The Structure and Function of Macromolecules

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The Structure and Function of Macromolecules

• Chapter 5

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Monomers, Polymers, and Macromolecules

• Monomers repeating units that serve as building
  blocks for polymers
• Polymers long molecule consisting of many
  similar or identical building blocks linked by
  COVALENT bonds
• Macromolecules LARGE groups of polymers
  covalently bonded 4 classes of organic
  macromolecules to be studied
• 1. Carbohydrates 3. Proteins
• 2. Lipids 4. Nucleic Acids

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Building Breaking Polymershttp//bcs.whfreeman
.com/thelifewire/content/chp03/0302002.html

• How do monomers link up to form polymers?
• Condensation reaction (specifically, dehydration
  synthesis)
• two molecules covalently bond and lose a water
  molecule in the process
• THIS TAKES ENERGY TO DO!
• How do polymers break back into monomers?
• Hydrolysis
• polymers are disassembled to monomers by adding a
  water molecule back
• Ex digestion of food

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The Synthesis and Breakdown of Polymers
As each monomer is added, a water molecule is
removed DEHYDRATION REACTION.
This is the reverse of dehydration is
HYDROLYSISit breaks bonds between monomers by
adding water molecules.
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Organic Compounds and Building Blocks

• Carbohydrates made up of linked monosaccharides
• Lipids -- CATEGORY DOES NOT INCLUDE POLYMERS (the
  grouping is based on insolubility)
• Triglycerides (glycerol and 3 fatty acids)
• Phospholipids
• Steroids
• Proteins made up of amino acids
• Nucleic Acids made up nucleotides

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CARBOHYDRATES

• Fuel Building Material
• http//bcs.whfreeman.com/thelifewire/content/chp03
  /0302002.html

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Carbohydrates Fuel and Building Material

• Carbs include sugars their polymers
• Carbs exist as three types
• 1. monosaccharides
• 2. disaccharides
• 3. polysaccharides (macromolecule stage)
• Made up of C, H, and O in a 121 ratio (CnH2nOn)
• Has carbonyl group (CO) and multiple hydroxyl
  groups (-OH)
• Size of carbon skeleton determines category

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The Structure and Classification of Some
Monosaccharides
REMEMBER location of carbonyl determines if is
an aldose (aldehyde sugar) or a ketose (ketone
sugar). See figure 5.3 in text.
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Monosaccharides

• Are major sources of energy for cells!
• Ex. Glucose cellular respiration
• Are simple enough to serve as raw materials for
  synthesis of other small organic molecules such
  as amino and fatty acids.
• Most common glucose, fructose, galactose

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Glucose, Fructose, Galactose

• Glucose
• made during photosynthesis
• main source of energy for plants and animals
• Fructose
• found naturally in fruits
• is the sweetest of monosaccarides
• Galactose
• found in milk
• is usually in association with glucose or
  fructose
• All three have SAME MOLECULAR FORMULA but differ
  structurally so they are ISOMERS!

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Disaccharides

• Consists of two monosaccharides joined by a
  GLYCOSIDIC LINKAGE a covalent bond resulting
  from dehydration synthesis.
• Examples
• Maltose 2 glucoses joined (C12H22O11)
• Sucrose glucose and fructose joined (C12H22O11)
• Lactose glucose and galactose joined (C12H22O11)

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Examples of Disaccharide Synthesis
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Polysaccharides

• These are the polymers of sugars the true
  macromolecules of the carbohydrates.
• Serve as storage material that is hydrolyzed as
  needed in the body or as structural units that
  support bodies of organisms.

These are polymers with a few hundred to a few
thousand monosaccharides joined by glycosidic
linkages.
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Storage Polysaccharides Starch and Glycogen

• STARCH AND GLYCOGEN are storage polysaccharides.
• Starch storage for plants
• Glycogen storage for animals

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Starch

• Starch is the storage polysaccharide of PLANTS
• made up of glucose monomers in alpha
  configuration (see fig. 5.7 pg. 67)
• Has a helical shape
• can be unbranched (amylose) or branched
  (amylopectin)
• Stored as granules in plants in the PLASTIDS
• these granules are stockpiles of glucose for
  later use carb BANK)
• You can find starch in potatoes and grains

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Glycogen

• Glycogen is the storage polysaccharide of ANIMALS
• extensively branched group of glucose units
• Stored in liver and muscle cells
• Glycogen bank in humans is depleted within 24
  hours and needs replenished by consuming food.

