Chemistry of Life 2.4: Organic Compounds

Polymers/monomer

Molecules made of a repetitive series of identical or similar subunits called monomers

Carbohydrates

Hydrophillic organic molecule, such as sugars or starches

Source of energy to be used quickly. All carbohydrates are eventually converted to glucose and is oxidized to make ATP

Monosaccharides

Simplest carbohydrates, simple sugars

Glucose - Blood sugar

Galactose

Fructose

Disaccharides

Sugar composed of two monosaccharides

Sucrose (glucose + fructose) - sugar cane/sugar beets - table sugar

Lactose ( glucose + galactose) - milk sugar

Maltose (glucose + glucose) - starch - malt beverage or germinating grains

Oligosaccharides / Polysaccharides

Oligosaccharides - Short chains of 3 or more monosaccharides

Polysaccharides - Long chains up to thousands of monosaacharides long - glycogen, starch and cellulose all made of glucose

Glycogen

Energy storage polysaccharide made by cells of the liver, mucles, brain, uterus, and vaginia.

Long, branched glucose polymer

Starch

Corresponding energy storage polysaccharide of plants.

Celluslose

Polysaccharide that gives strength to cell wall of plant. Principle component of wood, cotton, and paper.

Proteoglycans

Macromolecules where carbohydrates are the dominant component and proteins form the smaller component. Forms gels that hold cells and tissues together form a gelatinous filler in the umbilical cord and eye, lubricates the joints of the skeletal system and cartilage

Lipids

Hydrophobic organic molecule composed only of carbon, hydrogen, and oxygen with a high ration of hydrogen to oxygen.

Less oxidized than carbohydrates, and have more calories per gram

There are five types: fatty acids, triglycerides, phospholipids, eicosanoids, and steroids

Fatty Acids

Chain of 4 - 24 carbon atoms with a carboxyl group at one end and a methyl group at the other

Saturated Fatty Acids

Palmitic acid has as much hydrogen as it can carry

No more hydrogen can be added without exceeding four covalent bonds per carbon

“saturated with hydrogen”

Unsaturated Fatty Acids

Linoleic acid, carbon atoms are joined by double covalent bonds

Potential to share one pair of electrons with another hydrogen atom instead of adjacent carbon, more hydrogen can be added

Polyunsaturated fatty acids

Multiple C=C bonds (carbon-carbon)

Essential Fatty Acids

Most fatty acids that human need can be synthesized in the human body. Those that cannot and must be obtained from diet are known as essential fatty acids

Triglyceride

Three carbon alcohol called glycerol linked to three fatty acids

Liquid at room temp aka Oils.

Fat

Primarily energy storage

Concentration in adipose tissue (connective tissue), provides thermal insulation and act as shock absorbing cushion for vital organs

Phospholipids

Have phosphate groups linked to other functional groups

Phospholipids have two fatty acid “tails” that are hydrophobic but the phosphate “head” is hydrophilic, making them known as amphipathic which help to serve as structural foundation of cell membranes

Eicosanoids

20 carbon compounds derived from a fatty acid called arachidonic acid

Function hormone like chemical signals between cells

Prostaglandins

Most functionally diverse eicosanoids - five of the carbon atoms are arranged in a ring. Found in secretions of the bovine prostate gland, produced in all tissue.

Play in inflammation, blood clotting, hormone action, labor contractions, blood vessel diameter, and more

Steroids

Lipid with 17 carbon atoms arrange in 4 rings

Cholesterol

“parent” steroid from which all other steroids are synthesized

Cortisol

Progesterone

Estrogen

Testosterone

Bile Acids

Cholesterol is needed for is needed for normal body functions. It is important for cell membranes and required for proper nervous system function. Only 15% comes from diet, the other 85% is synthesized naturally in the body mostly by the liver

Proteins

Polymer of amino acids

Proteins are amphipathic (hydrophilic and hydrophobic)

Polypeptide of more than 50 amino acids

Amino acids

Central carbon atom with amino and carboxyl group bound to it.

