Biochemistry

1. Biochemistry The study of the chemical substances and processes that occur in plants, animals, and microorganisms.

2. Subjects a person needs to study to become a biochemist: • Biotechnology • Cell biology • Microbiology • Virology • Endocrinology • Neurobiology • Physics • Calculus • Inorganic chemistry • Organic chemistry • Genetics • Anatomy • physiology

3. Carbohydrates • The primary molecules responsible for short-term energy storage in living organisms • Carbohydrates have the general formula (CH2O)n . • Monosaccharide – a carbohydrate that cannot be broken down into simpler carbohydrates • Monosaccharaides rearrange in aqueous solutions to form ring structures • Simple carbohydrates

4. Carbohydrates • Disaccharides – a compound that can be decomposed into two simpler carbohydrates • Achieved by eliminating water to form the glycosidiclinkage which is broken down during digestion allowing the monosaccharaides to pass through the intestinal wall and enter the blood stream • Simple carbohydrate

5. Carbohydrates • Polysaccharides – long chainlike molecules composed of many monosaccharide units • A type of polymer • Complex carbohydrates • Starch • Starch has different properties than cellulose • Starch is common in potatoes and grains • Broken down during digestion • Cellulose’s linkages are indigestible by humans so it passes right through the intestines

6. Questions • Plants can grow to large sizes in pots even though their roots can’t extend beyond the boundaries of the pot. Provided with adequate amounts of water and sunlight, the plant can gain hundreds of time the mass of the seed from which the plant sprouted. Yet, very little of the mass of soil will have been taken up by the plant. Where does all that plant mass come from? Carbohydrates from photosynthesis contribute to the mass. • Corn seeds are coated with cellulose. What should happen to a seed that has been swallowed whole by a person? If coated with cellulose, it is indigestible and would pass right through • Table sugar is a disaccharide. What are the components of sucrose? Glucose and fructose • Why do plants store energy in the form of starch if the plants can’t utilize the starch directly as an energy source? They also store energy as fats and oils, but that’s in the next section. Within the cell it is approximately 75% water. Sugars are soluble and oils and starches are not. Starch is held in food vacuoles until the plant needs energy.

7. Lipids • Chemical components in the cell that are insoluble in water but soluble in nonpolar solvents. • Examples – fatty acids, fats, oils, phospholipids, glycolipids, and steroids • Lipids make up the containers that separate the interior of the cell from its external environment

8. Lipids • Fatty acids – carboxylic acids with long hydrocarbon tails • The R group contains 3-19 carbon atoms • Saturated fatty acids • Have no double bonds • Monounsaturated fatty acids • Have one double bond • Polyunsaturated fatty acids • Have more than one double bond

9. Lipids – Fats and Oils • Triglycerides – triesters composed of glycerol linked to three fatty acids • Formed by the reaction of glycerol with three fatty acids • Saturated fats – a triglyceride with saturated fatty acids • Solids at room temperature • Unsaturated fats – a triglyceride with unsaturated fatty acids • Liquid at room temperature

10. Other Lipids • Phospholipids – composed of glycerol linked to two fatty acids and one phosphate group • Glycolipids – composed of glycerol linked to a fatty acid chain, a hydrocarbon chain, and a sugar molecule • Nonpolar section = hydrocarbon and fatty acid, polar section = sugar molecule • Lipid bilayer – a structure formed by cell membranes • Steroids – lipids that contain the following four ring structures

11. Questions • Explain the arrangement of the phospholipids in the cell membrane. The phosphate head is hydrophilic and the hydrocarbon tail is hydrophobic so the tail orients inward away from the water and the polar head orients outward towards the water. • What are the intermolecular forces holding lipid molecules together and how does this explain why saturated fats are solids at room temperature and unsaturated fats liquids? It is from the dispersion forces within the carbon bonding. Saturated fats are linear due to all single bonds. Unsaturated fats are not linear due to double and triple bonds. • Phospholipids are unsaturated. What keeps the cell membrane from just flowing apart? Cholesterol holds the phospholipids in place along with the cytoskeleton. • How is the digestion and absorption of fats different from other foods? Fats are not digested and other foods are broken down into constituent components. Fats go into the circulatory system. • Bisphenol A can act as a hormone mimic. Which hormone does bisphenol A mimic and how does this happen? BisphenolA acts as estrogen because it has a similar shape so it can bind to the same receptors as estrogen.