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Structural Polysaccharides

• Cellulose and Chitin are structural
  polysaccharides
• Cellulose found in cell wall of PLANTS
• Chitin found in cell wall of FUNGI

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Cellulose

• Major component of plant cell walls
• most abundant organic compound on Earth
• Cellulose is a polymer of glucose, but all
  glucose molecules are in the beta configuration
• thus, cellulose is always straight, and this
  provides for strength (Ex. Lumber)

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Arrangement of Cellulose in Plant Cell Walls
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Cellulose and the Diet

• Few organisms possess the enzymes to digest
  cellulose
• Cellulose passes through the digestive tract and
  is eliminated in feces
• BUT, the fibrils of cellulose abrade the wall of
  the digestive tract and stimulate secretion of
  mucus which is necessary for smooth food passage
  so though cellulose is not nutritious, it is
  necessary
• Organisms that can digest cows (with help of
  bacteria), termites (with help of microbes), some
  fungi

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Chitin

• Another structural polysaccharide
• used by arthropods to build their exoskeletons
• Pure chitin is leathery, but when encrusted with
  calcium carbonate it hardens into shell form
• Also used by fungi in their cell walls (instead
  of cellulose)
• Similar to cellulose, but the glucose monomer has
  a nitrogen containing appendage

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Chitin, a structural polysaccharide exoskeleton
and surgical thread
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LIPIDS

• Energy Storage

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Lipidshttp//bcs.whfreeman.com/thelifewire/conten
t/chp03/0302002.html

• Does not include polymers only grouped together
  based on trait of little or no affinity for
  water
• Hydrophobic (water fearing)
• Hydrophobic nature is based on molecular
  structure consist mostly of hydrocarbons!
• REMEMBER hydrocarbons are insoluble in water
  b/c of their non-polar CH bonds!

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Lipids Highly Varied Group

• Smaller than true polymeric macromolecules
• Insoluble in water, soluble in organic solvents
• Serve as energy storage molecules
• Can act as chemical messengers within and between
  cells
• Include waxes and certain pigments
• Focus will be on fats, phospholipids, and steroids

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Fats -- Triglycerides

• Made of two kinds of smaller molecules glycerol
  and fatty acids (one glycerol to three fatty
  acids)
• Dehydration synthesis hooks these up 3 waters
  produced for every one triglyceride
• ESTER linkages bond glycerol to the fatty acid
  tails bond is between a hydroxyl group and a
  carboxyl group
• Glycerol is an alcohol with three carbons, each
  one with a hydroxyl group
• Fatty acid has a long carbon skeleton
• at one end is a carboxyl group (thus the term
  fatty acid)
• the rest of the molecule is a long hydrocarbon
  chain
• The hydrocarbon chain is not susceptible to
  bonding, so water H-bonds to another water and
  excludes the fats

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The Synthesis and Structure of a Fat, or
Triglycerol

• One glycerol 3 fatty acid molecules
• One H2O is removed for each fatty acid joined to
  glycerol
• Result is a fat

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Saturated vs. Unsaturated Fats

• Refers to the structure of the hydrocarbon chains
  of the fatty acids
• No double bonds between the carbon atoms of the
  chain means that the max of hydrogen atoms is
  bonded to the carbon skeleton (saturated)
• THESE ARE THE BAD ONES!!! they can cause
  atherosclerosis (plaque develop, get less flow of
  blood, hardening of arteries)!
• If one or more double bonds is present, then it
  is unsaturated
• and these tend to kink up and prevent the fats
  from packing together

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Examples of Saturated and Unsaturated Fats and
Fatty Acids 
At room temperature, the molecules of a saturated
fat are packed closely together, forming a solid.
At room temperature, the molecules of an
unsaturated fat cannot pack together closely
enough to solidify because of the kinks in their
fatty acid tails.
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Fat vs. Oil

• Most animal triglycerides are saturated
• Ex. Lard, butter
• These are solid at room temperature fat
• Plants and fish have unsaturated triglycerides,
  so they are liquid at room temp oil
• Ex. Vegetable oil, sunflower oil, cod liver oil

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Saturated and Unsaturated Fats and Fatty Acids
Butter and Oil
UNSATURATED
SATURATED
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Are lipids Bad?

• NO - Major function is energy storage
• Ex. Gram of fat stores more than TWICE the energy
  of a gram of polysaccharide
• Since plants are immobile, bulky storage of
  starch is okay animals needs mobility, so
  compact reservoir of fuel (fat or adipose tissue)
  is better
• Adipose tissue provides cushioning for organs and
  insulation for body

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Phospholipids

• Have only two fatty acid tails!
• Third hydroxyl group of glycerol is joined to a
  phosphate group (negatively charged)
• Are ambivalent to water tails are hydrophobic,
  heads are hydrophilic.
• When added to water, phospholipids self-assemble
  into aggregates that shield their hydrophobic
  portions from water
• Ex. micelles phospholipid droplet with the
  phosphate head on the outside (figure 5.13)
• At cell surface, get a double layer arrangement
  phospholipid bilayer

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The structure of a phospholipid
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Two structures formed by Self-assembly of
Phospholipids in Aqueous Environments
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Steroids

• Characterized by carbon skeleton consisting of
  four fused rings (see figure 5.14)
• Differences depend on the functional groups
  attached to the ring ensemble
• Cholesterol found in cell membranes of animals,
  is a precursor from which other steroids may be
  synthesized
• but if is found in high levels in the blood,
  contributes to atherosclerosis
• Many hormones are steroids
• Ex sex hormones

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Cholesterol A Steroid    

• Cholesterol is the molecule from which other
  steroids, including sex hormones, are
  synthesized.
• Steroids vary in the functional groups attached
  to their four interconnected rings (shown in
  gold)

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NUCLEIC ACIDS

• Polymers of Information

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NUCLEIC ACIDShttp//bcs.whfreeman.com/thelifewire
/content/chp03/0302002.html
POLYMERS OF INFORMATION BUILDING BLOCKS OF DNA
RNA
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What Determines the Primary Structure of a
Protein?

