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Almost all of the molecules a cell makes are composed of carbon atoms bonded to one

another and to atoms of other elements.

ORGANIC COMPOUNDS- Carbon-based molecules. Each carbon atom is a connecting point

from which a molecule can branch in up to four directions.

HYDROCARBONS- Compounds composed of only carbon and hydrogen atoms. Carbon

atoms, with attached hydrogens, can bond together in chains of various lengths to form

compounds.

CARBON SKELETON- The chain of carbon atoms in an organic molecule. May be branched

or unbranched.

Compounds with the same formula but different structures are called ISOMERS.

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The unique properties of an organic compound depend on the size and shape of its carbon

skeleton and on the groups of atoms that are attached to that skeleton.

FUNCTIONAL GROUPS- Affect a molecule’s function by participating in chemical reactions

in characteristic ways. These groups are polar, because their oxygen or nitrogen atoms

exert a strong pull on shared electrons.

This polarity tends to make the compounds containing these groups HYDROPHILIC (water-

loving) and therefore soluble in water.

A HYDROXYL GROUP consists of a hydrogen atom bonded to an oxygen atom, which in turn

is bonded to the carbon skeleton.

In a CARBONYL GROUP a carbon atom is linked by a double bond to an oxygen atom. If this

functional group is found at either end then it is called an ALDEHYDE, but if it is located in

the middle than it is known as a KETONE.

A CARBOXYL GROUP consists of a carbon double- bonded to an oxygen and also bonded to

a hydroxyl group. Mostly used as an acid.

An AMINO GROUP is composed of a nitrogen bonded to two hydrogen atoms and the

carbon skeleton. Normally acting as a base by picking up H+ ions.

A PHOSPHATE GROUP consists of a phosphorus atom bonded to four oxygen atoms.

A METHYL GROUP consists of a carbon bonded to three hydrogens. This molecule affects

the expression of genes.

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MACROMOLECULES- Gigantic chains covalently connected atoms.

Cells make most of their large molecules by joining smaller molecules into chains called

POLYMERS; a POLYMER is a long molecule consisting of many identical or similar building

blocks strung together. The building blocks of polymers are called MONOMERS.

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Cells link monomers together to form polymers by a DEHYDRATION REACTION, a reaction

that removes a molecule of water.

Each monomer has an H+ at one end an OH- at the other end. For each monomer added

to a chain, a water molecule is removed.

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Cells not only have to make polymers but also have to break them down. This process is

essentially the reverse of a dehydration reaction, because instead of removing a water

molecule, we add a water molecule. Both dehydration reactions and hydrolysis require the

help of enzymes to make and break bonds. Enzymes are specialized macromolecules that

speed up chemical reactions in a cells.

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The name CARBOHYDRATES refers to a class of molecules ranging from the small sugar

molecules dissolved in soft drinks to large polysaccharides, such as the starch molecules we

consume in pasta and potatoes.

The carbohydrate monomers are MONOSACCHARIDES. Monosaccharide's generally have

molecular formulas that are some multiple of CH2O. The two trademarks of sugars; a

number of hydroxyl groups and a carbonyl group.

It is convenient to draw sugars as if their carbon skeletons were linear, but in aqueous

solutions, most monosaccharide's form rings.

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Cells construct a DISACCHARIDE from two monosaccharide’s by a dehydration reaction.

The most common disaccharide is sucrose, which is made of a glucose monomer and a

fructose monomer.

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POLYSACCHRIDES are polymers of monosaccharides linked together by dehydration

reactions. Polysaccharides may function as storage molecules or as structural compounds.

STARCH, a storage polysaccharide in plants, consists entirely of glucose monomers. Starch

molecules coil into a helical shape.

Animal store excess sugar in the form of another glucose polysaccharide, called GLYCOGEN.

In animals glycogen is mainly stored in our liver and muscle cells.

CELLULOSE, the most abundant organic compound on earth, forms cable like fibrils in the

tough walls that enclose plant cells. A key feature of this polymer is that the branching

alternates at every junction.

Because humans don’t have enzymes to digest cellulose, therefore cellulose is not a

nutrient for humans

Another structural polysaccharide, CHITIN, is used by insects and crustaceans to build their

exoskeleton, the hard case enclosing the animal.

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LIPIDS are diverse compounds that are grouped together because they share one trait; they

mix poorly with water, if at all. Lipids consist mainly of carbon and hydrogen atoms linked

by non-polar covalent bonds. Lipids are HYDROPHOBIC (water-fearing).

A FAT is a large lipid made from two kinds of smaller molecules: glycerol and fatty acids.

Glycerol is an alcohol with three carbons, each bearing a hydroxyl group. A fatty acid

consists of carboxyl group and a hydrocarbon chain. The main function of fats is for storage.

