Lecture 1
39
Transcript of Lecture 1
Important Class Information from Syllabus
• Head TA• Grading TAs• Textbook• Grading Policy• Grading Scale• Lecture Outline (Tentative)• Enrollment
Important Class Information from Syllabus
• Quizzes
• Exams
• Grade Disputes
• Makeups
• Academic Misconduct
• Disability Services
• Arrive on time - leave only when class is over• Keep you informed of responsibilities and progress
throughout the quarter• Provide readings and quizzes that will help you organize
the content of this course• Strive to make the class interesting and relevant• Make sure that each student receives equal and fair
opportunity for learning and evaluation• Model patience and consider feedback
Expectations - InstructorI will…
Expectations - StudentYou will…
• Participate in class and by making contact with instructors when appropriate
• Stay up to date with assignments and material and take responsibility for your performance on quizzes and exams
• Demonstrate patience and seek clarification when/if a problem arises
• Show respect to teachers and fellow students by following the student code of conduct at all times
• Arrive on time and leave only when class is over• Maintain a sense of humor
Posting …
• Infectious Disease in the Developing World has been moved to 1180 Postle Hall.
Defining Biochemistry -the chemistry of biology (life)
• But what is life?• Ordered (Cellular)• Processes energy• Responds to environment• Regulation (homeostasis)• Growth/development• Reproduction• Evolution
But what is life really?
– Mechanistic not VitalisticSelf assembly - moving, sticky
molecules
Cellular
Modular
Genomic
Molecular Modules
Protein
Gene Whole Genome
++++++++ +++++++++
• Cells are modular (Made of modules)• Modules are proteins (for most part) • Proteins are coded by genes
• Genes are modular• Genes Diversify (Homologues)• Genes Duplicate, Genes Rearrange and Genes
Move
• Proteins Duplicate, Rearrange
Defining Biochemistry
• What is life really?– Modular – Emergent– Autopoietic - self-renewing– Genetic Continuity - direct filiation
• Organisms reproduce:– the organism– the mechanism
– Darwinian Evolution - natural selection based on propagation
• Also defines ancestry -
Copyright ©2001 by the National Academy of Sciences
Pace, Norman R. (2001) Proc. Natl. Acad. Sci. USA 98, 805-808
Tree of Life
Defining Biochemistry
• What is life really?– Modular – Emergent– Autopoietic - self-renewing– Genetic Continuity - direct filiation
• Organisms reproduce:– the organism– the mechanism
– Darwinian Evolution - natural selection based on propagation
• Also defines ancestry -
– Non-Darwinian Evolution - not based on ancestry
Defining Biochemistry
• What is life?– A set of self-propagating organic chemical
reactions producing modular, genetically continous, autopoietic, cellular organisms capable of Darwinian and non-Darwinian evolution
Defining Biochemistry
• What is life made of (organic)?– Organic (Carbon)
• Carbon bonds with many other elements• Carbons electrons are polarizable• Carbon is “compatible” with water• Carbon is relatively abundant
– Water-based
Defining Biochemistry - Constraints
1. Cellular -
• Prokaryote - average size 2.5um
• Eukaryote - average size 25um
• Multicellular organisms - 1mm
Prokaryote vs Eukaryote
• Eukaryotes:
• Membranes more folded• Compartmentalized• Larger genomes• Energy from inside• Multi-cellularity
• All changes necessary to overcome size limit imposed by relatively small surface area
Biochemical Constraints
2. Chemical• Legacy of Earth’s formation
– 6 common elements
• Carbon-based• Limited number of functional groups
– Elements that react with carbon– Page 5 in text
Water-based
Biochemical Constraints3. Thermodynamic - reactions must proceed
spontaneously Example: (respiration vs photosynthesis)
1. Chemical: Relies on oxidation reactions (catabolic)– Ultimately producing CO2
Photosynthesis: Relies on light between 300 - 1500nm for reduction reactions (anabolic)
2. Transport (Membranes/Gradients)3. Chemical currencies (ATP, NADH, etc)
Biochemical Constraints
4. EvolutionaryMolecules are selectedMolecules are limited by history
Pathways are selectedPathways are limited by histories
Organisms….
Molecular Selection
Biochemistry vs ChemistryDifferences
1. Occur in “Mild Conditions”
• Mild Conditions• 112 -113C record thermophiles on Earth• Growth can occur to -20 C• Pressure • Upper limit: Over 1000 atmospheres• Lower limit: Maintain liquid water
2. Occur at Great Rates and Specificity
• Enzymes– Complex– Specific– Typically catalyze a
Single reaction
3. Are Interdependent
• Many branch points
• Reverse pathways
• Interdependence is
an emergent property
4. Proceed in Pathways
Substrate Product
5. Are Regulated
• Occurs at Various Levels
– Enzyme Levels – Enzyme Activity
• Covalent Modification• Effector Molecules
Tomorrow: Defining Biochemistry
• What is life?– Water based
Water
• Relevant Facts
• 70 % Earth’s surface covered with water
• 70% of the Cell is composed of water
• Water is the only common substance that exists in all three states on earth
Water - Chemical Properties
• Valence electrons in water are shared in equal Sp3 hybrid orbitals
• The shape of water is a distorted – regular tetrahedron
Water - Chemical Properties• Water is polar due to the
difference in electronegativity between hydrogen and oxygen
Hydrogen Bonding
• 1. Hydrogen atom bonded
to an electronegative atom
with unpaired electrons
• 1. Cohesive – molecules held together-high surface tension
• 2. Moderates Temperature (specific heat)
• High melting point• High boiling point• 3. Excellent Solvent
Emergent Properties of Water
Properties of Water
e)weak nucleophile
a)Regular tetrahedronb)Hydrogen bondsc)Polard)Small Size (orientation
Water and Salt
Water and Sugar
Water and ProteinsWater and Proteins
Interactions can take place because water is a polar molecule
Unsolvated protein
molecule
Water interacts with the surface of
proteins
Ionic and polar regions onthe protein’s surface attract
water molecules.
–
Figure 3.7 (Campbell and Reece)
–
+
Properties of Water
e)weak nucleophile
a)Regular tetrahedronb)Hydrogen bondsc)Polard)Small Size (orientation
