Biomolecules

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Biomolecules

• The Raw Materials of Biotechnology
• The Molecules of Cells

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Organization of Life

• Entire organism
• System
• Tissue
• Cells
• Organelle
• Molecules
• Atoms

• Molecular/atoms lowest level of organization

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Elements of Life

• Organic chemistry
• Chemistry of Carbon
• CHNOPS
• Carbon
• Hydrogen
• Nitrogen
• Oxygen
• Phosphorus
• Sulfur
• Several Trace Minerals

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CARBON --The main event

• Forms a bond with
• 4 other atoms in which
• electrons are shared forming
• a covalent compound
• C

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CARBON -4 Bonds to other atoms

• H
• H C H
• H CH4

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CARBON -4 Bonds to other atoms

• H
• \
• H C OH
• H
• CH3OH

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CARBON -4 Bonds to other atoms

• H H
• H C C OH
• H H
• CH3CH2OH

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CARBON -4 Bonds to other atoms

• O
• H C H
• CH2O

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Four Main Types of Biomolecules

• All are polymers
• All are organic (C) compounds
• Carbohydrates
• Proteins
• Lipids
• Nucleic Acids
• Differ in terms of composition and function

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FunctionFour Main Types of Biomolecules

• Carbohydrates. Energy, support and
  recognition
• Proteins..Enzymes, structure,
  recognition, transport pigments,
  signals, movt
• Lipids..Cell membrane structure energy
  storage, signals cellular metabolism
  (VitK..)
• Nucleic Acids.Hereditary and protein
  information, energy, signals

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StructureFour Main Types of Biomolecules

• Carbohydrates. Polysaccharide..of simple
  sugars
• Proteins..Polypeptide..of amino acids
• Lipids..Insoluble in water..although
  common polymer glycerol and fatty acid
• Nucleic Acids.Polynucleotide..of
• nucleotides

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CarbohydratesWhat do they have in common?
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Carbohydrates-Common Features

• -OH Several OH (alcohol) groups
• This group LOVES water
• Makes sugars solids and water soluble
• CO C with a double bond to an oxygen
• Aldehyde or ketone
• Joins w/an OH to form a cyclic structure
• The resulting C (C-1) has OH/H
• Position of OH determines further bonding

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Monosaccharide-Fructose
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Monosaccharide Galactose
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Monosaccharide Glucose
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Comparing Two Different Sugars

• Open Chain

• Cyclic

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Disaccharides-Two sugars

• Loss of H and -OH

• Loss of Water !!!!!

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Disaccharide Lactose

• Lactose Milk Sugar
• Lactose Glucose and galactose
• Lactase Enzyme that digests lactose
• Most mammals express lactase only as juveniles
• Adults are lactose intolerant
• Once weaned NO MILK!!!!!

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Polysaccharides

• Starch...bonds between glucose can be digested
• Amyloseplant Glycogen animal

• Cellulosebonds between glucose cannot be
  digested by mammals

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SOboth are GLUCOSE ?????

• Starch stores glucose molecules for energy
• Amylose ? Maltose
• Amylase
• Maltose ? 2 Glucose
• Maltase
• Good for providing energy

• Cellulose is a rigid molecule of support
• Cellulose ? Cellobiose
• Cellulase
• Cellobiose ? 2Glucose
• Cellobiase
• Good for making paper

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Other carbohydrates
Chitin
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To Test for Carbohyrate
Benedict's Chemical test for reducing sugars To
test for the presence of monosaccharides and
reducing disaccharide sugars in food, the food
sample is dissolved in water, and a small amount
of Benedict's reagent is added. During heating
in a water bath, which is usually 4-10 minutes,
the solution should progress in the colors of
blue (with no glucose present), green, yellow,
orange, red, and then brick red or brown (with
high glucose present). Lugols Chemical test
for starch An indicator test for the presence of
starches Reacts by turning a dark-blue/black.
Stain starches due to iodine's interaction with
the coil structure of the polysaccharide
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FunctionFour Main Types of Biomolecules

• Carbohydrates. Energy, support and
  recognition
• Proteins..Enzymes, structure,
  recognition, transport pigments,
  signals, movt
• Lipids..Cell membrane structure energy
  storage, signals cellular metabolism
  (VitK..)
• Nucleic Acids.Hereditary and protein
  information, energy, signals

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Proteins

• Proteins (also known as polypeptides) are organic
  compounds made of amino acids.
• Proteins are essential parts of organisms
• Proteins participate in virtually every process
  
• within cells.
• Proteins make up half the dry weight of an
  Escherichia coli cell (other macromolecules such
  as DNA and RNA make up only 3 and 20,
  respectively).
• Proteins have diverse functions due to their
  ability to bind other molecules specifically and
  tightly

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Protein Function..!! WOW!!