In addition to storing energy, fatty tissue cushions vital organs and insulates the body. Some

fatty acids contain double bonds, which cause kinks (bends) in the carbon chain. Double

bonds prevent the maximum number of hydrogen atoms from bonding to a carbon

skeleton. Fatty acids and fats with double bonds in the carbon chain are said to be

UNSATURATED- having less than the maximum number of hydrogens. Fats with the

maximum number of hydrogens are said to be SATURATED. The kinks in unsaturated fats

prevent the molecules from packing tightly together and solidifying at room temperature.

Hydrogenation is when we add hydrogen to unsaturated fats, making them saturated.

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Phospholipids are the major components of cell membranes.

Phospholipids are structurally similar to fats, but they contain only two fatty acids attached

to glycerol instead of three. The hydrophilic and hydrophobic ends of multiple molecules

assemble in a bilayer of phospholipids to form membranes. The hydrophobic tails cluster in

the center, and the hydrophilic phosphate heads face the watery environment on both

sides of the membrane.

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Steroids are lipids whose carbon skeleton contains four fused rings.

Cholesterol is a common component in animal cell membranes, and animal cells also use it

as a starting material for making other steroids, including sex hormones.

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ANABOLIC STEROIDS are synthetic variants of the male hormone testosterone.

Testosterone causes a general build up of muscle and bone mass in males during puberty

and maintains muscle traits throughout life.

They can be used as a prescription to treat anemia and diseases that destroy body muscle.

However, some abuse these drugs, with serious consequences. Overdosing may cause

violent mood swings and deep depression. The liver may be damaged, leading to cancer.

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The most important roles of proteins is as enzymes, the chemical catalyst that speed and

regulate virtually all chemical reactions in a cell.

A protein is a polymer constructed from amino monomers

Each of our many thousands of different proteins has a unique 3D structure that

corresponds to a specific function

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Protein diversity is based on differing arrangements of a common set of just 20 amino

acids. AMINO ACIDS all have an amino group and a carboxyl group. The central carbon is

known as the alpha Carbon. Notice the amino group, carboxyl group, and the Hydrogen

atom attached to the alpha carbon which are common to amino acids. The R group (side

chain) consists of one or more carbon atoms with various chemical groups attached. The

structure of the R group determines the specific properties of each of the 20 amino acids

that are found in proteins.

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Cells join amino acids together in a dehydration reaction that links the carboxyl group of

one amino acid to the amino group of the next amino acid as a water molecule is removed.

The resulting covalent linkage is called a PEPTIDE BOND. A chain of amino acids,

POLYPEPTIDE

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The 3D shape is what determines its specific function. Their shapes enable them to

recognize and attach to its molecular target. The dependence of protein function on a

protein’s specific shape becomes clear when proteins are altered. In a process called,

DENATURATION, polypeptide chains unravel, losing their specific shape, and as a result

their function.

Changes in salt concentrations and pH can denature many proteins, as can excessive heat.

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The PRIMARY STRUCTURE- Is its unique sequence of amino acids. The three letter

abbreviations represent amino acids.

The SECONDARY STRUCTURE- In the second level of protein structure, parts of the

polypeptide coil or fold into local pattern. Coiling of a polypeptide chain results in a

secondary structure called an ALPHA HELIX; a certain kind of folding leads to PLEATED

SHEETS. The double helix and the pleated sheets are held together by hydrogen bonds.

The TERTIARY STRCUTURE- refers to the overall three-dimensional shape of a polypeptide.

The indentations and bulges arising from its particular arrangement of coils and folds give

the polypeptide the specific shape that fits to its function.

Many proteins consist of two or more polypeptide chains, or subunits. Such proteins have a

QUATERNARY STRUCTURE, resulting from the association of the subunits.

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Pauling was studying biological molecules, in 1953 he and a colleague discovered how

oxygen molecules attach to iron atoms of hemoglobin. He also discovered how an

abnormal hemoglobin molecule causes sickle-cell disease. And it was also Pauling who first

described the two fundamental secondary structures of proteins, the alpha helix and the

pleated sheets.

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The amino acid sequence of a polypeptide is programmed by a discrete unit of inheritance

known as a GENE. GENES consist of DNA one of the two types of polymers known as

NUCLEIC ACIDS. A gene does not put its genetic DNA information to work directly. It works

through an intermediary- the second type of nucleic acid known as RNA.

The monomers that make up nucleic acids are NUCLEOTIDES. A NUCLETIDE consists of a

Phosphate group, a Sugar, and a Nitrogenous base.

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The repeating of sugar to phosphate. Blue-yellow-blue-yellow….

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RNA usually consists of a single polynucleotide strand, but DNA is a DOUBLE HELIX, in

which two polynucleotides wrap around each other. The nitrogenous bases protrude from

the two sugar-phosphate backbones into the center of the helix. A pairs with T and G pairs

with C. The two strands are held together by hydrogen bonds between their based pairs.

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