12. Proteins • Polymers of amino acids • Amino acids – molecules containing an amine group, a carboxylic acid group, and an R group • Amino acids differ from each other only in their R group • The differences in the R group determine the structure and properties of the protein when the amino acids combine • The amino acids link together because the amine end of one amino acid reacts with the carboxylic end of another amino acid • Peptide bond – the bond between the amine end of one amino acid and the carboxylic end of another • Dipeptide – two amino acids linked together via a peptide bond • Polypeptides – more than two amino acids linked together via peptide bonds

13. Protein Structure • When amino acids link together to form proteins, the amino acids interact with one another, causing the protein chain to twist and fold in a very specific way. • The exact shape that a protein takes depends on the types of amino acids and their sequence in the protein chain. • The shape of proteins is crucial to their function. • Primary protein structure – the sequence of amino acids in its chain • Maintained by the covalent peptide bonds between individual amino acids • Changes in the amino acid sequence of a protein, even minor ones, can have devastating effects on the function of a protein • Hemoglobin transports oxygen in the blood • If glutamic acid is substituted for valine (only 2 of 584 amino acids changed) it results in sickle-cell anemia (often fatal before 30 years old)

14. Protein Structure • Secondary protein structure – refers to certain short-range periodic or repeating patterns often found along protein chains • Maintained by interactions between amino acids that are fairly close together in the linear sequence of the protein chain or adjacent to each other on neighboring chains • Alpha helix – the amino acid chain is wrapped into a tight coil in which the side chains extend outward from the coil (figure to left) • Maintained by hydrogen bonding interactions between NH and CO groups along the peptide backbone of the protein. • Beta pleated sheet – the chain is extended (as opposed to coil) and forms a zigzag pattern like an accordion pleat (figure to left) • Maintained by the peptide backbones of the chain interacting with one another through hydrogen bonding

15. Protein Structure • Tertiary protein structure – consists of the large-scale bends and folds due to interactions between the R groups of amino acids that are separated by large distances in the linear sequence of the protein chain • These interactions include the following: • Hydrogen bonds, Disulfide linkages, Hydrophobic interactions, Salt bridges • Fibrous proteins – tertiary structures in which coiled amino acid chains align roughly parallel to one another, forming long, water-insoluble fibers • Globular proteins – tertiary structures in which amino acid chains fold in on themselves, forming water-soluble globules that can travel through the bloodstream • Quaternary protein structure – describes how amino acid chains fit together • Maintained by the same kinds of interactions between amino acids as those that maintain tertiary structure

16. Questions • The primary structure of proteins occurs at the ribosome. Where in the cell do the other structures arise? Secondary and tertiary structures occur in the endoplasmic reticulum and quaternary structure occurs in the Golgi apparatus. • Where on the molecular structure would a protein-busting enzyme like pepsin attack the protein molecule? The peptide bond. • Name and describe four proteins that have different functions in the human body. Actin and myosin – muscle contractions and movement pepsin – digestive enzyme that works in the stomach to break down proteins Insulin – regulates glucose metabolism Oxytocin – stimulates contractions during childbirth somatotropin – growth hormone keratin – strengthens protective coverings (hair, quills, feathers, etc.) ovalbumin – storage protein found in egg whites hemoglobin – transports oxygen through the blood

17. Nucleic Acids • Nucleic acids – contain a chemical code that specifies the correct amino acid sequences for proteins and can be divided into two types deoxyribonucleic acid or ribonucleic acid • Deoxyribonucleic acid (DNA) – exists primarily in the nucleus of the cell • Ribonucleic acid (RNA) – exists throughout the entire interior of the cell • Nucleotides – individual units composing nucleic acids • Nucleotides have three parts: a sugar, a phosphate, and a base • Nucleotides link together via phosphate linkages to form nucleic acids (see image to left) • In DNA each nucleotide has the same phosphate and sugar but has different bases. The four bases are adenine (A), cytosine (C), guanine (G), and thymine (T). • In RNA, the base uracil (U) replaces thymine (T).

