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Biochemistry. Biochemistry is the study of the chemistry of living organisms Much of biochemistry deals with the large, complex molecules necessary for life as we know it However, most of these complex molecules are actually made of smaller, simpler units – they are biopolymers
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Biochemistry • Biochemistry is the study of the chemistry of living organisms • Much of biochemistry deals with the large, complex molecules necessary for life as we know it • However, most of these complex molecules are actually made of smaller, simpler units – they are biopolymers • There are four main classes of biopolymers – lipids, proteins, carbohydrates, and nucleic acids Tro: Chemistry: A Molecular Approach, 2/e
Lipids • Lipids are a family of compounds that are generally insoluble in water (ie. Non-polar). • Classes of Lipids: • Waxes = fatty acid and long chain alcohol (ester) • Fats & Oils = glycerol + three fatty acids • Phospholipids = glycerol + 2 fatty acids + phosphate + an amino alcohol • Sphingolipids = fatty acid + sphingosine + phosphate + an amino alcohol • Glycolipids = fatty acid + glycerol or sphingosine + one monosaccharide. • Steroids = a fused ring structure of three cyclohexanes and one cyclopentane.
Fatty Acids • Long chain carboxylic acids. • 12 – 18 Carbon’s are the most common. • Stearic acid is most often found in animal fat. CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2COOH And it can also be represented like this:
Fatty Acids • Can be saturated – all C-C single bonds. • Can be mono-unsaturated – one C-C double bond. • Ex) Oleic Acid found in olives and corn. • CH3(CH2)7CH=CH(CH2)7COOH • Can be poly-unsaturated – more than one C-C double bond. • Ex) Linoleic Acid found in soybeans and sunflowers. • CH3(CH2)4CH=CHCH2CH=CH(CH2)4COOH • In the Unsaturated acids, the cis isomer is usually found.
Physical Properties of Fats and Oils • The repeating zigzag shape of saturated fatty acids found in fats allows them to fit close together leading to strong attractions. As a result, a fat is solid at room temperature. • The unsaturated fatty acids found in oils do not stack together because of the double bonds. As a result, an oil is a liquid at room temperature.
Fats and Oils • Fats and oils are the most common lipids. • Often called triglycerides because they are a tri-ester of glycerol and three fatty acids. • Tristearin consists of three stearic acid molecules reacting with glycerol.
Reaction to Produce a Fat or Oil + 3 H2O
Steroids and Cholesterol • Steroids are any compounds containing the steroid nucleus (Pictured at right). • Cholesterol is the most important and abundant steroid in the body. • You cannot exist without this substance! • The sex hormones and the adrenocortical hormones depend on cholesterol for their synthesis.
Cholesterol and Hormones Cholesterol, Estrogen, and Testosterone
Carbohydrates • Simple Sugars have the formula Cn(H2O)n and were once thought to be “hydrates” of Carbon. • The Carbon cycle. ___________ • 6CO2 + 6H2O + energy C6H12O6 + 6O2 _____________
Types of Carbohydrates • Monosaccharides – do not hydrolyze into smaller units. • Disaccharides – consist of two mono units joined together – these will hydrolyze. • Polysaccharides – consist of many mono units and are sometimes called “complex carbohydrates.”
Monosaccharides • Have between three and eight C atoms. • Number of C’s determines whether it is a triose (3), tetrose (4), pentose (5), hexose (6), etc. • All have at least two –OH groups and the term polyhydroxy- is sometimes used. • Will also have either an aldehyde or ketone group. • Aldehyde = aldose and ketone = ketose. • Molecules are written with the C backbone in a vertical direction.
Monosaccharides • Ketose or Aldose? • How many chiral carbons?
Monosaccharides and Chirality • Large monosaccharides have several chiral C’s. • If the lowest chiral C has the OH group on the left, then it is called the L isomer. If it is on the right, then it is called the D isomer. • Hint: C’s with double to the O are not chiral and the -CH2OH groups are also not chiral.
Glucose • How many chiral carbons? • Is this the D or L isomer? • Note: D-glucose is oxidized in the body to produce energy and L-glucose cannot be oxidized.
Cyclic Structure • In solution, glucose and other mono-saccharides become cyclic.
Disaccharides • Composed of two mono units. • Some common ones are: • Sucrose = Glucose + Fructose • Lactose (Milk sugar) = glucose + galactose • Maltose = glucose + glucose • In the presence of water and an acid catalyst, these linked molecules will split apart back into their mono units.
