• molecules are made by living cells.
• these molecules are composed of carbon and the functional groups
• cells actually join small organic molecules together to form larger molecules called macromolecules.
• these molecules belong to 4 classes:
• carbs
• lipids
• proteins
• nucleic acids

Cells make carbs, proteins, and nucleic acids by linking smaller identical parts or subunits called monomers (one part)
into polymers (many parts).
 

Condensation Reaction (or dehydration reaction)

• Monomers are connected together by a reaction in which 2 molecules are covalently bonded to each other through loss of a water molecule.  
• Called a dehydration reaction b/c a water molecule is lost.
• When a bond forms between 2 monomers each contributes part of the water molecule that is lost:  one molecule provides a hydroxyl group and the other provides a hydrogen.
• To make a polymer the reaction repeated as monomers are added one by one.

Hydrolysis

• A process whereby polymers are disassembled to monomers
• hydrolysis is essentially the reverse of the dehydration reaction.
• hydrolysis means to break with water from the greek hydro (water) and lysis (break).
• bonds are broken by the addition of water molecules, a hydrogen from the water attaching to one monomer and a hydroxyl attaching to the adjacent monomer.
• eg of hydrolysis - digestion.  The bulk of the organic material in or food is in the form of polymers that are much too large to enter our cells.  within the digestive tract various enzymes attack the polymers, speeding up hydrolysis. the released monomers are then absorbed into the bloodstreamfor distribution to all body cells.  Those cells can then use dehydration reactions to assemble the monomers into new polymers that differ from the ones that were digested.

CARBOHYDRATES = sugars (Fuel and Building Material)

1. monosaccharides (single sugars)
2. disaccharides (double sugars, two monosaccharides)
3. polysaccharides (polymers of many sugars)

Monosaccharides

• molecular formula is some multiple of CH2O (e.g. glucose - C6H2O6)
• classified by several criteria:
• they have a hydroxyl group attached to each carbon except one, which is double bonded to an oxygen to form a carbonyl group.
• the size of the carbon skeleton ranges between 3 to 7 carbons longs.
• - OSE is a common ending for sugars (glucose and fructose)
• are major nutrients for cells (especially glucose)
• in cellular respiration, cells extract the energy stored in glucose molecules
• serve as the raw material for the synthesis of other types of small organic molecules, including amino acids and fatty acids.
• sugar molecules not immediately used are generally incorporated as monomers into disaccharides and polysaccharides.

Disaccharides

• Double sugar (consist of two monosaccharides joined by a glycosidic linkage, which is a covalent bond formed between two monosaccharides).
• The most prevalent disaccharide is sucrose.,
• e.g. sucrose (formed by condensation synthesis) 1-2 glycosidic linkage (fig. 5.5 in text)

Polysaccharides

• polymers of many monosaccharides.
• They consist of a few hundred to a few thousand monosaccharides linked together giving them a huge molecular weight.
• Two types of polysaccharides
• Storage polysaccharides are storage material, hydrolyzed (broken down) as needed to provide sugar for cells
• Plants store polysacc. as starch.  It consists entirely of glucose joined by 1-4 glycosidic linkages.
• Most animals, including humans have enzymes that break down or hydrolyze starch, making glucose available as a nutrient for cells.  The major soucres of starch in our diets are wheat, corn, rice, potatoes.
• Animals store polysacc. as glycogen.  We store glycogen in the liver and muscle cells
• and hydrolzye it for glucose when the need arises (i.e. energy). Storage time isn't long however, it lasts only a day. (see fig. 5.6)
• Structural Polysaccharides serve as building material for structures protecting cells or whole organisms
• e.g., in plants, cellulose is a major component of the tough walls that enclose plant cells (we commonly refer to it as fiber, because we can't digest it, but it is good to flush out your insides).  Cellulose is the most abundant compound on Earth (fig. 5.7 in text).
• Cellulose is a polymer of glucose, like starch, however, it differs in how the two glucose ring structures are interconnected alpha vs beta linkages.
• If you intertwine enough strands of cellulose with hydrogen bonds you will get strong fibrils which make up the cell walls of plants.
• eg., chitin. Chitin is a carbohydrate used by insects, spiders, etc. to build their exoskeleton

