The Molecules of Life

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Chapter 3

• The Molecules of Life

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Organic Molecules

• Contain C as a major element
• Study of organic chemistry or carbon chemistry
• C can make 4 covalent bonds
• Can get molecules branching off in 4 different
  directions
• develop very diverse carbon skeletons by binding
  with other C
• Usually bind with O, H or N most commonly
• CH4 (methane) is the simplest hydrocarbon

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Carbon Molecules
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Hydrocarbons

• Serve as fuels octane for cars and
  triglycerides for humans
• 3-D shape is also important in organic molecules
  as well as biological molecules
• What atoms on the C skeleton are also important

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Functional Groups
Ketone
Aldehyde
Sulfhydryl - S-H
Phosphate
Must know how to recognize and draw these!!
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Condensation Reaction

• Also called dehydration or polymerization
  reactions
• Take small subunits and build larger molecules
  macromolecules by the removal of H2O
• Same in all reactions that build larger molecules

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Hydrolysis Reactions

• Break large molecules apart to regenerate the
  subunits
• Need to break apart H2O to replace the H2O
  removed to make the macromolecule

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Macromolecules
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Carbohydrates

• Animals primary energy source
• Plants primary building blocks
• Monosaccharides simple sugars such as glucose
  and fructose
• same chemical formula but different arrangement
  of elements isomer
• gives sugar different properties, fructose is
  sweeter than glucose

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Sugars

• Disaccharides 2 sugars joined by dehydration
  reaction
• Many common ones lactose (Glc Gal) sucrose
  (Glc Fru)

• In aqueous environment sugars are ring structures
• Use the carbon skeleton structure as the
  beginning of other molecules needed in the cell

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Polysaccharide

• Complex carbohydrates long chains of sugars
• Starch many glucose, storage in plants, linear
  molecule
• Glycogen many glucose, storage in animals,
  branched molecule
• Cellulose many glucose, structural molecule,
  makes a fiber, most abundant organic compound on
  earth

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Carbohydrates

• Are very hydrophilic because of the OH groups
• Small sugars are very dissolvable in H2O but as
  they get larger in structure they become less
  soluble

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Lipids

• Hydrophobic or H2O hating
• see in salad dressings that separate
• Several types that are important
• fats
• steroids

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Fats

• Triglycerides are made of glycerol and 3 fatty
  acid chains (long hydrocarbon chains) connected
  by dehydration reaction
• Stores at least 2x the energy of sugars
• Fatty acid chains come in 3 types
• saturated no CC
• unsaturated 1 to a few CC
• polyunsaturated many CC

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Fats vs. Oil

• Fats have mostly saturated fatty acid side chains
  and are solids at room temperature
• tails will pack together firmly
• Oils have at least 1 unsaturated fatty acid tails
  and are liquids at room temperature
• CC makes a kink in the chain and therefore,
  cannot pack tightly

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Atherosclerosis

• Contributes to with high saturated fat diets
• Lipids build up on vessels, decrease blood flow
  and an increase of heart attacks and strokes
• Most plant oils are low in saturated fatty acids
  with the exception of tropical plant oils such as
  cocoa butter
• reason chocolate melts in your mouth

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Other Fats

• Hydrogenation process that converts unsaturated
  to saturated fatty acids
• Produces trans-fats (form of unsaturated fatty
  acids), worse than saturated ones
• Very healthy fat omega-3 fatty acid
• find in oily fish such as salmon and nuts
• decrease heart disease, relieves symptoms of
  arthritis and inflammatory bowel disease

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Steroids

• Different in structure and function but still
  lipids, hydrophobic
• Cholesterol is a 4 ring structure, implicated in
  heart disease but also important for cell life
  such as cell membranes, hormone starting point

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Anabolic Steroids

• Synthetic variant of testosterone
• THG new designer drug
• Very harsh side effects
• mood swings
• depression
• liver damage
• increased cholesterol
• shrunken testicles
• decrease in sex drive
• infertility

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Proteins

• Very elaborate many different ones, unique 3-D
  shape and function
• Made of amino acids
• Function as structural storage contractile
  transport also as defensive molecules such as
  antibody signal proteins and enzymes

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Amino Acids

• Must know structure of general amino acid
• Need to know the groups that they belong in
• Central C with
• COOH
• NH2
• -H group
• side group (R group) that makes each amino acid
  unique

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Non-polar and hydrophobic
Neutral
Hydrophilic
Acids
Bases
Polar
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Peptide Bonds

• Link amino acids together by a dehydration
  reaction between the incoming NH2 with the COOH
  group of the growing peptide change
• Backbone is N-C-C-N-C-C

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Polypeptide Chain

• gt 100 amino acids strung together
• Each protein has a unique order of amino acid
  letter is like a letter in an alphabet that
  spells out very long words
• Proteins are linear and not branched like
  polysaccharide

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Changes to the Alphabet

• One letter change can alter the conformation and
  function of a protein
• depends on where it is in the overall structure
  of the protein
• Substitute Val for Glu leads to sickle shaped red
  blood cell in low O2 concentration

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Protein Shape

• Polypeptide is not quite a protein until it folds
  into its proper shape and possibly join with
  other folded peptides
• Proteins have 3 levels of structure or a 4th
• 1? - unique sequence of AA, linear
• 2? - 2 folding patterns
• ? helices spiral
• ? sheets pleated
• 3? - overall shape of the protein
• 4? - if protein has multiple subunits that are
  necessary for the protein to function like
  hemoglobin

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3-D Structure

• Function follows form shape is crucial for
  function
• Surroundings dictate structure changes in
  temperature, pH or other environmental conditions
  proteins can unwind and lose shape
• denaturation
• cooked egg
• part of the reason you feel crappy when you have
  a fever proteins are not working well
• not all denaturation is permanent use chemicals
  in the lab to separate and purify proteins

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Nucleic Acid

• Information storing molecule made up of genes
  in a 4 letter alphabet
• building plan for proteins with an RNA
  intermediate (Ch 10)
• 2 types of nucleic acid
• RNA ribonucleic acid
• DNA deoxyribonucleic acid

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Building Blocks

• Nucleotide has 3 components
• nitrogenous base that can accept H base
• A, G, C and U for RNA
• A, G, C and T for DNA
• sugar
• ribose for RNA
• deoxyribose for DNA
• phosphate group

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Nitrogenous Bases
Adenine and Guanine are purines Thymine,
Cytosine and Uracil are pyrimidines
Uracil (U)
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Phosphodiester Bond

• Nucleotides linked together by phosphodiester
  bond
• Links the sugar (3 OH) of one nucleotide to
  the phosphate (5) of the incoming nucleotide
• The order of nucleotides is what makes DNA
  sequence unique

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DNA

• Double helix 2 strands of DNA that run
  anti-parallel
• Nitrogenous bases make the rungs of the ladder
  with H-bonds holding them together
• A and T 2 bonds
• G and C 3 bonds
• Strands are complementary to one another

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RNA

• Different from DNA in that it is single stranded
• Sugar is ribose
• Use U instead of T

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DNA and Protein

• Tape measure of evolution
• DNA is passed down to offspring and therefore so
  do the proteins that are expressed siblings are
  similar but not identical (except twins) compared
  to the general population
• Use similarities in DNA sequence to map
  relationships between populations
• the more closely related, the closer the sequence

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