Biochemistry I CHE 418 5418

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Biochemistry I(CHE 418 / 5418)

• Reading Assignment
• Berg et. al (2007) Chapter 1

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Biochemistry

• Study of the chemistry of life processes.
• The cell, as a living system, obeys the same
  laws of chemistry and physics that influence
  nonliving systems and reactions.
• A primary goal of biochemistry is to understand
  the cell in terms of the principles of chemistry
  and physics.

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Unifying Themes

• All life has a common ancestor
• Use DNA as genetic material
• Use same amino acids

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Life is divided into 3 domains
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Living Things are composed of Cells

• Cell Theory
• Organisms consist of one or more cell(s) and the
  cell is the basic unit of structure for all
  organisms
• all cells arise only from preexisting cells

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Domain Bacteria

• Prokaryotic cell
• lacks membrane bound organelles
• cell wall containing peptidoglycan.
• Gram negative thin layer of peptidoglycan
• Gram positive thick layer of peptidoglycan

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Domain Archaea

• Prokaryotic cell
• lacks membrane bound organelles
• Cell wall lacking peptidoglycan.

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Domain Eukarya

• Contain membrane bound organelles
• Four kingdoms

Nucleus Endoplasmic reticulum Golgi
apparatus Mitochondria Chloroplast Peroxisomes
Protists
Kingdom Plantae
Kingdom Fungi
Kingdom Animalia
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Kingdom Protista

• Single cellular (with a few multicellular)
• Have groups with characteristics of other three
  Eukaryotic kingdoms.
• Holding Kingdom

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Kingdom Fungi

• Cell
• Eukaryotic cell with cell wall containing chitin.
• Nutition
• Heterotrophic
• By absorption
• Motitlity
• Nonmotile
• Life cycle
• Haplontic life cycle
• Adult is haploid (n)
• Zygote is diploid (2n)
• Meiosis produces haploid spores
• Spores develop into adults
• Energy Storage
• glycogen

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Kingdom Plantae

• Cell
• Eukaryotic cell with cell wall containing
  cellulose.
• Nutition
• Autotrophic
• Photosynthetic
• Motitlity
• Nonmotile
• Life cycle
• Alternation of Generations
• Energy Storage
• starch

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Kingdom Animalia

• Cell
• Eukaryotic cell lacking cell wall
• Nutition
• Heterotrophic
• Ingest food
• Motitlity
• Motile
• By contractile fibers
• muscles
• Life cycle
• Diplontic
• Diploid adults (2n) that produce haploid gametes
  (n)
• Gametes are egg or sperm
• Energy Storage
• Glycogen

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Evolutionarily Diverse Organisms Have Proteins
with similar structure (and function)
Tata box binding protein
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The 5 Types Of Chemical Bonds Are Formed By
Electrons
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Units

• Length
• Angstrom (Å) 1 x 10 -10 m
• Energy
• Joule (J) energy required to move 1 meter
  against a force of 1 newton.
• Calorie (Cal) energy required to raise the
  temperature of 1 gram of water 1 degree celsius.
• 1Joule 0.239 cal.

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Covalent Bonds

• Covalent bonding between two atoms results from
  sharing a pair of electrons such that electron
  shells overlap.
• A? ?B ? AB
• Strong interactions!
• do not break spontaneously under physiological
  conditions.

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Hydrogen Bond

• Hydrogen Bonds Occur when a hydrogen atom is
  shared between 2 other atoms (both
  electronegative, such as O and N). See next slide
• Hydrogen bonds are strongest when the atoms
  sharing the hydrogen and the hydrogen are in a
  straight line. complementary
• In DNA, H bonds hold together strands.
• In Proteins, H bonds stabilize alpha helixes and
  beta sheets.

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Electronegativity
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Ionic Bonds

• Occur between full ( or -) or partial charges
• Important interactions at active site of enzymes.
• Coulombs law E kq q-
• r2
  D
• k proportionality constant ( 1389 kJ / mol OR
  332 kcal / mol)
• D dielectric constant (1 for vacuum 2 for
  hexane 80 for water)
• q charges of atoms
• r distance of separation (Å)

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Van der Waals Interactions

• Van der Waals weak forces between neutral atoms
  due to transient electrostatic interactions. At
  close distances any 2 atoms will show a weak
  attraction due to the dipole generated by the
  random movement of electrons (negative) around
  the nuclei (positive).

When atoms are too close they repulse each other,
and when too far they have little
attraction. Substrate specificity may come from
large numbers of van der Waals bonds resulting
from matching surfaces.
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Hydrophobic Interactions

• Nonpolar molecules cannot participate in H-bonds
  or ionic interactions. Water forms a cage or
  ordered structure around the nonpolar molecule.
  When two nonpolar molecules interact, the water
  molecules in the cage are displaced and
  interact with other water molecules rather than
  the nonpolar molecule. This interaction is more
  energetically favorable.
• An active site cleft may be strongly nonpolar,
  and therefore attract nonpolar substrates.
  Usually low free energy (G), enthalpy (H), but a
  gain in entropy (S).