• Structural. Bones,skin, nails, hooves, hair
• Enzymatic Digest sugar, makes DNA, makes fatty
  acids
• Transport Carries oxygen and fats in blood,
  Ca2/Cl-
• Contractile.. Muscles for movement, move
  chromosomes
• Hormone. regulate blood sugar, increase heart
  rate
• Immunity... Antibodies fight foreign substance
• Pigment.. Pigment in skin, eyes
• Recognition. On cell surfacesOther molecules
  (receptors)
• Toxins Stops nerve transmission, effects
  movement of ions, enzymes that destroy red
  blood cells

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Protein StructurePolypeptide

• Polymer of many amino acids
• Amino Acid
• H O
• H N C C OH
• H R
• Central Carbon
• R group

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Amino acids are distinguished by the R group

• Twenty different amino acid are found in proteins
• Most microorganisms and plants can biosynthesize
  all 20
• Animals (including humans) must obtain some of
  the amino acids from the diet.
• The amino acids that an organism cannot
  synthesize on its own are referred to as
  essential amino acids.
• Humans require 8 essential amino acids

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Amino acids combine by a dehydration synthesis
reaction

• Also called a condensation reaction

• An octapeptide

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Amino acids combine to form protein

• The order in which
• amino acids are bonded is called the sequence
• The sequence of amino acids determines the
  primary structure of a protein
• Determined by the genetic code (sequence of DNA)

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The chemical nature of R groups defines the
characteristics of the protein

• Some amino acid groups are attracted to each
  others
• Some amino acid groups are repelled by each other

• http//www.biog1105-1106.org/demos/105/unit1/prote
  instructure.html

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Four levels to protein structure

• Amino acid groups determine the overall shape of
  protein
• Proteins are not long straight molecules, but are
  usually folded into a 3-D shape

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Four levels to protein structure

• Structural proteins confer stiffness and rigidity
  to otherwise-fluid biological components.
• Most structural proteins are fibrous proteins.
• Polymerize to form long, stiff fibers that
  comprise the cytoskeleton, which allows the cell
  to maintain its shape and size

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Protein shape protein function
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Genetic Disease is due to Incorrect Proteins

• DNA
• RNA
• mRNA to be exact
• Protein

• Angelmans Syndrome
• Color Blindness
• Cystic Fibrosis
• Duchenne muscular dystrophy
• Hemophilia
• Sickle Cell Disease
• Tay Sacs
• Phenylketonuria
• Ataxia telangiectasia
• Gaucher disease
• Amyotrophic lateral sclerosis
• Parkinson Disease
• Huntington Disease
• Alzheimer Disease
• Cancer (Breast, Colon, etc..
• And the list goes on and on and on

• Central Dogma of Molecular Biology

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Changes in DNA Change in Protein Change in
Function

• DNA
• Transcription
• RNA
• mRNA to be exact
• Translation
• Protein

• Regulation of transcription determines genes
  expressed (and proteins produced)
• Shortly after or even during synthesis, the
  residues in a protein are often chemically
  modified by post-translational modification
• Alters the physical and chemical properties,
  folding, stability, activity, and ultimately, the
  function of the proteins.

• Gene Expression

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Detecting Proteins

• Chemical test used for detecting the presence of
  peptide bonds.
• In a positive test, a copper(II) ion is reduced
  to copper(I)
• Forms a complex with the nitrogen and carbon of
  the peptide bonds in an alkaline solution.
• A violet color indicates the presence of proteins

• Alternative protein assays include
• UV spectroscopy
• Lowry protein assay
• Bicinchoninic acid protein assay (BCA)
• Amido black protein assay

• Biuret test

• Other Tests

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Brown Recluse Spider Toxin Effect on Red Blood
Cells

