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What is biochemistry?

What is biochemistry?. Advanced organic chemistry? Cell biology? Molecular biology? The most fun and interesting subject in science (personal bias)?

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What is biochemistry?

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  1. What is biochemistry? • Advanced organic chemistry? • Cell biology? • Molecular biology? • The most fun and interesting subject in science (personal bias)? • The study of life on a molecular level. Or, the formal term of bios = life meaning biochemistry is the science concerned with the chemistry of various molecules that occurs in living cells • Biochemistry encompasses large areas of cell biology, molecular biology, and molecular genetics • Biochemistry is essential to all of the life sciences (biomedical and plant sciences) All advanced degrees require that biochemistry is one of the first courses • This class will be taught not - as an advanced organic but as an encompassing science that should help tie several of your classes together

  2. Biochemistry I • We will be studying the four macro-biomolecules - proteins, DNA/RNA, lipids and carbohydrates, and whenever possible putting them into biomedical context • What are YOUR expectations of this class? • Ask yourself why you need this course • What are my expectations of this class? • Work hard but have fun with the semester/year • Push you intellectually and make you think about how life works around you - like a mechanic understands an engine, you will understand how a cell/tissue/organ/body works

  3. What is Critical Thinking?

  4. What is Critical Thinking? • The critical habit of thought, if usual in society, will pervade all its mores, because it is a way of taking up the problems of life. Men educated in it cannot be stampeded by stump orators ... They are slow to believe. They can hold things as possible or probable in all degrees, without certainty and without pain. They can wait for evidence and weigh evidence, uninfluenced by the emphasis or confidence with which assertions are made on one side or the other. They can resist appeals to their dearest prejudices and all kinds of cajolery. Education in the critical faculty is the only education of which it can be truly said that it makes good citizens. William Graham Sumner, Folkways, 1906

  5. What is Critical Thinking? • Critical thinking is the intellectually disciplined process of actively and skillfully conceptualizing, applying, analyzing, synthesizing, and/or evaluating information gathered from, or generated by, observation, experience, reflection, reasoning, or communication, as a guide to belief and action. In its exemplary form, it is based on universal intellectual values that transcend subject matter divisions: clarity, accuracy, precision, consistency, relevance, sound evidence, good reasons, depth, breadth, and fairness

  6. What is Critical Thinking? • My down and dirty version: • Thinking about what and why rather than just accepting some fact or comment. • Asking questions to answer “does this make sense”? And answering that based on fact not “feelings or blind faith”.

  7. Study Tips • Do not cram, too much material and topics build on the next from the first day. • Read the study tips on my homepage • Write an outline, ask yourself what does all of this mean in a few words • Test Tip • The tests are multiple guess, short answer and essay • DO NOT read the question and then look for and answer. Think of the answer and then find if. Looking for a likely answer will nearly always cause problems

  8. This semester: • pH, buffers and amino acids • Protein structure and function • Enzymes and kinetics • Carbohydrates • Lipids and fats • Metabolism • Biochemical source of diseases • Real life and interesting examples • Next semester: More metabolism, • Diabetes, Cancer, • Nutrition, Signal Transduction

  9. … and now the fun begins... • Functional Groups - One of the reasons why organic chemistry is a prerequisite for the class • Just for review – know and be able to draw each of the structures in fig 1-2..

  10. Also know… • Disulfide • Thioester • Anhydride (2 carboxylic acids) • Guanidino • Imidizole

  11. Also know… • Disulfide • Thioester • Anhydride (2 carboxylic acids) • Guanidino • Imidizole R1-S-S-R2

  12. Also know… • Disulfide • Thioester • Anhydride (2 carboxylic acids) • Guanidino • Imidizole R1-S-S-R2 R1-C-S-R2 = O

  13. R1-C-O-C-R2 = = O O Also know… • Disulfide • Thioester • Anhydride (2 carboxylic acids) • Guanidino • Imidizole R1-S-S-R2 R1-C-S-R2 = O

  14. R1-C-O-C-R2 = = O O R NH - - HN=C - NH2 Also know… • Disulfide • Thioester • Anhydride (2 carboxylic acids) • Guanidino • Imidizole R1-S-S-R2 R1-C-S-R2 = O

