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Biochemistry

Biochemistry. Agenda. Introduction Water Structure Properties Bonding Macromolecules Structure Functions . Energy Flow Catabolic vs. Anabolic Laws of Thermodynamics Enzymes Structure and Classification Mechanisms of Reactions Environment and Enzyme Activity Enzyme Inhibition.

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Biochemistry

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  1. Biochemistry

  2. Agenda • Introduction • Water • Structure • Properties • Bonding • Macromolecules • Structure • Functions • Energy Flow • Catabolic vs. Anabolic • Laws of Thermodynamics • Enzymes • Structure and Classification • Mechanisms of Reactions • Environment and Enzyme Activity • Enzyme Inhibition

  3. Biochemistry • Biochemists discuss chemistry with biologists, and biology with chemists, thereby confusing both groups. Among themselves, they talk about baseball. • Credit:  Anonymous

  4. Biochemistry • Biology = study of living things • Chemistry = study of atoms and molecules • Biochemistry = study of atoms and molecules in living things

  5. Water • Staple of life • Has several interesting and important properties • High surface tension • High boiling point • Density dependent on temperature • Cohesion and adhesion

  6. Water and Bonds • Water has a dipole charge • Partially separated along the molecule • The oxygen-hydrogen bond = Hydrogen (H) bond • 1 oxygen can bond to 2 hydrogens • Leads to water lattice

  7. Water and Bonds • Oxygen has 2 non-bonding electrons • These are H-bond Acceptors • The hydrogen atoms are H-bond donors

  8. Water and other molecules • Based on structure, other molecules may be: • Hydrophilic- water loving; bonds with and dissolves in water • Hydrophobic- water fearing; repels water and does not dissolve • Amphipathic- contains both hydrophilic and hydrophobic areas

  9. Macromolecules • Amino Acids • Carbohydrates • Lipids • Nucleic Acids • These 4 molecules make up the make up most of the important molecules in biomolecularproceses

  10. Amino Acids • Amino acids all have a common core structure • Amino acids are the building blocks of proteins, and have an important role in energy metabolism and in cellular signaling. • They are also a small but important part of cell membranes.

  11. Carbohydrates • Carbohydrates are molecules of the empirical formula Cn(H2O)n where n usually ranges from 3–7. • They are found in sugars and starches and make up parts of nucleotides (the energy currency of a cell, and the building blocks for genetic information). • They are also present in some components of all cell membranes. • They are the central components of energy-producing pathways in biology.

  12. Carbohydrate (glucose)

  13. Lipids • Lipids are closely related to hydrocarbons (compounds containing hydrogen and carbon atoms exclusively), although they usually have other atoms beside C and H. • Characterized by limited solubility in water, lipids are essential components of membranes, and are important energy stores in plants and animals.

  14. Lipid Structure

  15. Nucleic Acids • Nucleic Acids contain a carbohydrate component joined to one of four carbon- and nitrogen-containing ring compounds called bases. • They make up the energy currency of the cell • When joined end-to-end (polymerized) into DNA or RNA chains, form the genetic information of a cell.

  16. Nucleic Acid Structure

  17. More on Macromolecules • We are going to revisit the 4 macromolecules we talked about previously • What are the 4?

  18. Amino Acids • Structure • Carboxyl Group • Amino Group • Side Chain or R Group • Hydrogen • All of these around a central Carbon • When a lot of these (maybe a 1000+) are put together they form proteins

  19. Amino Acids • These chains of amino acids that form proteins are called polymers • They (the amino acids) form Peptide Bonds • Peptide Bond is when the amino group is next to, and forms a covalent bond with, the carboxyl group of the next amino acid • A polymer of peptide bonds = Polypeptide

  20. Amino Acids as Proteins • For this polypeptide chain to become a protein it has to assume a very specific shape. • This is called Conformation • There are 4 levels of Protein Structure • Primary- sequence of amino acids • Secondary- the coils and folds that take shape because of the sequence • Tertiary- the overall shape due to interactions of R groups • Quaternary- the overall shape/ final product

  21. What happens if Proteins don’t fold correctly? • They don’t work (properly). • Another way proteins mess up is called Denaturation. • Excessive heat, pH imbalance, or other chemical imbalances can cause bonds to break • This makes the shape change • Leading to the protein not working right

  22. Carbohydrates • Carbohydrates give your body energy. • Candy or soda gives you energy • Candy and soda have sugar • Sugars are Carbohydrates

  23. Carbohydrates • Sugars can vary on how they are put together • The most simple of these is the Monosaccharide • Mono means 1 • Sacchar means sugar • Monosaccharide’s are formulas of the same unit • CH2O • Glucose is the most common Monosaccharide

  24. Carbohydrates • Disaccharides are sugars composed of 2 monosaccharides • Di means 2 • Glucose + Glucose = Maltose • Joined by a glycosidic linkage • Covalent bond between monosaccharides • Polysaccharides are sugars with a few hundred to a few 1000 monosaccharides • Commonly Used for Storage

  25. Carbohydrates • Storage Polysaccharides may include • Starch: storage for plants • Made entirely of glucose • Glycogen: storage for animals • Polymers of glucose • Widely branched

  26. Carbohydrates • Polysaccharides may also be structural. • Cellulose: polymers of glucose • The glycosidic linkages differ • The key component in plant structure • Chitin: composed of glucose with a Nitrogen-containing appendage • Makes up the exoskeleton of insects, spiders, and crustations

  27. Lipids • Lipids are a very broad group • All have a very low affinity for water • They don’t like it • Lipids may be: • Fats • Phospholipids • Steroids

  28. Lipids as Fats • Fats are made up of glycerol and fatty acids • Glycerol is an alcohol • Fatty acids are long carbon chains • Usually 16-18 units long • Basically carboxyl groups

  29. Lipids as Fats • Common fat is a triglycerol or triglyceride • Means 3 fatty acids for 1 glcerol • Saturated vs Unsaturated • Plants and Fish = unsaturated • Animals= saturated • Because of the kink in unsaturated fats, they cannot pack closely together. Because of this they are better for you. Lots of saturated fat leads to cardiovascular disease.

  30. Lipids as Phospholipids • Phospholipids are the main components of cell membranes. • They are made of a phosphate head and 2 fatty acid tails. • The phosphate head is hydrophilic • Fatty acid tails are hydrophobic • Makes phospholipids amphipathic

  31. Lipids as Steroids • Steroids are lipids with a carbon skeleton consisting of 4 fused rings • Several different types of steroids • Depends on functional groups (kind of like the R group of amino acids) • One type is cholesterol • Part of animal cell membranes • Often a precursor for other steroids

  32. Lipids as Steroids • Other steroids may include hormones, such as: • Testosterone- male hormone • Estrogen- female hormone • Anabolic steroids are also lipids, but have as many adverse side effects as positive ones. • Back-ne, anyone?

  33. Nucleic Acids • Nucleic Acids are the building blocks of DNA and RNA • 2 groups • Purines = Adenine and Guanine • Pyrimidines= Thymine, Cytosine, and Uracil • All are composed of 3 parts • Phosphate group, pentose sugar, and nitrogen based • We will be talking a lot more about them, later.

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