• Venom released by the brown recluse spider
  contains a complex collection of enzymes.
  Primarily protein-based, the brown recluse
  spider's venom has antigenic and locally
  destructive properties. Among other
  subcomponents, esterases, hyaluronidases and
  proteases have been isolated from recluse spider
  venom through various purification techniques. Of
  these, Sphingomyelinase-D has been identified as
  the primary substance with a toxic effect on red
  blood cells.
• Sphingomyelinase-D directly causes hemolysis,
  which damages red blood cell walls and leads to
  the leakage of the red, oxygen-bearing protein
  known as hemoglobin. Anemia may result. After red
  blood cell casts are discarded, they are filtered
  through the kidneys and can cause renal failure.
• Brown recluse venom triggers the aggregation of
  platelets and endothelial swelling in order to
  combat harm caused to red blood cells. White
  blood cells are brought to the area of the
  injury. However, instead of forming blood clots
  where needed, these white blood cells form blood
  clots in capillaries, resulting in necrosis.

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FunctionFour Main Types of Biomolecules

• Carbohydrates. Energy, support and
  recognition
• Proteins..Enzymes, structure,
  recognition, transport pigments,
  signals, movt
• Lipids..Cell membrane structure energy
  storage, signals cellular metabolism
  (VitK..)
• Nucleic Acids.Hereditary and protein
  information, energy, signals

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Lipids-What are they?

• Sometimes used as a synonym for fats
• Fats are a subgroup of lipids called
  triglycerides
• Lipids are defined as molecules that are
  hydrophobic or amphiphilic
• Hydrophobic..they dont dissolve in water
• Amphiphilic nature some lipids form structures
  such as vesicles, liposomes, or membranes in a
  water environment

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Lipids What are they?

• The main biological functions of lipids include
• Energy storage
• Structural components of cell membranes
• Important signaling molecules.

• Broad group of molecules that includes
• Fats Waxes
• Sterols
• Fat-soluble vitamin
• (such as vitamins A, D, E and K),
• Monoglycerides,
• Diglycerides,
• Phospholipids,
• and others.

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LipidsWhat are they?

• Made of mostly C-H
• Some oxygen
• Some phosphorus
• Might see nitrogen
• Made of mostly C-H
• Thats why they are hydrophobic

• They Dont like waterThey Dont like water..They
  dont like water

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Three general groups

• Triglycerides
• Phospholipids
• Steroids

Remember mostly carbon and hydrogen!
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Triglycerides

• Animal fat and plant oils
• Energy storage molecules
• Composed of glycerol and fatty acids

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Fat VS. OilIts all in the Fatty Acids

• Saturated fats..All C-C single bonds
• Molecules pack together wella solid or fat--at
  room temperature

• Unsaturated fats..A few to many C C double
  bonds
• Molecules dont pack togethera liquidor oilat
  room temperature

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Phospholipids

• Found primarily in cell membranes
• Similar to triglycerides exceptthese have a
  phosphate group
• Makes the molecule capable of interactions with
  water

• Phosphate polar head

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Phospholipids

• Phosphate A negative charge
• Hydrophilic-phosphate (head)
• Hydrophobic-fatty acid (tail)
• Make membrane bilayer in water environment (like
  the cell)

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Phospholipids make up membranes
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Sterols

• Overlapping rings of C-H
• Complex molecules with many functions
• Horomone
• Pigments
• Vitamins
• Cholesterol one of most important

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Sterols
Testosterone
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Test for lipids

• Grease-spot test for lipids has been used for
  centuries.
• Produce a translucent stain on paper or fabric

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Fatty Acids used to make SOAP

• Consists of sodium or potassium salts of fatty
  acids
• Made by reacting common oils or fats with a
  strong alkaline solution (the base, NaOH) in a
  process known as saponification.
• The fats are split from glycerol by the base,
  yielding alkali salts of fatty acids (crude soap)
  and glycerol

• https//anitagrant.com/images/stories/ingredients/
  SiteUpdates/SAPprocess.gif

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FunctionFour Main Types of Biomolecules

• Carbohydrates. Energy, support and
  recognition
• Proteins..Enzymes, structure,
  recognition, transport pigments,
  signals, movt
• Lipids..Cell membrane structure energy
  storage, signals cellular metabolism
  (VitK..)
• Nucleic Acids.Hereditary and protein
  information, energy, signals

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Nucleic Acids

• A nucleic acid is a polymer composed of chains of
  monomeric nucleotides.
• The most common nucleic acids are
  deoxyribonucleic acid (DNA) and ribonucleic acid
  (RNA).

