MCB 100 January 30, 2019

1. MCB 100 January 30, 2019 Biological Macromolecules Proteins, Lipids, Polysaccharides and Nucleic Acids

2. Chemical Composition of an Escherichia coli Cell % Total Weight % Dry Weight Organic Compounds Proteins 15 50 Nucleic Acids RNA 6 20 DNA 1 3 Carbohydrates 3 10 Lipids 2 8 Miscellaneous 2 6 Inorganic Compounds Water 70 Ions and Minerals 1 3 Macromolecule = large molecule Polymer = a large molecule made of many smaller molecules stuck together in long chains

6. Proteins – polymers of amino acids held together by peptide bonds Lipids – amphipathic molecules that form the matrix of cell membranes – fatty acids and glycerol components are held together by ester bonds Polysaccharides (also known as complex carbohydrates) – polymers of sugars held together by glycosidic bonds Nucleic Acids – polymers of nucleotides held together by phosphodiester bonds

7. Proteins – polymers of amino acids held together by peptide bonds Lipids – amphipathic molecules that form the matrix of cell membranes – fatty acids and glycerol components are held together by ester bonds Polysaccharides(also known as complex carbohydrates) – polymers of sugars held together by glycosidic bonds Nucleic Acids – polymers of nucleotides held together by phosphodiester bonds

8. Amino Acids and Proteins Proteins are large globular molecules. There are many different types of proteins found in a typical cell and each type has a different function. Some proteins are found in the cytoplasm and others are embedded in the cell membrane. Some Functions of Proteins: - some act as part of the structure of the cell - many act as enzymes that catalyze biochemical reactions - others transport substances through the cell membrane - some regulate expression of genes or control other cell functions The function of a protein is determined by it’s solubility, shape and the three dimensional arrangement of organic functional groups on it’s surface.

9. 2-D Protein Gel Electrophoresis Gel electrophoresis is a way to separate large biological molecules like DNA fragments and proteins. In 2-D protein gels each spot is a different type of protein molecule. Gels like this can be used to characterize the population of proteins present in a particular type of bacterial culture or in a particular type of plant or animal tissue.

10. Structure of amino acids All amino acids contain nitrogen in the form of an amino group. They also always have a carboxylic acid group. The amino groups and the carboxylic acid groups are involved in the formation of the bonds that join amino acids into long chains to make proteins.

11. Formation of a Peptide Bond • The formation of a peptide bond requires a free carboxylic acid group and a free amino group. • A molecule of water is produced when the two amino acids are joined. • Note how the dipeptide has a free amino group and a free carboxylic acid group. Another amino acid can be attached by the formation of another peptide bond.

12. Structure of an Oligopeptide • Since each amino acid has an amino group and a carboxyl group, a linear chain of great length can be made. • The oligopeptide shown is a pentapeptide (oligo = few, penta = 5) • Most proteins are chains of 100 – 1000 amino acids.

13. Proteins are linear chains of amino acids • Typical proteins consist of 200 – 400 amino acids, but some are smaller than this and others are larger. The key factor that determines the structure and ultimately the function of an enzyme is the sequence of amino acids found in the protein.

14. The Folding of a Protein to Its Final Shape Primary Structure: - The sequence of amino acids in the chain - Determined by the genetic information encoded in the mRNA - Determines the final shape and function of the protein Secondary Structure: - Local folding of a protein chain - Alpha helix and Beta sheet are common motifs - Stabilized by interactions between backbone groups that are fairly close to each other in the primary sequence Tertiary Structure: - Final folding of a single protein chain to its globular form - Stabilized by interactions between groups on side chains that may be far apart in the primary sequence but close together in the final 3-D shape Quaternary Structure: - The noncovalent attraction of two or more separate protein chains to form a functional unit - Stabilized by interactions between groups on side chains that may be far apart in the primary sequence but close together in the final 3-D shape

15. Structure of a Typical Protein Lysozyme: an enzyme that breaks down bacterial & fungal cell walls

17. AMINO ACIDS GROUPED BY TYPES OF SIDE CHAINS NON-POLAR (hydrophobic) AROMATIC Glycine (mostly hydrophobic) Alanine Phenylalanine Leucine Tyrosine Isoleucine Tryptophan Valine Proline POLAR (hydroxyl or amide groups)ACIDIC SerineAspartic acid ThreonineGlutamic acid Asparagine Glutamine SULFUR CONTAININGBASIC MethionineLysine CysteineHistidine Arginine

22. DNA – Protein Interactions Some DNA-binding proteins are involved with the regulation of gene expression. A zinc-finger is a motif or fold seen in some DNA binding proteins. Functional groups on the alpha helices of the protein stick to functional groups in the major groove of the DNA double helix. Zinc finger-DNA. Note three alpha helices pointing into the major groove, each recognizing 3 bp of DNA. The Zinc binding domain is a structural element for protein folding, not directly involved in DNA binding.From: kahn@biochem.umd.edu

