BIOC/CHEM/MMG 205
BIOCHEMISTRY I
FALL 2004
Contacts
Margaret A. (Peggy) Daugherty
e-mail: [email protected]
phone: Temporary phone 656 - 0344
office: Temporary Office Given B418
Office Hours: Tuesday 5 - 7 pm Given C443
and by appointment
Martin Case (will provide office hours)
e-mail: [email protected]
phone: x6-8246
office: Cook A321
Teaching Assistant: Pete Brescia
e-mail: [email protected]
Office hours: Tuesday 3:30 - 4:30; Thursday 10:30 - 11:30
Office location: Given Building (C447/414 same room!)
BIOC 205
Protein structure & function
Hints to success!
Keep up with the reading (please!)
*Required material
Reading assignments
Lectures (powerpoints are an outline)
What I say in class
What I write on the board (low-tech counts!)
Homework counts!
Clue! Homework & review questions reflect the
type of questions I’ll ask on an exam.
Goal: Be able to apply what you learn, not just do
rote memorization of facts
Amino acids: correct ionization at pH 7.0
Orange: hydrophobic
Green: Polar, uncharged
Magenta: acidic (polar, charged)
Blue: basic (polar, charged)
Lecture 1:
Review of Fundamentals
Margaret A. Daugherty
Fall 2004
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Figure 1.8
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I: Living systems are highly organized (heirarchy)
CELLS AND ORGANIZATION
organelles
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The universal phylogenetic as determined by ribosomal RNA sequences analyses
(Carl Woese “On the Evolution of Cells” PNAS 99 (2002) pp 8742-8747.
pathogenic
halophiles
thermoacidophiles
methanogens
“extremophiles”
archae
PROGENOTE (3.5 billion)
eukaryote
cytosol
Storage granules
Cell membrane
prokaryote
ORGANIZATION OF CELLS
flagella
Cell wall
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CELLS: What is the distribution of biomolecules?
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CELLS: An aside…..
Cells are densely packed with protein, nucleic acids…..
Water 70%
Protein 15%
Nucleic acids 7%
Polysaccharides 3%
Lipids 2%
Small molecules 2%
Inorganic ions 1%
RNA
II: Biological Structures Serve Functional Purposes
DNA
Examples of proteins
III: Living systems are engaged in energy transformation
ATP
NADH
&
NADPH
NADH
lacks phosphate
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III: Living systems are engaged in energy transformations
Key point: energy flows through an organism
Apparent steady-state system:
energy & material are consumed and used
to maintain stability and order!
Thermodynamically:
Open system
Isothermal
Insert figure 1.17
Glucose is the universal “fuel” for cells
METABOLISM: USE OR PRODUCE ENERGY IN A
SEQUENCE OF MANAGED REACTIONS
“Enzymes”
control the
steps in
breakdown
of glucose
ENZYMES AND BIOLOGICAL FUNCTION
Uncatalyzed = 33 seconds
Catalyzed = 100 nanoseconds!
Enzymes are proteins that carry out chemical reactions
carbonic anhydrase
CO2 + H20 ---> HCO3- + H+
Carbonic Anyhdrase Mechanism:
Zn, H20, displacements, rearrangements But, always returning to the same start!
http://www.bio.cmu/edu/Courses/03231/ProtStruc/BCTmech.htm#bctmech
IV: Living systems can self-replicate
1) Genetic information is encapsulated in a linear sequence of
four bases (ATCG)
2). Structure is such that it is compatible with any sequence
3). The double helical nature of DNA makes it such that it
has an internal template for its own replication & repair.
DNA IS OUR GENETIC MATERIAL (of course!)
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Biomolecules are held together by covalent bonds
O, C, H, N, P, S make up 99% weight of most organisms
BIOMOLECULES ARE POLYMERS
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-COO-
1’-OH
BIOMOLECULES HAVE DIRECTIONALITY
5’-PO 4-
H3+N-
4’-OH
RNA
Biomolecules have discrete structures!
DNA
Examples of proteins
3’-OH
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STRUCTURAL COMPLEMENTARITY DETERMINES
BIOMOLECULAR INTERACTIONS
LOCK & KEY
Lysozyme binding to
an antibody
INDUCED FIT
(enzymes)
Hexokinase
binding it’s
substrate
glucose
CH2
H 2C
86 kJ/mol
9.3 kJ/mol
enthalpic
0.3 kJ/mol
20 kJ/mol
3 kJ/mol
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entropic
Bond Strength
Non-covalent interactions give rise to structure
“Hydrophobic interactions”
Non-covalent interactions are WEAK but
their abundance makes them important!
REVIEW
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1). Chemistry allows us to understand biology
2). There are 4 distinct properties of living organisms
3). Living organisms are organized in a hierarchical fashion
4). Structure serves function
5). Living systems use energy (ATP, NADPH, NADH)
6). Living systems replicate via DNA; DNA is ideally suited to be the
genetic material.
7). Cells descended from a common ancestor
8). Bacterial cells are different from eukaryotes.
9). Cells are densely packed; biomolecules distributed throughout.
10). Covalent bonds play a major role in biomolecular structure
11). Non-covalent interactions are weak and abundant.
12). Non-covalent interactions are important because they permit the
flexibility needed for life.
13). Structural complementarity is necessary for biomolecular
interactions.