LIPIDS - hydrophobic compounds

• they are the one class of large biological molecules that does not include polymers.
• a family of compounds grouped together because they are all hydrophobic.
• they are mostly hydrocarbons but they may have some polar bonds associated with oxygen.
• Three families of lipids:
• Fats are large molecules constructed from two kinds of smaller molecules: glycerol and fatty acids from a dehydration reaction.  glycerol is an alcohol and a fatty acid is a hyrocarbon of about 16 or 18 carbon atoms.
• The nonpolar C-H bonds in the tails of fatty acids are the reason fats are hydrophobic.
• Fats separate from water b/c the water molecules hydrogen bond to one another and exclude fats.
• A common eg. of this is the separation of vegetable oil (a liquid fat) from the aqueous vinegar solution in a bottle of salad dressing.
• In making a fat, 3 fatty acids each join to a glycerol and the resulting fat is called a triacylglycerol.
• Fatty acids can vary in length and in the number and locations of double bonds.  saturated vs. unsaturated grants.    these terms refer to the structure of the hydrocarbon tails of the fatty acids.  I
• saturated fatty acid - no double bonds between the carbon atoms composing the tail, as many hydrogen atoms as possible are bonded to the carbon skeleton
• eg., animal fats are saturated (e.g. bacon grease, lard, and butter) and are solids at room temperature.
• unsaturated fatty acid  - has one or more double bonds, formed by the removal of hydrogen atoms from the carbon skeleton.
• eg., Plant fats are unsaturated and are liquid at room temperature and are referred to as oils
• Phospholipids - structurally related to fats, but have only two fatty acid chains instead of 3 like fats and they have a phosphate group.
• The phosphate group is negatively charged and additional small molecules that are charged or polar, can be linked to the phosphate group to form a variety of phopholipids.
• The tails of these groups exclude water but the charged phophate side forms a hydrophilic head that has an affinity for water.
• At the surface of a cell phopholipids are arranged in a double layer (bilayer).  The hydrophilic heads of the molecules are on the outside of the bilayer, in contact with the aqueous solution inside and outside the cell.  The hydrophobic tails point toward the interior of the membrane, away from the water.
• The phopholipid bilayer forms a boundary between the outside of the cell and its external environment; in fact, phospholipids are the main components of cell membranes.
• Steroids - carbon skeletons consisting of 4 interconnected rings
• e.g. cholesterol a component of the membranes of animal cells. Also cholesterol is an important precursor to other steroids by adding or subtracting different functional groups

PROTEINS

• account for more than 50% of dry weight of cells
• A human has tens of thousands of different proteins including
• structural proteins (e.g., keratin for hair)
• storage proteins (e.g., casein, protein of milk,  source of amino acids for baby mammals)
• enzymatic proteins (e.g., digestive enzymes hydrolyze polymers of food)
• others (see Table 5.1 in text).
• Proteins are structurally complex, but are all comprised of amino acids (the monomers of proteins)

amino acids

• organic molecules possessing both carboxyl and amino functional groups --COOH and NH2
• the general formula for an amino acid (p.68 in text)
• 20 kinds of amino acids.
• Cells build proteins from various combinations of the 20 amino acids
• Amino acids consist of
• an alpha carbon bonded to a hydrogen
• a carboxyl group
• an amino group
• a variable portion (side chain) symbolized by the letter R.
• The physical and chemical properties of an amino acid are determined by the side chain.
• the side chain determines the unique characteristics of a particular amino acid.

I will not hold you responsible for knowing the molecular structure of all twenty amino acids, however, you should be able to identify whether one is polar, non-polar, electrically charged and if electrically charged whether it is acidic or basic.

How can I tell if an amino acid is polar, nonpolar, acidic or basic?
1. The R group is different for every amino acid - learn to distinguish the R group from the nonvariable portions of the amino acids
2.  Remember the chemistry learned in Ch.2 and 4

Nonpolar R groups will share electrons equally
Polar R groups - electrons will not be shared equally (funcational groups such as sulfhydryl or alcohal groups)
Carboxyl groups (p.54) are acidic and are composed of COOH
Amino groups (p.54) are basic and have N in them

How do we link amino acid monomers to form a protein polymer?

• Condensation synthesis (fig. 5.16 in text)
• when two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, an enzyme can join the amino acids by means of a dehydration reaction.
• The resulting bond is a peptide bond.
• N-C-C-N-C-C = polypeptide backbone
• when the process is repeated over and over it results in a polypeptide.
• At one end of the polypeptide chain is a free amino group and at the opposite end is a free carboxyl group.
• The chain has polarity with an amino end (N-terminus) and a carboxyl end (C terminus).

