Biochemistry

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Biochemistry

• Biochemistry is the study of the chemistry of
  living organisms
• Much of biochemistry deals with the large,
  complex molecules necessary for life as we know
  it
• However, most of these complex molecules are
  actually made of smaller, simpler units they
  are biopolymers
• There are four main classes of biopolymers
  lipids, proteins, carbohydrates, and nucleic acids

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Lipids

• Lipids are a family of compounds that are
  generally insoluble in water (ie. Non-polar).
• Classes of Lipids
• Waxes fatty acid and long chain alcohol (ester)
• Fats Oils glycerol three fatty acids
• Phospholipids glycerol 2 fatty acids
  phosphate an amino alcohol
• Sphingolipids fatty acid sphingosine
  phosphate an amino alcohol
• Glycolipids fatty acid glycerol or
  sphingosine one monosaccharide.
• Steroids a fused ring structure of three
  cyclohexanes and one cyclopentane.

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Fatty Acids

• Long chain carboxylic acids.
• 12 18 Carbons are the most common.
• Stearic acid is most often found in animal fat.

CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH
2COOH
And it can also be represented like this
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Fatty Acids

• Can be saturated all C-C single bonds.
• Can be mono-unsaturated one C-C double bond.
• Ex) Oleic Acid found in olives and corn.
• CH3(CH2)7CHCH(CH2)7COOH
• Can be poly-unsaturated more than one C-C
  double bond.
• Ex) Linoleic Acid found in soybeans and
  sunflowers.
• CH3(CH2)4CHCHCH2CHCH(CH2)4COOH
• In the Unsaturated acids, the cis isomer is
  usually found.

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Physical Properties of Fats and Oils

• The repeating zigzag shape of saturated fatty
  acids found in fats allows them to fit close
  together leading to strong attractions. As a
  result, a fat is solid at room temperature.
• The unsaturated fatty acids found in oils do not
  stack together because of the double bonds. As a
  result, an oil is a liquid at room temperature.

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Fats and Oils

• Fats and oils are the most common lipids.
• Often called triglycerides because they are a
  tri-ester of glycerol and three fatty acids.
• Tristearin consists of three stearic acid
  molecules reacting with glycerol.

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Reaction to Produce a Fat or Oil
3 H2O
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Steroids and Cholesterol

• Steroids are any compounds containing the steroid
  nucleus (Pictured at right).
• Cholesterol is the most important and abundant
  steroid in the body.
• You cannot exist without this substance!
• The sex hormones and the adrenocortical hormones
  depend on cholesterol for their synthesis.

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Cholesterol and Hormones
Cholesterol, Estrogen, and Testosterone
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Carbohydrates

• Simple Sugars have the formula Cn(H2O)n and were
  once thought to be hydrates of Carbon.
• The Carbon cycle.
• ___________
• 6CO2 6H2O energy ? C6H12O6 6O2
  _____________

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Types of Carbohydrates

• Monosaccharides do not hydrolyze into smaller
  units.
• Disaccharides consist of two mono units joined
  together these will hydrolyze.
• Polysaccharides consist of many mono units and
  are sometimes called complex carbohydrates.

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Monosaccharides

• Have between three and eight C atoms.
• Number of Cs determines whether it is a triose
  (3), tetrose (4), pentose (5), hexose (6), etc.
• All have at least two OH groups and the term
  polyhydroxy- is sometimes used.
• Will also have either an aldehyde or ketone
  group.
• Aldehyde aldose and ketone ketose.
• Molecules are written with the C backbone in a
  vertical direction.

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Monosaccharides

• Ketose or Aldose?
• How many chiral carbons?

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Monosaccharides and Chirality

• Large monosaccharides have several chiral Cs.
• If the lowest chiral C has the OH group on the
  left, then it is called the L isomer. If it is
  on the right, then it is called the D isomer.
• Hint Cs with double to the O are not chiral and
  the -CH2OH groups are also not chiral.

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Glucose

• How many chiral carbons?
• Is this the D or L isomer?
• Note D-glucose is oxidized in the body to
  produce energy and L-glucose cannot be oxidized.

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Cyclic Structure

• In solution, glucose and other mono-saccharides
  become cyclic.

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Disaccharides

• Composed of two mono units.
• Some common ones are
• Sucrose Glucose Fructose
• Lactose (Milk sugar) glucose galactose
• Maltose glucose glucose
• In the presence of water and an acid catalyst,
  these linked molecules will split apart back into
  their mono units.

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Sucrose
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Polysaccharides

• This is essentially a polymer of glucose units
  (usually).
• Plant Starch exists in two forms Amylose and
  Amylopectin.
• Amylose is a long,continuous chain of glucose
  molecules. Typically has 250 4000 units.
• Amylopectin is a branched chain of glucose
  molecules. Branches are about every 25 units.

