BiologicalMolecules

Chapter 3

Topoisomerase protein bound to DNA

Carbon in Biological Molecules

• Organic molecules– Derived from living organisms– Contain a carbon backbone

• Inorganic molecules– CO2, CO, and all molecules without carbon

Carbon

• Carbon is versatile and can form up to4 covalent bonds.

• Because it can make so many differentbonds, Carbon is present in nearlyevery structure in a cell.

6 CCarbon12.01

Carbon

• Most organic molecules have a carbonbackbone.– A chain of carbon atoms bonded together.

• Branching off of the backbone are a variety offunctional groups.– Small molecules with a specific function that

determine the chemical nature of the largermolecule.

6 CCarbon12.01

Organic Molecules oftencontain Functional Groups

C6H12O6

• A modular approach: small organicmolecules, subunits, are combined toform larger molecules.

• Monomers, “one part”, single subunits.– Example: sugars

• Polymers, “many parts”, long chains ofmany subunits.– Example: starches

Synthesis of Organic Molecules Dehydration Synthesis• “To form by removing water.”

1. A hydrogen ion (H+) is removed from onesubunit.

2. A hydroxyl group (OH-) is removed from thea second subunit.

3. The two subunits can now covalently bondand the H+ and OH- can form water.

Hydrolysis

• “To break apart with water”

• Water is ionized and the H+ and OH-

bind to each new subunit.

• The major way our digestive systembreaks down food.

Types ofBiologicalMolecules

CarbohydratesLipids

ProteinsNucleic Acids

RNA Polymerase protein synthesizingRNA strand from a template DNA helix.

C6H12O6 =

“Chemical Structure”

“Space-Filling Model”

“Ball and Stick Model”

=“Chemical Formula”

Carbohydrates• Molecules composed of carbon, hydrogen,

and oxygen in a ratio of ~1:2:1 --> (CH2O)n

• Monosaccharide: composed of one sugar.– Glucose, fructose, galactose

glucose

• Disaccharide: composed of two sugars.– Short-term energy storage.– Created by dehydration synthesis of two

monosaccharides.– Examples: sucrose, maltose, lactose

• Polysaccharide: composed of many sugars.– Long-term storage– Structural materials– Starches, glycogen, cellulose

• Polysaccharide: composed of many sugars.– Long-term storage– Structural materials– Starches, glycogen, cellulose

Lipids

• Composed almost entirely of carbon andhydrogen.

• Hydrophobic and insoluble in water.

• 3 classes of lipids:– Oils, fats, and waxes– Phospholipids– Steroids, and other “fused-ring” compounds

Oils, Fats, and Waxes

• Formed bydehydration ofglycerol andfatty acid subunits.– Fatty acids are long

strands of CH2 with acarboxylic acidfunctional group(-COOH) on the end.

Oils, Fats, and Waxes•Saturated fatty acids:all excess bonds occupied byhydrogen atoms.

•Usually solid at roomtemperature.

•Unsaturated fatty acids:double-bonded carbon atoms,resulting in fewer hydrogenatoms.

•Liquid at room temperature.

Trans Fats• Chemically modified

unsaturated fats byhydrogenation.– Example: partially-

hydrogenated soybeanoil.

• Keeps oils solid atroom temperature

• Difficult to metabolize.

C

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C

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C

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C

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C

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Saturated Fat (butter, lard)

C

H

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C

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HC

H

HC

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cis-Unsaturated Fat (oils)

C

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H

C

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trans-Unsaturated Fat (margarine)

C

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Phospholipids• Makes up the plasma membrane

surrounding cells.• Consists of

– Phosphate-nitrogen “head” (hydrophilic)– 2 fatty acid “tails” (hydrophobic).

Cell Membrane:a Phospholipid Bilayer

Hydrophilic “Head”

Hydrophobic “Tail”

Phospholipid

Lipid Bilayer

The hydrophobicinterior of themembrane inhibitswater movement,preventing leaks.

Steroids• 4 carbon rings fused together with

functional groups.• Formed by a similar biochemical

pathway as other lipids.• All are synthesized from cholesterol.

– Cholesterol comesfrom animalderived foods.

– Most animalssynthesize all theyneed.

Cholesterol• Aids in keeping the membrane fluid and protects

neurons in the brain.• Non-polar.• Carried through the bloodstream on lipoproteins.

– High-density lipoproteins (HDL) = "good" cholesterol.– Low-density lipoproteins (LDL) = "bad" cholesterol.

• LDL is ~100x largerthan HDL.

• LDL can be depositedin arteries formingplaques.

Proteins

• Composed of chains ofamino acids.

• Many different functions:– Enzymes guide chemical

reactions.– Structural proteins:

collagen, keratin.– Movement: actin and

myosin.– Defense: antibodies.

ATP Synthase

Collagen

Actin

Myosin

AntibodyProtein crystal structures from the RCSB Protein Data Bank

Amino Acids

• All amino acids share the same generalstructure:– Amino group (NH2)– Carboxylic group (COOH)– Variable group (R)

• 20 different amino acids, each with adifferent ‘R’ group.

The Twenty Amino Acids

Protein Synthesis

• Proteins are synthesized by a dehydrationreaction between two amino acids.

• Short amino acid chains are called peptides.• Longer amino acid chains (>50 aa) are called

polypeptides.

Proteins have 4 Levels of Structure1. Primary structure: sequence of amino acids.2. Secondary structure: helix or ß-sheet held together

by hydrogen bonds.3. Tertiary structure: complex 3-dimensional shape

of the polypeptide.4. Quaternary structure: individual polypeptides

subunits can link to form a larger protein.

Keratin andHair Texture

• Disulfide bondsbetween amino acids(cysteine) in keratinresult in curly, wavy, orstraight hair.

Curly Hair

Nucleic Acids• Long chains of nucleotide subunits.

– Nucleotides consist of a 5-carbon sugar, aphosphate group, and a nitrogen-containingbase (the variable group).

• Nucleotides are covalently linked via theirphosphate groups to form nucleic acids.

Two Main Typesof Nucleotides

• Ribose nucleotides(subunit of RNA)– Ribonucleic acid (RNA) is

copied from DNA and isinvolved in protein synthesis.

• Deoxyribose nucleotides(subunit of DNA)– Deoxyribonucleic acid (DNA)

contains the genetic materialof all living organisms.

DNA

• Linked deoxyribosenucleotides form asingle-stranded DNA(ssDNA) molecule.

• Two ssDNA chainsbind with hydrogenbonds between thenitrogen-containingbases to form ahelical structure.

• Other nucleotides:– Cyclic AMP (adenosine monophosphate)

– Intracellular messenger.– Adenosine triphosphate, ATP

– Energy currency of all cells.– NAD+ and FAD

– Electron carriers.

Homework

Chapter 3

Thinking Through the Concepts, Review Question #5

Applying the Concepts #1