Polysaccharides • This is essentially a polymer of glucose units (usually). • Plant Starch exists in two forms: Amylose and Amylopectin. • Amylose is a long,continuous chain of glucose molecules. Typically has 250 – 4000 units. • Amylopectin is a branched chain of glucose molecules. Branches are about every 25 units.
Polysaccharides • Animal Starch is also called ___________. This is essentially a branched chain as well. • Branches are about every 10 – 15 units. • ____________, found in cell walls of plants and animals, is also a long chain of glucose units much like amylose.
Polysaccharides • The linkage between each unit in cellulose is different (b linkage) and is resistant to hydrolysis. • Human’s do not possess the enzymes to break this material down for energy as some animals do. • We often refer to this material in our diet as “fiber.”
The Amino Acids • Are the building blocks of all proteins. • Twenty different versions of these. • All contain the carb. acid and amine functional groups. • Center C is called the alpha Carbon and it is chiral (except in Glycine) • Abbreviated by three letter designations.
Amino Acids • The R groups can be non-polar, polar, acidic, or basic. Serine Alanine Non-polar R group Acidic R Group
The Peptide Bond • Amino acids link together by the reaction of a carboxylic acid on one with the amine of another. • The linkage between the two is called a peptide bond.
Peptide Formation • Reaction to form peptide bond between any two amino acids is a condensation type:
Primary Structure • Chains of 3 – 50 amino acids are called polypeptides. • When more than 50 amino acids are joined, we usually call it a protein. • The specific sequence of amino acids in a protein is called the primary structure. • Our DNA codes for only a limited number of specific sequences for making proteins. • Approximately 100,000 different proteins found in humans.
Secondary Structure • This refers to how the amino acids along the polypeptide are arranged in space. • The three most common types are: • Alpha Helix - which is a corkscrew shape of the chain that results from Hydrogen bonding between every fourth amino acid. All of the R groups then are pointed outward. • Beta-Pleated Sheet – rows of amino acids are held flat with HB keeping them rigid. • Triple Helix – is three peptide chains woven together like a braid. HB is also a powerful force that holds this together.
Tertiary Structure • This is the overall 3D shape of the protein. • The types and interactions of the R groups are important in this area. • Globular proteins, like hemoglobin and insulin, have a very compact and round shape. The non-polar R groups point inward and the polar R groups point outward and this makes these proteins soluble in water. • Fibrous proteins, like keratin (hair, skin), consist of long, thin, fibrous shapes. Cross-linking is an important aspect and determines whether you have curly or straight hair.
Nucleic Acids • Basic structure is a polymer of four different bases. • Each nucleotide consists of three parts: a sugar, a base, and a phosphate group.
Nucleotide Structure • Each nucleotide has three parts – a cyclic pentose, a phosphate group, and an organic aromatic base • The pentoses are the central backbone of the nucleotide • The pentose is attached to the organic base at C1 and to the phosphate group at C5 • The phosphate groups then link to each other to form a polymer
DNA and RNA • Deoxyribonucleic Acid is found primarily in the nucleus of the cell. • Ribonucleic Acid is found throughout the cell. • The sugar molecule Ribose differs by a single oxygen atom.
Bases • In DNA, the four cyclic bases are Adenine, Guanine, Cytosine, and Thymine. In RNA, Thymine is replaced by Uracil.
Base Pairing in DNA • The bases in nucleic acids are complementary – they precisely pair with another base. • Adenine pairs with Thymine via two hydrogen bonds • Guanine pairs with Cytosine via three hydrogen bonds
Genetic Structure • Each sequence of three nucleotides is called a codon • A codon codes for one amino acid • AGT = Serine • ACC = Threonine • This is universal for all living things!
DNA Double Helix • Base pairing generates the helical structure • In DNA, the complementary bases hold strands together by H-bonding • allow replication of strand
Protein Synthesis • Transcription → translation • In nucleus, DNA strand at gene separates and a complementary copy of the gene is made in RNA • messenger RNA = mRNA • The mRNA travels into the cytoplasm where it links with a ribosome • At the ribosome, each codon on the RNA codes for a single amino acid, and these are joined together to form the polypeptide chain Tro: Chemistry: A Molecular Approach, 2/e
Protein Synthesis Tro: Chemistry: A Molecular Approach, 2/e