• Nucleic acids are universal in living things, as
  they are found in all cells and viruses
• Named for their role in the cell nucleus

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Nucelic Acid-FunctionThese molecules carry
genetic information or form structures within
cells

• DNA is responsible for the long-term storage of
  information
• DNA is often compared to a set of blueprints
• DNA contains the instructions needed to construct
  other components of cells, such as proteins and
  RNA molecules.

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The three types of RNA

• mRNA roles is the transcribed genetic information
  from deoxyribonucleic acid (DNA)
• rRNA acts as assembly site for protein synthesis
  in complexes or protein and RNA known as
  ribosomes,
• tRNA serves as an essential carrier molecule for
  amino acids to be used in protein synthesis.

• RNA includes
• mRNA (messenger)
• tRNA (transfer)
• rRNA (ribosomal)

• All used in protein synthesis

• All encoded in the DNA

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Nucleic Acid-Structure

• The monomers from which nucleic acids are
  constructed are called nucleotides.
• A sequence of nucleotides forms a polymeric chain
  that has the ability to interact with another
  chain or other parts of the chain

• A double-stranded nucleic acid consists of two
  single-stranded nucleic acid chains held together
  by hydrogen bonds, such as in the DNA double
  helix.
• RNA is usually single-stranded, but any given
  strand may fold back upon itself to form
  secondary structure as in tRNA and rRNA.

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Nucleic Acid - Structure
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Nucleotides

• Each nucleotide consists of three components
• A carbon to carbon ringed structure with
  nitrogen
• Called a nitrogenous base
• Either a purine or a pyrimidine
• A 5-carbon sugar and
• A phosphate group.

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Nucleic acid types differ in the structure of the
sugar

• DNA contains
• 2-deoxyribose
• RNA contains ribose
• The only difference is
• the presence or absence of a a OH (hydroxyl
  group) on the second carbon

• That OH makes RNA less stable---easily degraded

• RNA is a transient molecule..

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Nitrogenous bases found in the two nucleic acid
types are different

• Adenine, cytosine, and guanine are found in both
  RNA and DNA
• Thymine only occurs in DNA and uracil only occurs
  in RNA.

• DNA A T C G

• RNA A U C G

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All nucleotides have a phosphate group

• Phosphate as found in phospholipids
• HPO4
• Found between two adjacent nucleotides in a
  polypeptide
• Sugar phosphate backbone

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Nucleotides are joined in a polymer

• The addition of a nucleotide requires a
  nucleotide tri-phosphatethe energy necessary
  to create the bond between adjacent nucleotide is
  found in the phosphates that leave

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Creating a new nucleotide istemplate
driven..DNA WILL BE COPIED

• Making a new DNA or RNA polynucleotide requires a
  DNA molecule to be copied.
• DNA is copied by matching complementary bases

• Adenine pairs with Thymine (or Uracil in RNA)

• Cytosine pairs with Guanine

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Strict Complementary Rules

• Resulting DNA molecule
• Two chains of twisted nucleotides
• (two strands-a double helix)
• Arranged anti-parallel
• Just enough room for a purine (double ring) and a
  pyrimidine (single ring).This determines the
  match

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Base Pairs are Complementary

• Two chains are held together by a weak
  interaction between the bases
• C G AT
• The bond holding the nucleotides together within
  the strand is very strong

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DNA Sequence

• Order of bases on the polynucleotide chain is
  called the DNA sequence
• This determines the message encoded by the
  molecule
• ATTCGCTTGAACT..

• Although DNA is represented by a sequence of
  letters, it is important to remember that each
  nucleotide has a sugar and a phosphate

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RNA is very similar

• Uses uracil instead of thymine
• -OH group on the second carbon of the sugar
• (its ribosenot deoxyribose)
• Single stranded

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Recall the Central Dogma of Molecular Biology

• DNA
• Transcription
• RNA
• mRNA to be exact
• Translation
• Protein

• TACCGTCTCGAA
• AUGGCAGAGCUU
• mRNA to be exact
• Amino Acids.

• How is RNA Translated?

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Genetic Code 3 Nucleotides

• AUGGCAGAGCUU
• AUG GCA GAG CUU
• 1st 2nd 3rd 4th amino acid amino
  acid amino acid aacid
• Met Ala Glu Leu

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Nucleotides are used for energy and signaling
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Detecting DNA/RNA

• Electrophoresis with dyes that bind DNA
• Best is Ethidium Bromide
• Sybersafe with comparable sensitivity

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