

LEARN MORE

SEE ANIMATIONof AMYLASE

PROTEIN CONFORMATION ALSO DEPENDS ON PHYSICAL ENVIRONMENT

•pH•Salt concentration•Temperature

http://www.desktopfotos.de/Downloads/melt_cd.jpg

http://www.nealbrownstudio.com/adm/photo/163_nb_fried_egg.jpg

See a movieChoose narrated

LEARN MORE

Proteins that have denatured are biologically inactive

Once conditions change, protein may need help returning to its functional shape.

Facilitation of folding

NUCLEIC ACIDSNUCLEIC ACIDS

Nucleic Acids

Nucleic acids are polymers composed of units known as nucleotides. The main functions of nucleotides are: information storage (DNA), protein synthesis (RNA) energy transfers (ATP and NAD).

Nucleic AcidsNucleic acids are polymers composed of units known as nucleotides.

Nucleotides consist of a pentose (5C) sugar, a nitrogenous base, and a phosphate. Sugar and phosphate alone = nucleoside

Nucleic Acids

The sugars are either:

ribosedeoxyribose

OR

Nucleic Acids Nitrogeneous bases can be:

Purines (Adenine and Guanine) ~ double-ring Pyrimidines (Cytosine, Thymine and Uracil)

~ single-ring

Deoxyribonucleic acid (DNA) Nitrogen base attached to

sugar at C-1

Phosphate attached to sugar at C-5

Phosphate attached to next nucleoside at C-1 by

phosphodiester linkage

Each strand has a 3’ and 5’ end

http://staff.um.edu.mt/acus1/3Molgen.htm

DNADeoxyribonucleic acid (DNA) is the physical carrier of inheritance for 99% of living organisms.

Image from: http://sbchem.sunysb.edu/msl/dna.gif

Deoxyribonucleic acid (DNA)

Deoxyribose sugar

Nitrogeneous bases:A, C, G and T

DOUBLE HELIX sugar & phosphates

make up sides of ladder

nitrogen bases form steps

Deoxyribonucleic acid (DNA)Strands run antiparallel

http://www.biology.arizona.edu/biochemistry/problem_sets/large_molecules/06t.html

Deoxyribonucleic acid (DNA)

Complementary strands H bonds ~ between paired bases van der Waals ~ between stacked bases

http://staff.um.edu.mt/acus1/3Molgen.htm

Ribonucleic acid (RNA)Ribose sugar

Nitrogeneous bases:A, C, G, and U

SINGLE STRANDED

http://www.biology.arizona.edu/biochemistry/problem_sets/large_molecules/06t.html

RNARNA functions in protein synthesis.

There are three types of RNA:

Messenger RNA (mRNA) ~ blueprint for construction of a protein.

Ribosomal RNA (rRNA) ~ construction site where the protein is made.

Transfer RNA (tRNA) ~ truck delivering the proper amino acid to the

site at the right time.

Deoxyribonucleic acid (DNA)Ribonucleic acid (RNA)

DNA → RNA → protein

NUCLEOTIDES can transfer and store energy

Adenosine triphosphate (ATP)

NUCLEOTIDES can transfer and store energy

NAD+

NADP+

FADCoenzyme A

Energy and electron carriers used in photosynthesis andrespiration

More on this next unit!