18. Nucleic Acids • The order of bases in a nucleic acid chain specifies the order of amino acids in a protein. • Codon – a sequence of three bases that code for one amino acid • Genetic code – the code that links a specific codon to an amino acid (discovered 1961) • Gene – a sequence of codons within a DNA molecule that codes for a single protein • Chromosomes – contain genes and are located within the nuclei of cells. • Humans have forty-six

19. DNA Structure • Cells synthesis only the proteins that are specific to their function • DNA is stored in the nucleus as a double-stranded helix • The bases on each DNA strand are directed toward the interior of the helix, where the hydrogen bond to bases on the other strand • Each base is complimentary – capable of precise pairing – with only one other base • Adenine (A) only hydrogen bonds with thymine (T) • Cytosine (C) only hydrogen bonds with guanine (G)

20. DNA Replication • When a cell is about to divide, the DNA within its nucleus unwinds and the hydrogen bonds joining the complementary bases break, forming two single parent strands • With the help of enzymes, a daughter strand complementary to each parent strand (with the correct complementary bases in the correct order) is formed. • Hydrogen bonds between strands reform resulting in two complete copies of the original DNA, one for each daughter cell

21. Protein Synthesis • Dietary protein is split into its constituent amino acids during digestion • These amino acids are reconstructed into the correct protein needed by the organism in the organism’s cell • The process is directed by nucleic acids. • To make a particular protein, the gene unravels. • The segment of DNA corresponding to the gene acts as a template for synthesis of a complimentary copy of that gene in the form of another nucleic acid – mRNA. • mRNA moves to the cell structure within cytoplasm called a ribosome, where protein synthesis occurs • mRNA chain that codes for the protein moves through the ribosome • As ribosome reads each codon the corresponding amino acid is brought into place and a peptide forms with the previous amino acid • As mRNA moves through ribosome, the protein is formed

22. Protein Summary • DNA contains the code for the sequence of amino acids in proteins. • A codon – three nucleotides with their bases – codes for one amino acid. • DNA strands are composed of four bases, each of which is complementary – capable of precise paring – with only one other base. • A gene – a sequence of codons – codes for one protein. • Chromosomes are molecules of DNA found in the nuclei of cells. Humans have 46 chromosomes. • When a cell divides, each daughter cell receives a complete copy of the DNA – all forty-six chromosomes – within the parent cell’s nucleus. • When a cell synthesizes a protein, the base sequence of the gene that codes for that protein is transferred to mRNA. The mRNA them moves out to a ribosome, where the amino acids are linked in the correct sequence to synthesize the protein. The general sequence is DNA → RNA → Protein • DNA is transcribed to mRNA in the nucleus. The mRNA can move out of the cell’s nucleus and into the ribosome (a cell structure within cytoplasm). The ribosome reads the mRNA’s codons and pairs it with the corresponding amino acid mediated by tRNA forming the protein.

23. Questions • Explain the chemistry (intermolecular bonds) behind transfer RNA and the building of an amino acid sequence. Hydrogen bonds make tRNA the shape they are (clover-like). Base pairing allows tRNA to attach to ribosome. Hydrogen bonds to amino acid. • How can heat affect the performance of proteins and nucleic acids? What is the connection between homeostasis and the performance of proteins and nucleic acids? Denatures and changes function so it will not function properly. Homeostasis is normal function and it happens in a narrow temperature and pH range. • Describe how mutagens and teratogens affect organisms? Do they affect nucleic material or are there other pathways causing changes in development? Mutagens can change DNA (nucleic material). Teratogens cause birth defects (i.e. alcohol).

24. Things to know for test… • Complex carbohydrates versus simple carbohydrates • Saturated fats versus unsaturated fats • Phospholipids have a hydrophilic polar end and a hydrophobic nonpolar end • Glycolipids are nonpolar • Amino acids contain an amine, carboxylic acid, and an R group (R=hydrocarbon chain) • Protein structures • Primary protein refers to… amino acid sequence • Secondary protein refers to… repeating pattern • Tertiary protein refers to… large scale twists and folds • Quaternary protein refers to… arrangement of chains • Nucleotide contains a sugar, phosphate, and base groups • DNA and RNA use a sequence of three bases codes for an amino acid