  15. R1-C-O-C-R2 = = O O R NH - - HN=C - NH2 Also know… • Disulfide • Thioester • Anhydride (2 carboxylic acids) • Guanidino • Imidizole R1-S-S-R2 R1-C-S-R2 = O R -C=CH N HN C H

  16. Prokaryotic Cellular Organization

  17. Eukaryotic Cellular Organization

  18. The Plasma Membrane • Composed of a phospholipid bilayer and proteins. • The phospholipid sets up the bilayer structure • Phospholipids have hydrophilic heads and fatty acid tails. • The plasma membrane is fluid--that is proteins move in a fluid lipid background

  19. The Plasma Membrane • Phospholipids: • Two fatty acids covalently linked to a glycerol, which is linked to a phosphate. • All attached to a “head group”, such as choline, an amino acid. • Head group POLAR – so hydrophilic (loves water) • Tail is non-polar -hydrophobic • The tail varies in length from 14 to 28 carbons.

  20. The Plasma Membrane • Proteins: • Integral proteins: • Embedded in lipid bylayer – serve as “ion pumps” • They pump ions across the membrane against their concentration gradient • Peripheral proteins: • Bound to membrane surface by ionic bonds. • Interact with components of the cytoskeleton • Anchored proteins: • Bound to surface via lipid molecules

  21. The nucleus • Contains almost all of the genetic material • What it contains is called the nuclear genome – this varies greatly between plant species. • Surrounded by nuclear envelope- double membrane - same as the plasma membrane. • The nuclear pores allow for the passage of macromolecules and ribosomal subunits in and out of the nucleus.

  22. The Endoplasmic reticulum • Connected to the nuclear envelope • 3D-network of continuous tubules that course through the cytoplasm. • Rough ER: Synthesize, process, and sort proteins targeted to membranes, vacuoles, or the secretory pathway. • Smooth ER: Synthesize lipids and oils. • Also: • Acts as an anchor points for actin filaments • Controls cytosolic concentrations of calcium ions

  23. The Endoplasmic reticulum • Proteins are made in the Rough ER lumen by an attached ribosome. • Protein detaches from the ribosome • The ER folds in on itself to form a transport vesicle • This transport vesicle “buds off” and moves to the cytoplasm • Either: • Fuses with plasma membrane • Fuses with Golgi Apparatus

  24. The Golgi Network • Proteins or lipids made in the ER contained in transport vesicles fuse with the Golgi. • The Golgi modifies proteins and lipids from the ER, sorts them and packages them into transport vesicles. • This transport vesicle “buds off” and moves to the cytoplasm. • Fuse with plasma membrane.

  25. The Golgi Network

  26. The Mitochondria • Contain their own DNA and protein-synthesizing machinery • Ribosomes, transfer RNAs, nucleotides. • Thought to have evolved from endosymbiotic bacteria. • Divide by fusion • The DNA is in the form of circular chromosomes, like bacteria • DNA replication is independent from DNA replication in the nucleus

  27. The Mitochondria Site of Cellular Respiration • This process requires oxygen. • Composed of three stages: • Glycolysis--glucose splitting, occurs in the cell. Glucose is converted to Pyruvate. • Krebs cycle--Electrons are removed--carriers are charged and CO2 is produced. This occurs in the mitochondrion. • Electron transport--electrons are transferred to oxygen. This produces H2O and ATP. Occurs in the mito.

  28. The Chloroplast • Contain their own DNA and protein-synthesizing machinery • Ribosomes, transfer RNAs, nucleotides. • Thought to have evolved from endosymbiotic bacteria. • Divide by fusion • The DNA is in the form of circular chromosomes, like bacteria • DNA replication is independent from DNA replication in the nucleus

  29. The Chloroplast • Membranes contain chlophyll and it’s associated proteins • Site of photosynthesis • Have inner & outer membranes • 3rd membrane system • Thylakoids • Stack of Thylakoids = Granum • Surrounded by Stroma • Works like mitochondria • During photosynthesis, ATP from stroma provide the energy for the production of sugar molecules

  30. Cellular Organization - Simple comparison of prokaryotes and eukaryotes

  31. Organelles with their principle function

  32. The End Any Questions?

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