Biochemistry

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Biochemistry

• Using Organic chemistry for Life

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Clicker

• Why are organic molecules important to biology?
• Living objects are constructed mostly of organic
  molecules.
• Organic molecules are so varied that they are
  capable of many different functions.
• Only God knows for sure and shes not saying.
• Look, Im here, isnt that good enough?

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Organic molecules are Life

• If you think of all the different things an
  organism needs to do
• Create energy
• Repair itself.
• Grow
• Transport materials
• Hold its structure
• Fend off invaders
• Protect from hostile nature (heat, light, storms,
  electricity)
• Reproduce
• Store blueprints
• Store memories
• Acquire sensory data
• Process sensory data
• Lots of functions require lots of molecules

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Lipids

• Lipids are water-insoluble components of cells
  including fats, fatty acids, oils, phospholipids,
  glycolipids, and steroids.
• Your body is mostly water (aids transport,
  temperature control), so if every molecule in
  your body were water soluble, youd melt into a
  salty puddle!!!
• Lipids, among other uses, make up cell membranes
  to keep you from collapsing into a puddle!

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Fatty Acids

• Guess what kind of acid?
• Carboxylic acid!!!
• A fatty acid is a long alkane/alkene chain with a
  carboxylic acid on the end!

Myristic acid (common name) Tetradecoic acid
(IUPAC name) Butterfat or coconut oil
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• Oleic acid (common name)
• cis-octadec-9-enoic acid)
• In olive oil, peanut oil

What does the cis mean? It means the two H are
on the same side!
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Fatty Acids
Stearic Acid C18H36O2 a saturated fatty acid
Oleic Acid C18H36O2 a monounsaturated fatty
acid
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Fatty Acids
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Structure and Melting Point

• Larger fatty acid Higher melting point
• Double bonds decrease the melting point
• More DB lower MP
• Saturated no DB
• Monounsaturated 1 DB
• Polyunsaturated many DB

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Its all about the solubility

• The alkane/alkene portion of the molecule is
  water insoluble. Why?
• Its non-polar. Water is polar. Remember, like
  dissolves like.
• The carboxylic acid portion is water soluble.
  Why?
• The carboxylic acid (C0 and OH) is polar, and
  so is water.

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If I throw oleic acid in water

• What happens?
• It forms little micelles (beads) with the
  hydrophobic tails all mixed together and the
  hydrophilic acid portion facing the water.
• This is why oil and water dont mix

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Lipid Bilayer
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Fats and oils

• Triglycerides
• Youve heard the term, what does it mean? A
  triglyceride is actually a combination of
  glycerol (a triol) and 3 fatty acids. Its
  actually a tri-ester!

glycerol
Myristic acid
3

O
C(CH2)11CH3
Trimystirin
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Fats and oils

• This a saturated fat the hydrocarbon chain is
  an alkane, no double bonds.

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Fats and oils

• An unsaturated fat would have double bonds. If
  we did the same reaction with oleic acid.

Oleic acid
glycerol
3

O
CH3
(CH2)4
C (CH2)7
C
Triolein
O
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Tristearin a simple triglyceride found in lard
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Triglycerides

• Saturated triglycerides tend to be at
  room temperature.
• Solid
• Liquid
• Gas
• All of the above, it depends on the type.

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Triglycerides

• Saturated triglycerides tend to be solids at room
  temperature because of
• Van der Waals forces
• Hydrogen bonding
• Dipole-dipole interactions
• A and B
• B and C

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Triglycerides

• Unsaturated triglycerides tend to be
  at room temperature.
• Solid
• Liquid
• Gas
• All of the above, it depends on the type.

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Triglycerides

• Unsaturated triglycerides (oils) tend to be
  liquids at room temperature because of
• Van der Waals forces
• Hydrogen bonding
• Dipole-dipole interactions
• A and B
• B and C

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Triglycerides

• They are big molecules. They tend to form solids
  due to a combination of Van der Waals forces and
  dipole forces. BUT, unsaturated molecules can be
  sterically hindered so that the polar parts cant
  get near the other polar parts. That leaves us
  with just Van der Waals forces and it reduces
  the melting point relative to saturated molecules.

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Trioleina simple triglyceride found in olive oil
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Other Lipids

• Phospholipids take a triglyceride and replace
  one of the fatty acids with a phosphate group.
• Glycolipids Use glucose instead of glycerol.
• These are ideal for cell walls they are strong
  and have a polar end and non-polar end. The
  polar end faces the inside (aqueous) part of the
  cell and the non-polar ends are internal.

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Phospholipids

• Esters of glycerol
• Glycerol attached to 2 fatty acids and 1
  phosphate group
• Phospholipids have a hydrophilic head due to
  phosphate group, and a hydrophobic tail from the
  fatty acid hydrocarbon chain
• part of lipid bilayer found in animal cell
  membranes

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Phosphatidyl Choline
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Glycolipids

• similar structure and properties to the
  phospholipids
• the nonpolar part composed of a fatty acid chain
  and a hydrocarbon chain
• the polar part is a sugar molecule
• e.g., glucose

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Glucosylcerebroside(found in plasma membranes of
nonneural cells)
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Steroids

• Steroids are lipids with a four-ring central
  structure.

OH
CH3
CH3
O
Testosterone
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Steroids
testosterone
cholesterol
estrogen b-estradiol
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Carbohydrates

• Structurally much simpler than lipids.
• Carbohydrates are polyhydroxy aldehydes or
  ketones.

Glucose (C6H12O6) a monosaccharide
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Carbohydrates

• You can actually string together monosaccharides
  to make more complicated carbohydrates.
• But even monosaccharides have variety!