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Polysaccharides

• Animal Starch is also called ___________. This
  is essentially a branched chain as well.
• Branches are about every 10 15 units.
• ____________, found in cell walls of plants and
  animals, is also a long chain of glucose units
  much like amylose.

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Polysaccharides

• The linkage between each unit in cellulose is
  different (b linkage) and is resistant to
  hydrolysis.
• Humans do not possess the enzymes to break this
  material down for energy as some animals do.
• We often refer to this material in our diet as
  fiber.

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Amino Acids and Proteins
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The Amino Acids

• Are the building blocks of all proteins.
• Twenty different versions of these.
• All contain the carb. acid and amine functional
  groups.
• Center C is called the alpha Carbon and it is
  chiral (except in Glycine)
• Abbreviated by three letter designations.

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Amino Acids

• The R groups can be non-polar, polar, acidic, or
  basic.

Serine
Alanine
Non-polar R group
Acidic R Group
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The Peptide Bond

• Amino acids link together by the reaction of a
  carboxylic acid on one with the amine of another.
• The linkage between the two is called a peptide
  bond.

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Peptide Formation

• Reaction to form peptide bond between any two
  amino acids is a condensation type

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Primary Structure

• Chains of 3 50 amino acids are called
  polypeptides.
• When more than 50 amino acids are joined, we
  usually call it a protein.
• The specific sequence of amino acids in a protein
  is called the primary structure.
• Our DNA codes for only a limited number of
  specific sequences for making proteins.
• Approximately 100,000 different proteins found in
  humans.

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Secondary Structure

• This refers to how the amino acids along the
  polypeptide are arranged in space.
• The three most common types are
• Alpha Helix - which is a corkscrew shape of the
  chain that results from Hydrogen bonding between
  every fourth amino acid. All of the R groups
  then are pointed outward.
• Beta-Pleated Sheet rows of amino acids are held
  flat with HB keeping them rigid.
• Triple Helix is three peptide chains woven
  together like a braid. HB is also a powerful
  force that holds this together.

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Alpha Helix Beta-Pleated Sheet
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Tertiary Structure

• This is the overall 3D shape of the protein.
• The types and interactions of the R groups are
  important in this area.
• Globular proteins, like hemoglobin and insulin,
  have a very compact and round shape. The
  non-polar R groups point inward and the polar R
  groups point outward and this makes these
  proteins soluble in water.
• Fibrous proteins, like keratin (hair, skin),
  consist of long, thin, fibrous shapes.
  Cross-linking is an important aspect and
  determines whether you have curly or straight
  hair.

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Tertiary Structure
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Overview of Protein Structures
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Albumin
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Lysozyme
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Nucleic Acids

• Basic structure is a polymer of four different
  bases.
• Each nucleotide consists of three parts a sugar,
  a base, and a phosphate group.

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Nucleotide Structure

• Each nucleotide has three parts a cyclic
  pentose, a phosphate group, and an organic
  aromatic base
• The pentoses are the central backbone of the
  nucleotide
• The pentose is attached to the organic base at C1
  and to the phosphate group at C5
• The phosphate groups then link to each other to
  form a polymer

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DNA and RNA

• Deoxyribonucleic Acid is found primarily in the
  nucleus of the cell.
• Ribonucleic Acid is found throughout the cell.
• The sugar molecule Ribose differs by a single
  oxygen atom.

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Bases

• In DNA, the four cyclic bases are Adenine,
  Guanine, Cytosine, and Thymine. In RNA, Thymine
  is replaced by Uracil.

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Base Pairing in DNA
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Base Pairing in DNA

• The bases in nucleic acids are complementary
  they precisely pair with another base.
• Adenine pairs with Thymine via two hydrogen bonds
  
• Guanine pairs with Cytosine via three hydrogen
  bonds

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Linking Nucleotides
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Linking Nucleotides
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Genetic Structure

• Each sequence of three nucleotides is called a
  codon
• A codon codes for one amino acid
• AGT Serine
• ACC Threonine
• This is universal for all living things!

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DNA Double Helix
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DNA Double Helix

• Base pairing generates the helical structure
• In DNA, the complementary bases hold strands
  together by H-bonding
• allow replication of strand

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DNA Replication
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Protein Synthesis

• Transcription ? translation
• In nucleus, DNA strand at gene separates and a
  complementary copy of the gene is made in RNA
• messenger RNA mRNA
• The mRNA travels into the cytoplasm where it
  links with a ribosome
• At the ribosome, each codon on the RNA codes for
  a single amino acid, and these are joined
  together to form the polypeptide chain

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Protein Synthesis
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