CHEMISTRY REFRESHER FOR BIO 311C

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CHEMISTRY REFRESHERFORBIO 311C

• Roshani Cowmeadow, Ph.D.
• Program Coordinator
• UT Learning Center

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• DAY ONE TOPICS
• Structure of an Atom
• Electrons, protons, neutrons
• Atomic number, mass number, atomic weight,
  isotopes
• Electron configuration and energy levels
• Periodic trends
• Moles/Molarity
• Molar Mass
• Calculating the molarity of a solution

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• DAY TWO TOPICS
• pH
• Acids and bases (strong vs. weak)
• pH calculations
• Functional Groups
• Organic compounds
• Six biologically important functional groups

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pH
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pH

• Concentration of H
• Acid or Base

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pH

• In pure water, some H2O molecules break apart
• H2O H OH-
• The H immediately reacts with another water
  molecule, so its really more like this
• 2 H2O H3O OH-

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pH

• 2 H2O H3O OH-

In pure water, at 25ºC (77ºF)
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0.0000001 Molar H?Thats a hard number to
remember!

• pH scale
• pH -log H
• pH -log (1.0 x 10-7)
• pH 7

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pH
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Acids and Bases
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How do you change pH?

• Add something acidic, like Hydrochloric Acid

H 0.0000001 M H 1.0 x 10-7 pH 7
H 0.0000100 M H 1.0 x 10-5 pH 5
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How do you change pH?

• Or add something basic, like Sodium Hydroxide

H 0.000000100 M H 1.0 x 10-7 pH 7
H 0.000000001 M H 1.0 x 10-9 pH 9
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Why does pH matter?

• These ions are trouble theyre looking for
  bonds to disrupt
• Can disrupt hydrogen bonds
• Can disrupt protein conformation
• Can change charge differential (potential) of a
  cell.
• And more

H
OH-
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Biological Systems and pH
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Buffers

• Stabilize pH
• Often consist of weak acids or bases
• Example bicarbonate

CO32- 2 H2O ? HCO3- H2O OH- ? H2CO3 2
OH- H2CO3 2 H2O ? HCO3- H3O H2O ? CO32- 2
H3O
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How do you tell pH without a pH meter?

• Acidic ? Tastes sour
• Basic ? makes hands feel soapy

But Why??
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So why do Acids taste sour?
Your tongue has proton receptors
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So why do bases make your hands feel soapy?
base
triglyceride (fat)
soap
glycerol
(R chain of carbon and hydrogen atoms)
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Functional Groups
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Carbon

• Organic compounds contain carbon
• Carbon is very versatile because it can make 4
  bonds
• Examples of organic compounds
• glucose cholesterol
  tryptophan

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Functional Groups

• Collections of atoms in a molecule that perform a
  certain function.
• 6 types very important for biology
• Hydroxyl group
• Carbonyl group
• Aldehydes
• Ketones
• Carboxyl group
• Amino group
• Sulfhydryl group
• Phosphate group

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Hydroxyl Group (-OH)

• Composed of hydrogen and oxygen
• Polar
• Compounds with
• -OH are known as alcohols

H
O
Ethanol
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Carbonyl Group (-CO)

• Carbon double bonded to oxygen
• Polar
• If at end of molecule aldehyde
• If in middle of molecule ketone

O
C
R
R
Acetone
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Carboxyl Group (-COOH)
O

• Carbon double bonded to oxygen, single bonded to
  a hydroxyl
• Function as acids

C
O
H
R
Formic Acid
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Amino Group (-NH2)

• Nitrogen with 2 hydrogens
• Function as bases

N
H
H
Glycine
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Sulfhydryl Group (-SH)

• Composed of sulfur and hydrogen
• Compounds are known as thiols or mercaptans
• Stinky!
• Function like OH groups

S
H
Ethanethiol
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Phosphate Group (-PO4H3)

• Phosphate plus four oxygens, with or without
  hydrogens.
• Functions as weak acid
• Phosphodiester bonds important for energy storage
  and DNA properties

O
H
O
P
H
O
H
O
ATP
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Thank you for coming!

• Please visit the UT Learning Center for
• Tutoring
• Advice
• More classes
• JES 332A
• www.utexas.edu/student/utlc