Carbon-based compounds

• Chapter 4~ Carbon & The Molecular Diversity of Life

Organic chemistry…

The Chemistry of CarbonForms a tetrahedral shape when bound to 4 molecules

Tetravalence- 4 e- in outer shell

Hydrocarbons• Only carbon & hydrogen

(petroleum; lipid ‘tails’)• Covalent bonding; nonpolar• High energy storage• Isomers (same molecular formula,

but different structure & properties)– structural~differing covalent

bonding arrangement– geometric~differing spatial

arrangement – enantiomers~mirror images

• pharmacological industry (thalidomide)

Prefixes

• Organic compounds are named with prefixes

• Plain hydrocarbons end with –ane – Double bonds= ene– Side groups change

names (ex: -OH = -ol)

Functional Groups

• Attachments that replace one or more of the hydrogens bonded to the carbon skeleton of the hydrocarbon

• Each has a unique property from one organic compound to another

• Hydroxyl Group – H bonded to O– alcohols– polar (oxygen)– solubility in water

• Carbonyl Group– C double bond to O– At end of H-C: aldehyde– Otherwise: ketone

• Carboxyl Group – O double bonded to C to hydroxyl– carboxylic acids (dissociation= H+)– covalent bond between O and H– Polar

• Amino Group– N to 2 H atoms– “amines”– acts as a base

• Sulfhydral Group– sulfur bonded to H– Thiols– Can cross-link with each other

• Methyl Group– C bonded to 3 H’s– Affects

shape/configuration

• Phosphate Group– phosphate ion

covalently attached by 1 O to the C skeleton

– Negatively charged

ATP= NRG

- ATP is the main energy source for cells.

- One phosphate group is cleaved off to form ADP and energy is released

Macromolecules

Chapter 5~The Structure & Function of Macromolecules

Polymers

• Covalently bonded monomers

• Condensation (dehydration) reaction– One provides a –OH while the

other provides a H to form a water molecule

• Hydrolysis– bonds between monomers are

broken by adding water (ex:digestion)

Carbohydrates• Monomer =

Monosaccharides – CH2O formula– multiple hydroxyl (-OH) groups

and 1 carbonyl (C=O) group:• aldehyde (aldose) sugar- group at end • ketone (ketose) sugar- group in center

• broken down during cellular respiration

• raw material for amino acids and fatty acids

Putting them together

• Disaccharides – glycosidic linkage

(covalent bond between 2 monosaccharides)

• Sucrose (table sugar)– most common

disaccharide

Functions of Carbohydrates

• Storage:– Starch= glucose monomers– Plants: roots/plastids – Animals: glycogen/fat

• Structure:– Cellulose~ most abundant organic

compound – Chitin~ exoskeletons; cell walls of

fungi; surgical thread

Lipids• Monomers: Triacyglycerol (triglyceride)

– Carboxyl group = fatty acid– Ester linkage: 3 fatty acids to 1 glycerol molecule

• Fats, phospholipids, steroids• Hydrophobic• Non-polar C-H bonds in fatty acid ‘tails’• Saturated vs. unsaturated fats; single vs.

double bonds

Saturated vs. Unsaturated

Phospholipids

• Two fatty acids instead of three– phosphate group attaches

to one -OH

• ‘Tails’ = hydrophobic• ‘Heads’ = hydrophilic

Phospholipids in formation

- Micelle (phospholipid droplet in water)

- Bilayer (double layer)- cell membranes

Steroids

• Lipids with 4 fused carbon rings

• Ex: cholesterol...– cell membranes– precursor for other steroids

(sex hormones)– “Good” (HDL) vs “Bad”

(LDL) cholesterol• atherosclerosis

Proteins• Importance:

– instrumental in nearly everything organisms do

– 50% dry weight of cells– most structurally sophisticated

molecules known• Monomer = amino acids (20)

– central carbon atom– carboxyl (-COOH) group– amino group (NH2)– H atom– variable group (R)

Amino Acid R- Groups

Variable (R-) group characteristics:

• R- group interactions determine shape and function– Nonpolar (hydrophobic)

• Gly, Ala, Val, Leu, Ile, Met, Phe, Trp, Pro

– Polar (hydrophilic)• Ser, Thr, Cys, Tyr, Asn, Gln

– Acids• Asp, Glu

– Bases• Lys, Arg, His

Putting them together

• Polypeptides formed by a dehydration reaction.– peptide bonds~ covalent bond of carboxyl group to

amino group

3-D Structure

• Proteins function is determined by their structural conformation

• Amino acid sequence determines how it will fold– Affinity of A.A’s for each other, etc.

• Chaperonins- proteins that assist in folding of other proteins– Segregate and protect proteins and allow them to fold

w/o any “bad influences”• Four levels of protein structure

Primary Structure• Linear structure of Amino Acids• Molecular Biology:

– each protein has a unique primary structure of amino acids

• Examples:– One amino acid substitution in hemoglobin

causes sickle-cell anemia

Secondary StructureCoils & folds caused by

hydrogen bonds • Alpha Helix:

– Coiling~ every 4th AA• fibrous proteins, keratin

• Pleated Sheet:– Parallel sheets w/ H bonding

between them• globular proteins, spider silk

Tertiary Structure• Protein takes on irregular

contortions from R group bonding– Hydrogen bonds between

polar side groups– Hydrophobic molecules

undergo van der Waals interactions

– Disulfide bridges form between cystine –SH groups

– Ionic bonds between + and -

Quaternary Structure• 2 or more polypeptide chains

aggregated into 1 macromolecule– Collagen (connective tissue

that makes up 40% of body structure)

– Hemoglobin (Oxygen binding protein in red blood cells)

* 3-D structure of proteins discovered w/ X-ray crystallography and nuclear magnetic resonance (NMR)

Denaturation

• If protein shape is changed, it cannot function properly– Heat, pH change,

chemical treatment, etc.• Sometimes proteins can

be “renatured” if environment is restored to normal (rare)

Nucleic Acids

• 2 types:– Deoxyribonucleic acid

(DNA)– Ribonucleic acid (RNA)

• Storage and transmittance of genetic information

• DNA RNA protein

• Monomers= nucleotides

• Each nucleotide is composed of:– nitrogenous base– pentose sugar– phosphate group

“Polynucleotides”

• Joined by phosphodiester linkages– covalent bonds

between phosphate groups

Nitrogenous bases• Purines always pair

w/ Pyrimidines

• DNA- - A & T- G & C

• RNA-- A & U - G & C

DNA

• In nucleus• Codes for proteins (like

blueprints)• Double helix

– 2 strands held together by H-bonds between bases

– Complimentary base pairing

• Sugar = deoxyribose• Bases- A, G, C, T

Watson and Crick

• James Watson and Francis Crick discovered the double helix structure of DNA in 1953.

RNA• Single stranded• Several types:

– Ex: mRNA, rRNA, tRNA

• Acts as messenger between DNA in nucleus and ribosomes in cytoplasm

• Sugar= ribose• Bases- A, G, C, U