Carbons 2, 3, 4, and 5 are all chiral 4
different atoms are attached
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Carbohydrates

• But even monosaccharides have variety!
• Mannose is an optical isomer of glucose
  differing only in the relative 3D orientation of
  the -OH

Mannose
Glucose
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Intramolecular rearrangement

• Glucose can actually react with itself by
  addition to the carbonyl to form a 6 membered
  ring (5 or 6 membered rings are more stable and,
  therefore more likely)

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Intramolecular rearrangement
O

• Equivalent representations of glucose. Similar
  pairs of structures exist for all sugar.
• Glucose is an example of one type of sugar,
  called an aldose because of the aldehyde group
  in the linear structure.

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Fructose (C6H12O6)

• Fructose is a ketose. Its structure is similar
  to aldoses (like glucose) but it is a ketone in
  the linear representation rather than an
  aldehyde.
• Notice Fructose is a structural isomer of
  glucose!

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Dehydration returns!

• Monosaccharides can be linked together via
  dehydration reactions to form glycosidic
  linkages.
• A glycosidic linkage is really just an ether
  linkage created by dehydration of 2 alcohols!

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Dehydration returns!

• While it might seem that we can create the
  linkage using multiple different alcohol (-OH)
  sites to form the bond, there is one OH that is
  more reactive than all the others!

Because of the presence of the O next to it, this
C-OH bond is more reactive!
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Dehydration returns!

• The dehydration reaction that creates the
  glycosidic linkage occurs preferentially at
  this site!

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Dehydration returns!
OH
OH
H
H
OH
C
OH
C
H
H
C
C
C
C
H
OH
H
OH
H2O
H
H
H
H
C
C
C
C
CH2
CH2
O
OH
OH
O
O
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Size matters..

• If 2 sugar molecules can form a glycosidic
  linkage, then the most reactive site is used.
  BUT, theres no reason why you cant use the less
  preferred sites.
• Carbohydrates are polysaccharides formed by
  multiple glycosidic linkages between sugar
  molecules.

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Clicker Question

1. Im here
2. Im not here

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Amino Acids

• Amino Acids are building blocks of proteins.
• Amino Acids are exactly what the name suggests
  amines AND carboxylic acids

Glycine
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a - Amino Acids

• Glycine is the simplest of the a - amino acids.
  The a refers to the carbon immediately next to
  the carbonyl group. To be an a - amino acid, the
  amine must be bonded to this carbon.

Glycine
a
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Different substituents, different a - amino acid

• If the a carbon has different substituents
  (besides the 2 Hs of glycine) it is a different
  amino acid.

CH2
CH2
C 0
OH
OH
Serine
Aspartic acid
Glycine
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Lets think together
bases

• Amines are
• Carboxylic acids are
• What happens when you mix an acid and a base
  together?
• They neutralize each other!

acids
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How would that neutralization occur?

• The COOH is an acid, the NH2 is a base. Any
  COOH can donate a proton to any NH2. Some
  amino acids are stronger acids/bases than others
  based on the side group, but they are all
  acids/bases.

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Base form of Glycine
Amphoteric form of Glycine


-
Zwitterion form of Glycine
Acid form of Glycine
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Which one is it?

• If you had a beaker full of glycine in distilled
  water at 25 C and 1 atm of pressure, which one
  would be the dominant form?

Base form of Glycine
Amphoteric form of Glycine

Zwitterion form of Glycine
Acid form of Glycine
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Which one is it?

• Could you ever have any of the other forms?
• Sure! Change the pH!

Base form of Glycine
Amphoteric form of Glycine

Zwitterion form of Glycine
Acid form of Glycine
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What happens if I mix serine and glycine?

• Lets make H2O!

Glycine
Serine
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Dehydrationnot always a bad thing! Called
condensation

Glycine
Serine
OR
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Dehydrationnot always a bad thing! Called
condensation
OR
Peptides
H2O
H2O
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Protein structure

• One way to look at protein information is in
  the sequence of the amino acids.
• Consider the alphabet, with 26 letters.
• If you had 26 amino acids, how many 3 letter
  words could you write?
• 17,576 (26x26x26)
• 456,976 Four letter words
• 11,881,376 Five letter words
• 141 trillion 10 letter words

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Structure and Function

• Unlike words, proteins are 3-D objects. The
  function of a given protein is determined by its
  sequencewhich amino acid follows which amino
  acid called the primary structure, but it is
  also determined by the secondary, tertiary, and
  even quarternary structure.

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Secondary structure

• Once the amino acids are in a sequence, it is
  possible for them to form superstructures by
  hydrogen bonding with each other across chains.
• Secondary structure is a multi-amino acid
  structure.

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Secondary structure

• An alpha helix (a-helix) is a right-handed
  (clockwise) spiral in which each peptide is in
  the trans conformation. The amine group of each
  peptide bond runs upward and parallel to the axis
  fo the helix the carbonyl points downward.
• A ß-pleated sheet consists of neighboring chains
  that are anti-parallel to each other. Each
  peptide bond is trans and planar. The amine and
  carbonyl point toward each other.

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Tertiary structure

• Once the amino acid sequences are arranged into
  secondary superstructures, these secondary
  structures can be arranged differently relative
  to each other. A kind of super-superstructure.
• This tertiary structure is usually constructed
  largely by disulfide bonds between cysteine amino
  acid groups.

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Quarternary structures

• Some proteins are made up of multiple polypeptide
  subunits (different chains of amino acids). Each
  subunit has its own primary, secondary, and
  tertiary structure.
• The subunits are arranged relative to each other
  in quarternary super-super-superstructures