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What is the most important precious
valuable compound?

• WATER

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Facts about Water

• Water has unique physical properties that make it
  suitable to serve as the matrix of life
• H2O
• boiling point 100o C (212o F)
• melting point 0o C (32o F)
• F.W. 18
• High Heat of Vaporization
• 540 calaries/1g (liquid to gas)
• Universal Solvent
• High Surface Tension
• Density of solid water (ice) is less than density
  of liquid water.
• Ionize
• 70 of cell mass

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Universal Solvent

• Many compounds dissolve in water to form a
  solution.
• Solution - uniform molecular mixture of two or
  more substances.
• solvent - substance in the greatest quantity
• solute - substance in lesser amount.
• Substances are categorized depending on
  interaction with water
• hydrophilic - (water loving) - dissolves in water
• hydrophobic - (water fearing) poorly soluble in
  water

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High Surface Tension

• Surface tension - measure of how difficult it is
  to break the surface of the liquid.
• Insects walking on water
• skipping rock on water
• needle floating on water
• Water is
• Cohesive - attractive to self.
• Adhesive - attractive to surfaces.
• Solid water (ice) is less dense
• than liquid water.
• Ice floats on water ---see the movie Titanic
• Ponds freeze at top insulating the remaining
  water

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Why is water so important to life?

• Water is a liquid at physiological temperatures
• Water has an unusually high boiling point

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Why is water so important to life?

• 3. Water is a good thermal regulator. Large
  amount of heat is required to change its
  temperature.
• ?T ?H/Cp
• It takes 1 cal to raise 1 g water 1 deg C
• Smaller Cp ? Greater ?T

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Why is water so important to life?

• 4. Water provides very effective heat
  dissipation.
• Q ?Hvap
• Evaporation of 1g water dissipates 540 cal.

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Why Does Water Have Such Unusual Properties?

• Shape of the molecule
• Hydrogen bond -
• weak intermolecular bond formed between the d
  charge of the H and d- charge of the oxygen
• millisecond duration
• requires energy to break

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Hydrogen bonds explain

• High Boiling Point /Freezing point
• High Heat of Vaporization
• Universal Solvent
• High Surface Tension Adhesive / Cohesive forces
• Density of solid water (ice) is less than density
  of liquid water.

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Water Can Ionize

• H2O H OH- hydrogen
  hydroxide
• ion ion
• (1x 10-7 moles/L)
• A measure of the concentration of hydrogen ion
  H in solution is the pH.
• (Actually, the hydrogen ions do not exist free in
  solution, but combine with another water to form
  hydronium ion, H3O)

pH -log H
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Kw
How did we get this? Keq HOH_
H2O Water is 55.5M K 1.8 x 10 -16 Kw
KH2O HOH- Kw 1.8 x 10-16 X 55.5 Kw
1.0 x 10-14
If you know the hydrogen concentration you can
calculate the hydroxyl concentration and vise
versa. pKw pH pOH 14
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pH Scale

• Measures H
• scale is continuum from 0 - 14
• 7 is neutral
• Neutral - neither acidic or basic
• 0 - 6.99 is acidic
• 7.01 - 14 is basic (alkaline)
• one pH unit change represents 10 fold change in
  H
• What is the pOH and OH- at each point?

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pH Scale

• Compounds may be categorized as
• Acid - molecule that dissociates in water to
  release hydrogen ion(s)
• raises hydrogen ion concentration
• lowers pH .
• Base - molecule that in water either takes up a
  hydrogen ion or releases a hydroxide ion.
• reduces hydrogen ion concentration
• raises pH.

Blood pH 7.35 7.45 H 40 nM
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pH of specific tissues and fluids are maintained
at precise values
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pH Scale

• Strong acid - dissociates 100 releasing all
  possible hydrogen ions.
• HCl H Cl-
• Weak acid does not dissociate 100.
• H2CO3 H HCO3-
• (weak acid) (proton)
  (conjugate base or salt)

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Buffer

• Buffer - substance that tends to resist pH
  changes in a solution thus stabilizing its
  relative pH.
• Weak acids and conjugate bases
• buffer works one pH unit either side of pKa
  (buffering range).
• Characteristics
• Buffering capacity
• pH
• See p. A2

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pH Scale

• Carbonic acid is a weak acid that buffers blood.
• H2CO3 H HCO3-
• (carbonic acid) (hydrogen ion)
  (bicarbonate)

H
OH-
H2O
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A Derivation of the Henderson-Hasselbalch
Equation

• 1. Consider a buffering mixture

WEAK ACID
PROTON
CONJUGATE BASE
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A Derivation of the Henderson-Hasselbalch
Equation

• 2. Write the acid dissociation constant (Ka)?

concentration in moles / liter mole
6.022 X 10 23 particles
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A Derivation of the Henderson-Hasselbalch
Equation

• 3. Take the logarithm in base 10 of both sides.

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A Derivation of the Henderson-Hasselbalch
Equation

• 4. Multiplying through on both sides by -1.