23. Above: Hemoglobin Right: Cell Membrane Structure

25. Antigen-Antibody Complex

26. The Active Site of a Serine Protease From: www.researchgate.net/profile/Rima_Chauduri

27. Proteins – polymers of amino acids held together by peptide bonds Lipids – amphipathic molecules that form the matrix of cell membranes – fatty acids and glycerol components are held together by ester bonds Polysaccharides (also known as complex carbohydrates) – polymers of sugars held together by glycosidic bonds Nucleic Acids – polymers of nucleotides held together by phosphodiester bonds

28. Fatty acids and Lipids hydrophilic end hydrophobic end

29. (Top) Two Dimensional Diagram of a Segment of a Cell Membrane (Lipid Bilayer Only) (Bottom) Three Dimensional Diagram of a Segment of a Cell Membrane (Lipid Bilayer with embedded proteins)

30. Fats are long-term energy storage molecules that are more hydrophobic than phospholipids.

31. Sterols are lipids that are found in the membranes of eukaryotic cells. Cholesterol is found in animal cell membranes. Ergosterol is found in fungal cell membranes. Phytosterol is found in plant cell membranes. Bacteria generally don’t have sterols in the membranes, except Mycoplasma and Ureoplasma have ergosterol. CholesterolErgosterolA Phytosterol (Sitosterol)

32. Proteins – polymers of amino acids held together by peptide bonds Lipids – amphipathic molecules that form the matrix of cell membranes – fatty acids and glycerol components are held together by ester bonds Polysaccharides (also known as complex carbohydrates) – polymers of sugars held together by glycosidic bonds Nucleic Acids – polymers of nucleotides held together by phosphodiester bonds

33. Sugars and Polysaccharides Simple sugars have the general formula (CH2O)n. That is: a certain number of carbon atoms with an equal number of water molecules worth of hydrogen and oxygen. Hence sugars are called carbohydrates. Glucose (or dextrose) is an example of a small sugar, or monosaccharide with the formula C6H12O6. Polysaccharides such as starch and cellulose are formed by linking together dozens or even hundreds of simple sugar units.

35. Sugars have many polar groups: hydroxyls & carbonyls. This makes sugars very soluble in water. Sugars can be broken down (oxidized) to yield energy. Sugars can be joined to each other by glycosidic bonds. A disaccharide is made by joining two simple sugars. A trisaccharide is made by joining three simple sugars. Polysaccharides are made by joining manysugars. Polysaccharides can be sugar storage molecules. (starch) Polysaccharides are important components of cell walls. Polysaccharides can be slimy or sticky substances.

36. Sugars can be linked by glycosidic bonds. The suffix used in the name of a sugar is: -ose.

37. A modified sugar has some change from the standard (CH2O)n formula. Examples: glucosamine has an amino group on carbon-2, N-acetylglucosamine has an acetic acid (ethanoic acid) attached to that amine, N-acetylmuramic acid is like n-acetyl- glucosamine with an additional group attached to carbon-3. Chitin, the cell wall material in fungi, is a polymer of N-acetyl- glucosamine. Bacterial cell walls contain N-acetylmuramic acid.

38. Starch

39. Polysaccharides Cellulose a component of plant cell walls, a glucose polymer held together by beta-1,4-linkages Chitin a component of the exoskeleton of insects and other arthropodsChondroitin a component of cartilage

40. Glycoproteinsglyco- : pertaining to sugar A glycoprotein is a protein with sugar groups attached.

42. Glycolipids One or more sugar groups attached to fatty acid chains.

43. Lipopolysaccharide LPS bacterial endotoxin O - antigen LPS is a complex glycolipid found on the outer surface of the outer membrane of Gram-negative bacteria.

44. Proteins – polymers of amino acids held together by peptide bonds Lipids – amphipathic molecules that form the matrix of cell membranes – fatty acids and glycerol components are held together by ester bonds Polysaccharides (also known as complex carbohydrates) – polymers of sugars held together by glycosidic bonds Nucleic Acids – polymers of nucleotides held together by phosphodiester bonds

45. Nucleic Acids and Nucleotides Nucleic acids are polymers of nucleotides DNA A double stranded molecule that can be up to 100 million base pairs long. DNA is the genetic material in all cellular life forms. A chromosome contains a single large molecule of DNA. A chromosome can carry enough information to encode thousands of genes. EXAMPLE: E. coli chromosome is about 4 million base pairs long and about 5000 genes. RNA mRNA: carries genetic information to direct synthesis of 1 – a few proteins rRNA: part of the structure of the ribosome, which makes new proteins tRNA: facilitates the correct alignment of amino acids for protein synthesis Nucleotides dATP, dCTP, dGTP and dTTP are precursors of DNA synthesis ATP, CTP, UTP and GTP are precursors of RNA synthesis and are also energy rich molecules that are used to assist in pushing biosynthetic reactions