A protein consists of one or more polypeptide chains twisted and folded upon themselves to form a particular 3-D shape or conformation.
 

• The conformation of a protein is important for how a protein functions (fig. 5.20 in text).
• 4 Levels of Protein Structure
• Primary Structure is the unique sequence of amino acids of a protein.
• e.g., lysozyme (antibacterial enzyme present in our tears ) - it consists of a single polypeptide chain that is 129 aa long.
• the primary structure of a protein is basically the amino acid sequence of the protein
• lysozyme, like all proteins, is coded for by specific pieces of DNA and the position of each and every amino acid in the protein is important for its function.
• A change in the amino acid structure can affect the proteins configuration and make it not function properly. For instance, sickle cell anemia is due to a mutation leading to a different amino acid in position 6 (Val instead of a Glu) (see fig. 5.19 in text).
• Molecular biologists have sequenced hundreds of protein sequences.  HUMAN GENOME PROJECT
• Secondary Structure is the folding of a polypeptide chain due to the formation of hydrogen bonds at regular intervals along the polypeptide backbone or skeleton.
• Two types:
• alpha helix (a hydrogen bond between every fourth peptide bond)
• beta pleated sheet (hydrogen bonds between parallel regions)
• not all proteins have alph ahelix and beta pleated sheets, but lysozyme has both.  Lysozyme is a fairly typical globular protein that has stretches of alpha helix that are separated by nonhelical regions.
• In contrast, some fibrous proteins, like alpha-keratin, which is the structural protein of hair, have the alpha helix formation over their length.
• Pleated sheets also dominate the secondary structure of some fibrous proteins, such as the silk produced by many insects and spiders.
• Tertiary Structure is structure of the protein from bonding between side chains or R groups of the various amino acids.
• Hydrophobic interactions:  as a polypeptide folds into its functional conformation, amino acids with hydrophobic (nonpolar) side chains usually congregate in clusters at the core of the protein, out of contact with water.
• H bonds between polar side chains and ionic bonds between positively and negatively charged side chains also help stabilize tertiary structure.
• disulfide bridges, which are strong, covalent bonds, also reinforce the tertiary structure of the protein.   Disulfide bridges form when 2 cysteine monomers (have sulfhydryl groups) are brought close together by the folding of the protein.
• Quaternary Structure is structure due to interaction of more than one polypeptide chain or subunit  (some proteins consist of more than one polypeptide chain)
• eg - collagen is an aggregation of 3 subunits supercoiled into a larger triple helix.

In a cell, proteins spontaneously arrange themselves into their 3 dimensional shapes after being synthesized

• proteins can denature or unwind if conditions change.
• Misshapen, denatured proteins are no longer biologically active.
• Proteins can denture from changes in
• salt concentration
• pH
• temp
• eg. - the white part of an egg (albumin) becomes opaque during cooking because the denatured proteins are insoluble and solidified from heat

NUCLEIC ACIDS

• The amino acid sequence for a protein comes from a gene.
• Genes are made of DNA, which is a polymer of belonging to the class of compounds called nucleic acids.
• 2 types of nucleic acid
• DNA - deoxyribonucleic acid
• RNA - ribonnucleic acid
• These molecules enable living organisms to reproduce their complex equipment from one generation to the next.
• DNA is the genetic material you get from your parents.
• DNA can replicate itself, and make RNA, which makes protein.

Nulceotides

• the monomers of nucleic acids
• 3 parts of a nucleotide
• a nitrogenous base, which is joined to
• a pentose (five carbon) sugar, which in turn is bonded to
• a phosphate group (see fig. 5.27)

Nitrogenous bases

• pyrimidines
• cytosine (C)
• thymine (T)
• uracil (U)
• has a 6-membered ring of carbon and nitrogen atoms.
• purines
• adenine (A
• guanine (G)
• larger, with the 6 membered ring fused to a five-membered ring.
• The specific pyrimidines and purines differ in the functional groups attached to the rings.
• Uracil is found only in RNA and Thymine only in DNA

polynucleotide

• nulceic acids are polynucleotides - they consist of many nucleotides
• consist of a phosphate backbone with different nitrogenous bases being the appendages of the backbone
• the nucleotides are linked by covalent bonds called phophodiester linkages between the phosphate of one nucleotide and the sugar of the next.
• DNA molecules of cells actually consist of 2 polynucleotides that spiral around an imaginary axis to form a double helix.  This 3D image was discovered in 1953 by Watson and Crick (who won the Nobel prize for this discovery)