- log Ka

- log H
-
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A Derivation of the Henderson-Hasselbalch
Equation

• 5. Substitute
• -log Ka pKa and
• - log H pH

pKa

pH
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A Derivation of the Henderson-Hasselbalch
Equation

• 6. Rearrange

pKa

pH

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Henderson-Hasselbalch Equation
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Mathematics of Log10 (A refresher)

• Logs used extensively in pH calculations We use
  log10 exclusively in pH calculations
• Definition If b 10a then log10b a
• Multiplication
• log(ab) loga logb
• e.g. log (2 X 108) log2 log108
• 0.3 8
• 8.3
• Division
• log(a/b) loga logb
• e.g. log (2 X 10-8) log (2/10-8)
• 0.3 8
• 7.7

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Thermodynamics

• Thermodynamics distinguishes between a system and
  its surroundings.

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The First Law of Thermodynamics

• The First Law of Thermodynamics states that the
  total energy of a system and its surroundings is
  constant.
• Other ways to state this
• The energy content of the universe is constant
• Energy can be neither created nor destroyed

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The Second Law of Thermodynamics

• The Second Law of Thermodynamics states that the
  total entropy (S) of a system plus that of its
  surroundings always increases.
• Entropy (S) is a measure of randomness or disorder

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Thermodynamics terms

• S Entropy
• Disorder or randomness
• H Enthalpy
• Heat content
• T Absolute Temperature
• In degrees Kelvin
• G Gibbs free energy

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Gibbs Free Energy (?G)

• ?G ?H system - T?Ssystem
• ?G must be negative for a process to occur
  spontaneously.

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Human Genome Project

• 15 year project to sequence the entire human
  genome
• Start 1990 completed 2003 ( two years early)
• The facts
• 3164.7 million bases (3 billion)
• 99.9 identical between individuals
• 3 encodes for proteins
• 50 is repetitive junk DNA
• 1.4 million single nucleotide changes (SNPs) have
  been identified.
• 25,000 Genes
• Average gene is 3000 base pairs in size
• Largest gene is dystrophin at 2.4 million bases

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Human Genome Project (Cont)

• What We Still Don't Understand A Checklist for
  Future Research
• Exact gene number, exact locations, and functions
  
• Gene regulation
• DNA sequence organization
• Chromosomal structure and organization
• Noncoding DNA types, amount, distribution,
  information content, and functions
• Coordination of gene expression, protein
  synthesis, and post-translational events
• Interaction of proteins in complex molecular
  machines
• Predicted vs experimentally determined gene
  function
• Evolutionary conservation among organisms
• Protein conservation (structure and function)
• Proteomes (total protein content and function) in
  organisms
• Correlation of SNPs (single-base DNA variations
  among individuals) with health and disease
• Disease-susceptibility prediction based on gene
  sequence variation
• Genes involved in complex traits and multigene
  diseases
• Complex systems biology, including microbial
  consortia useful for environmental restoration
• Developmental genetics, genomics
• http//www.ornl.gov/sci/techresources/Human_Genome
  /project/journals/insights.html

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Human Genome Project (Cont)

• The draft sequence already is having an impact
  on finding genes associated with disease. Over 30
  genes have been pinpointed and associated with
  breast cancer, muscle disease, deafness, and
  blindness. Additionally, finding the DNA
  sequences underlying such common diseases as
  cardiovascular disease, diabetes, arthritis, and
  cancers is being aided by the human variation
  maps (SNPs) generated in the HGP in cooperation
  with the private sector. These genes and SNPs
  provide focused targets for the development of
  effective new therapies.
• One of the greatest impacts of having the
  sequence may well be in enabling an entirely new
  approach to biological research. In the past,
  researchers studied one or a few genes at a time.
  With whole-genome sequences and new
  high-throughput technologies, they can approach
  questions systematically and on a grand scale.
  They can study all the genes in a genome, for
  example, or all the transcripts in a particular
  tissue or organ or tumor, or how tens of
  thousands of genes and proteins work together in
  interconnected networks to orchestrate the
  chemistry of life.
• Post-sequencing projects are well under way
  worldwide. (See GenomicsGTL). These explorations
  will result in a profound, new, and more
  comprehensive understanding of complex living
  systems, with applications to agriculture, human
  health, energy, global climate change, and
  environmental remediation, among others.
• http//www.ornl.gov/sci/techresources/Human_Genome
  /project/journals/insights.html

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pH Problems

• 1. What are the pH and pOH of the following
  solutions?
• a. 0.1 M HCl
• 0.1 M H2SO4
• 2. For the dissociation of formic acid (HCOOH),
  the pH is 3.75. At pH 4.75, what is the ratio
  of formate (HCOO-) to formic acid?

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pH Problems

• 3.Calculate the ratio of HPO42- / H2PO- at pH of
  5.7, 6.7 and 8.7.

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pH problems

• 4. At a normal blood pH of 7.4, the sum of
• HCO3_ CO2 25.2 mM. What is the
  concentration of HCO3 and CO2 (pKa for HCO3_ /
  CO2 6.1)?