Unformatted text preview: Instructor: Whitney Yin TAs: Qingchao Eric Meng http://www.whitney.yin.cm.utexas.edu/CH369.htm https://www.whitney.yin.cm.utexas.edu/CH36 9.htm Course info Course Text book: Essential Biochemistry by Pratt and Cornely Textbook, ~$80, electronic WileyPlus $53.00 Electronic version of textbook Wiley access (internet explorer preferred) Syllabus will be posted on blackboard and Web. Office hours: Whitney Yin: Thurs: 12pm, MBB3.422 Eric Meng: Wed. Weekly reviews: Thus: 56pm. Location: TBA Edit your UT profile Edit your UT profile If your directory information is selected as “confidential”, you will not be able to receive group mail. Please contact TAs to be added on the mailing list. Ch. 1 Chemical Basis of Life Ch. 1 Chemical Basis of Life What is Life? What is Life? What Is Life? is a nonfiction book on science for the lay reader written by physicist Erwin Schrödinger. In the book, Schrödinger introduced the idea of an "aperiodic crystal" that contained genetic information in its configuration of covalent chemical bonds. What is life? What is life? Mission: You are a member of team that is about to be sent to Mars to search for life. What will you look for? What is the sign for life? Credit: HiRISE, MRO, LPL (U. Arizona), NASA Dark Sand Cascades on Mars Dark Sand Cascades on Mars What is Biochemistry? What is Biochemistry?
The study of chemistry of life. It overlaps with cell biology, genetics, immunology, microbiology pharmacology and physiology Biochemistry has traditionally been a science of reductionism and attempts to explain the whole by breaking it into smaller parts and examining each part separately. nding of each molecule's physical structure and chemical reactivity ad to an understanding of how molecules cooperate form larger functiona Why biochemistry? Why biochemistry? Identification of molecules involved in important biological processes, e.g., DNA synthesis Pharmaceutical development
What is (are) the effective molecules? Drug testing Quantification for biological reactions Topics of biochemistry Topics of biochemistry What are the chemical and three dimensional structures of biological molecules? Who do biological molecules interact with each other? Who does the cell synthesize and degrade biological molecules? How is energy conserved and used in cells? What are the mechanisms for organization biological molecules and coordinating their activities? How is generic information stored, transmitted and expressed? Biochemical reactions differ from general chemical reactions All biochemical reactions occurred in living cells in WATER, at neutral pH at 37 °C; Only a small subsets of atoms occur in biomolecules, such as C, N, O and H. Living vs. not living
Living organisms use a set of chemical reactions, metabolism, to maintain life. They processes allow organisms to Grow, Reproduce, Maintain their structures. Periodic Table of Elements Periodic Table of Elements Major small biomolecules Major small biomolecules Building blocks How do organism perform complicated How do organism perform complicated functions with such simply components? Polymerization DNA is composed of deoxynucloeitdes (4) RNA is composed of nucleotides (4) Proteins is composed of amino acids (20) Polysaccharides is composed of carbohydrates or monosaccharides (~1000) Consider a 5component polymer:
1 2 3 4 5 5 Total combinations DNA: 4 4 20 1 4 20 1 4 20 1 4 20 1 45 = 512 205 =3200000 protein: 20 Poly1 Sacharride An average protein contains ~400 aa, that’s 10520 combinations! What are we made of? What are we made of? 1. Amino acids
COOH NH2 (Carboxyl group) C H (Amino group) R -There are 20 amino acids, which have the same structures except the R group; -These 20 amino acids are the components of almost all proteins. Hydrophobic Hydrophilic Positively charged Negatively charged Biopolymers form welldefined three dimensional structures Structure of human endothelin. 2. Nucleotides 2. Nucleotides
Ο Ο P Ο O Ο P Ο Ribose Ribose – RNA Deoxyribose DNA Phosphate Nucleotides Nucleotides Structured nucleic acids Structured nucleic acids 3. Lipids 3. Lipids
Hydrocarbon Carboxylic acid Palimitate Cholesterol formula (CH2O)n 4. Carbohydrates 4. Carbohydrates Structure of polysaccharides Structure of polysaccharides Origin of life Origin of life Where is the first molecule come from? How do they evolve? What is the selection pressure? What is the most ancient What is the most ancient biological molecule? RNA world? Nucleotides can be made in the absence of protein RNA has catalytic activity, e.g., they can cleave and ligate RNA. It has not been shown that nucleotides can replicate themselves. Protein world? Amino acids can be made in the absence of nucleotides. Protein can replicate DNA and RNA. But they need nucleic acids to replicate proteins. Devices for generating nucleosides Devices for generating nucleosides
HCN, HCOH, P Energy in biological Energy in biological system Why don’t our genes fall apart, or become more random ? How do biological reaction occur simultaneously? The secret of live – using energy to The secret of live – using energy to maintain the biological structures First law of thermodynamics First law of thermodynamics Energy can neither be created nor destroyed during a chemical reaction Energy can only be converted between the two forms Chemical bonds can be viewed as potential energy Heat associated with reaction energy is call enthalpy. ∆H Gibbs free energy Gibbs free energy
∆ G = (energy of products) – (energy of reactants) reactant product Energy changes during reactions Energy changes during reactions Energy requirement Energy requirement Gibbs free energy or free energy, G Enthalpy, H – heat content in a system; Entropy, S – measurement of the degree of disorder or randomness. G = H – TS ∆ G = Gproduct – Greactant = ∆ H T∆ S
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