Chapter 23: Biological Chemistry Biochemistry is the area of chemistry that focuses on the study of compounds and processes occurring in living systems. Important classes of biological compounds that we will be responsible for: Carbohydrates: molecules composed of C, H and O in a 1 to 2 to 1 ratio (carbohydrates play a role in providing nutrients to cells) Lipids: a molecule with a large percentage of C and H atoms that produce a non-polar substance (lipids are generally not soluble in water but would be soluble in non-polar solvents) Proteins: are polymers of amino acids (an amino acid has a NH2 group and an CO2H group in the same molecule), proteins often act as the building blocks of cells) Nucleic Acids: are the molecules that carry genetic information, they are polymers made from repeating phosphate, sugar, and a nitrogenous bases (two major types are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA))

Carbohydrates: molecules composed of C, H and O in a 1 to 2 to 1 ratio (carbohydrates play a role in providing nutrients to cells) Sugars (called saccharides) are carbohydrates Sugars are broken into two categories: aldoses and ketoses (the –ose ending is used to indicate that the molecule is a sugar) An aldose contains an aldehyde carbonyl group in its open chain form A ketose contains a ketone carbonyl group in its open chain form A monosaccharide (called a simple sugar) contains a single aldose or ketose molecule while a disaccharide molecule consists of two monosaccharide molecules that join together. A polysaccharide contains many monosaccharaides joined together into a chain,

Glucose is a aldahexose: alda because of the aldehyde group, hex because of 6 carbons, -ose because it is a sugar

Ring formation in Glucose: One of the lone pairs on an OH group (the one in red) will react with the carbonyl carbon of the aldehyde (shown in blue) to form a six membered ring that contains an oxygen atom (this ring is called a pyran). The a and b symbols refer to the direction that the new OH group points (up or down respectively) in the figure.

1) Fructose is a ketohexose: keto because of the ketone group, hex because of 6 carbons, -ose because it is a sugar Ring formation in fructose is similar to what happens with glucose. The difference is that the ketone carbon is carbon 2 in the chain (the aldehyde was carbon 1). As a result, a five member ring forms instead of the 6 that formed with glucose. 2) The a form 3) The b form

Sucrose is a disaccharide that results when glucose and fructose undergo a condensation reaction together. The condensation reaction is much like the ring forming reaction of glucose except that water is expelled from the new molecule.

Starch and Cellulose are both polysaccharides made of repeating glucose units Starch uses a linkages and is digestible while Cellulose uses b linkages and cannot be digested by humans

Lipids: because of their non-polar nature, lipids are not soluble in water, they are said to by hydrophobic (water fearing). Fats are important types of lipid. Fats consist of long chain fatty acids (carboxylic acid) bound to a glycerol molecule (called a triglyceride). A fat can be saturated (no C=C double bonds) or unsaturated (one or more C=C double bonds) Phospholipid a fat like molecule where one of the fatty acids of a triglyceride has been replaced with a phosphate group Steroid is a type of lipid that has a very specific ring structure-three six membered rings fused together with a five member ring attached (see figure) Cholesterol is another example of this type of lipid. If a fat is reacted with water and base (a reaction called saponification) you will produce fatty acids and glycerol.

Phospholipid bilayers: the long alkane like “tails” are non-polar and will dissolve each other but will repel water (hydrophobic) while the phosphate head groups are ionic and will be soluble in water (hydrophilic)

Cholesterol is another example of a lipid.

Amino Acids: here are 20 essential amino acids that you need in your diet.

Proteins are made of poly-amino acids The amide link between the two amino acids is called a peptide bond The primary structure is simply listing the order in which the amino acids occur in the protein. The secondary structure is the shape that the polypeptide chain adopts (a helix or pleated sheet) The tertiary structure is the shape that large section of the polypeptide adopt as they fold or curl back on themselves The quaternary structure is the shape that occurs when multiple chains interact to form a larger structure. Hydrogen bonding, dipole-dipole, and dispersion forces all play roles in determining the shape.

Disulfide Bridges can also influence the shape of a protein. When you get a perm, your hair is held in place while chemicals are added to help the cysteine chains that are close together to form disulfide bridges. As a result, the hair will remain in the shape that it was held after the perm. This will last until the disulfide bridges naturally break down. If you have very curly hair, the protein in your hair contains a more cysteine than someone with straight hair. If you have your hair straightened, the chemicals they use break apart the disulfide bridges and allow the hair to become straight. Over time, the disulfide bridges will naturally start to reform and the hair will become curly again.

Enzymes are proteins that act as catalysts. The shape of the protein causes it to only catalyze a specific type of reaction because only molecules with a very specific shape can interact correctly with the enzyme. This is called the Lock and Key Enzyme Model. After a substrate undergoes a reaction controlled by the enzyme, the enzyme releases the products and is unchanged by the reaction. Protein secondary, tertiary, and quaternary structure depend upon the environment (temperature, pH, salt concentration, etc….). If the environment changes, the protein will change shape and this can alter the ability of the protein to act as an enzyme. This process is called denaturation.

Nucleic Acids: Chains of nucleotides containing a sugar bonded to a phosphate and an organic base. A nucleotide is one phosphate group bonded to the 5’ position on the sugar ribose (or deoxyribose) which is then bonded to an organic base (called a nitrogenous base).

In DNA, the polymer chain is constructed of ester type linkages between a phosphate group and the OH groups of the sugar ribose (note that the ribose is missing one OH group and hence the name deoxyribonucleic acid (DNA)) A small section of DNA The phosphate backbone repeats exactly the same throughout the DNA molecule, the part that changes so that the molecule can carry genetic information is the nitrogenous bases

Nitrogenous bases used in DNA and RNA (the red H indicates where the base would be linked to the ribose backbone)

What single feature tells you which chain is RNA and which is DNA? A small section of RNA A small section of DNA What single feature tells you which chain is RNA and which is DNA?

DNA is double stranded (the two strands run in opposite directions) which are linked together by hydrogen bonding interactions occurring between the nitrogenous bases. Here two representations are shown (famous a helix on the right).

During DNA replication, the double stranded DNA molecule is separated while the strand is copied. DNA carries genetic information in the form of genes (large sections of the DNA molecule that perform specific functions). RNA has several uses and takes on different forms depending upon the use. mRNA (messenger RNA) carries instructions for making proteins out into the cytosol tRNA (transfer RNA) transfers amino acids to the ribosome rRNA (ribosomal RNA) becomes part of the ribosome where protein synthesis takes place