There are 20 amino acids that make proteins

Peptides

Any molecule made up of 2 or more amino acids joined by peptide bonds

Named for how many amino acids are in them

dipeptides - two

tripeptides - three

oligopeptides - few than 10-15 (example is oxytoxic, 9 amino acids)

polypeptides - more than 15

proteins - more than 50

Describe a proteins primary structure

A protein’s sequence of amino acids, encoded in gene

Most basical structure

Describe a proteins secondary structure

Coiled/folded shaped held together by hydrogen bonds

Most commonly alpha helix or b sheet

Most proteins have multiple alpha and B sheet regions joined by segments of less orderly areas.

Describe a proteins tertiary structure

More folding/bending into globular and fibrous shapes

Hydrophobic radicals are avoiding water while the hydrophilic are going to it, the Van der Waals force is at play and helps the structure Globular proteins - can resemble tangled ball of yarn have a structure well suited for proteins that are in cell membranes and proeins that move freely through body fluids such as enzymes and antibodies

Fibrous proteins - slender filaments better suited in muscle contraction, provide strength to skin, hair, and tendons. Examples include myosin, keratin, and collagen

Describe a proteins quaternary structure

two or more polypeptide chains associating through noncovalent forces such as ionic bonds or hydrophilic/hydrophobic interactions

Only occurs in some proteins

Why does a protein being able to change structure matter?

Because subtle reversible changes are necessary for situations such as enzyme function, muscle contraction, open/closing of pores in the cell membrane

What is denaturation?

Drastic usually permanent changes in structure due to things like heat or pH change making the protein unable to preform their normal function

Best example is cooking an egg

Protein Functions

Structure - add structure that is needed such as keratin giving structure to bone, cartilage and skin

Communication - help with cell to cell communication - hormones are an example. Hormones or other molecules that reversibly bind to a protein is a ligand

Membrane transport - can form tunnels in cell membranes that govern what passes through the membrane and when, can also act a carrier to bind to particles and move them through membranes especially important in muscles and nerve activity

Catalyst - Metabolic pathways of the body are controlled by enzymes which are globular proteins that work as catalysts

Recognition/protection - Glycoproteins in the immune system act as recognizers - antibodies and other proteins then act as attackers and neutralize organisms that invade the body, or as clotting proteins

Movement - are the basis of movement, which is the fundamental part of life

Cell adhesion - bind cells together, examples include sperm to egg, immune cell to sick cells, and keeping tissues together

Enzymes / substrate

A protein that is a biological catalyst - allowing biochemical reactions to occur in the body at normal temperatures

A substrate is what the enzyme is acting upon

-ase is added and indicts the enzymes action

An enzyme is not consumed in the reaction it catalyzes, allowing it to be used over and over

Cofactors

2/3 of human enzymes need a nonprotein partner to help them

Inorganic cofactors include iron, copper, zinc, magnesium, and calcium

They can work by binding to the enzyme and making it fold into the shape that is needed at an activation site

Coenzymes are organic cofactors include niacin, riboflavin, and other water soluble vitamins

Metabolic Pathways

Chain of reactions with each step catalyzed by a different enzyme

A → B → C → D - A is the initial reactant, B+C are intermediates and D is the end product and each step needs a different enzyme to go off

The pathway can be turned on or off when they are needed

Nucleotides

Organiz compounds with three principle components: single or double carbon-nitrogen ring called nitrogenous bae, a monosaccharide, and one or more phosphate groups

ATP is one of the best known nucleotides

ATP - adenosine triphosphate

Most important energy transfer molecule in the body

Gains energy from exergonic reactions such as glucose oxidation and releases within seconds

Short lived molecule, usually consumed within 60 seconds of its formation.

Nucleic Acids

Polymers of nucleotides

DNA deoxyribonucleic acid (DNA) is the largest 100 million - 1 billion nucleotides long

RNA ribonucleic acid range from 70 to 10,000 nucleotides long