• Gene unit of inheritance that determines the
  sequence of amino acids
• made of DNA (polymer of nucleic acids)
• Building blocks of nucleic acids are nucleotides
  
• phosphate group, pentose sugar, nitrogenous base
  (A,T,C,G,U)

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Two Categories of Nitrogenous Bases

• Pyrimidines and Purines
• Pyrimidines smaller, have a six-membered ring of
  carbon and nitrogen atoms (C , U, T)
• Purines larger, have a six- and a five-membered
  ring fused together (A, G)

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NUCLEIC ACIDS consist of phosphate group,
pentose sugar, nitrogenous base
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Nucleic Acids

• Exist as 2 types DNA and RNA
• DNA -- double stranded (entire code)
• sugar is deoxyribose
• never leaves nucleus
• bases are A,T,C,G
• involved in replication and protein
  synthesis
• RNA -- single stranded (partial code)
• sugar is ribose
• mobile nucleus and cytoplasm
• bases are A,U,C,G
• involved in Protein Synthesis

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Summary of Flow of Genetic Info

• DNA ? RNA ? protein
• transcription
  translation
• Transcription in nucleus of cell opens up DNA
  double helix, copies section needed for protein
  manufacture, this makes messenger RNA (mRNA)
• Translation -- mRNA travels out of nucleus to
  cytoplasm to a ribosome (site of protein
  manufacture) ribosomal RNA (rRNA) anchors the
  transcript in the ribosome, transfer RNA (tRNA)
  brings in correct amino acid by reading 3 amino
  acids at a time (codon)

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DNA?RNA?Protein A Diagrammatic Overview of
Information Flow in a Cell
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PROTEINS

• Structural Storage Transport Catalysts

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Proteinshttp//bcs.whfreeman.com/thelifewire/cont
ent/chp03/0302002.html

• Account for over 50 of dry weight of cells
• Used for structural support
• (see page 72) storage
• transport
• signaling
• movement
• defense
• metabolism regulation (enzymes)
• Are the most structurally sophisticated molecules
  known
• Are polymers constructed from 20 different amino
  acids

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Hierarchy of Structure

• Amino acids building blocks of proteins
• 20 different amino acids in nature
• Polypeptides polymers of amino acids
• Protein one or more polypeptides folded and
  coiled into specific conformations

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• All differ in the R-group (also called side
  chain)
• The physical and chemical properties of the
  R-group determine the characteristics of the
  amino acid.
• Amino acids possess both a carboxyl and amino
  group.

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How Amino Acids Join

• Carboxyl group of one is adjacent to amino group
  of another, dehydration synthesis occurs, forms a
  covalent bond
• PEPTIDE BOND
• When repeated over and over, get a polypeptide
• On one end is an N-terminus (amino end)
• On other is a C-terminus (carboxyl end)

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Making a Polypeptide Chain
Note dehydration synthesis. Note carboxyl
group of one end attaches to amino group of
another. Note peptide bond is formed. Note
repeating this process builds a polypeptide.
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Proteins Function Depends on Its Conformation

• Functional proteins consist of one or more
  polypeptides twisted, folded, and coiled into a
  unique shape
• Amino acid sequence determines shape
• 2 big categories 1. Globular
• 2. Fibrous
• Function of a protein depends on its ability to
  recognize and bind to some other molecule.
  CONFORMATION IS KEY!

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Lysozyme
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Four Levels of Protein Structure

• Primary Structure unique sequence of amino
  acids (long chain)
• Secondary Structure segments of polypeptide
  chain that repeatedly coil or fold in patterns
  that contribute to overall configuration
• are the result of hydrogen bonds at regular
  intervals along the polypeptide backbone
• Tertiary Structure superimposed on secondary
  structure irregular contortions from
  interactions between side chains
• Quaternary Structure the overall protein
  structure that results from the aggregation of
  the polypeptide subunits

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The Primary Structure of a Protein
This is the unique amino acid sequencenotice
carboxyl end and amino end! These are held
together by PEPTIDE bonds!!!
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The Secondary Structure of a ProteinAlpha Helix
Beta Pleated Sheet
BOTH PATTERNS HERE DEPEND ON HYDROGEN BONDING
BETWEEN CO and N-H groups along the polypeptide
backbone. Alpha Helix delicate coil held
together by H-bonding between every fourth amino
acid Beta pleated sheet two or more regions of
the polypeptide chain lie parallel to one
another. H-bonds form here, and keep the
structure together. NOTE only atoms of
backbone are involved, not the amino acid side
chains!
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Tertiary Structure of a Protein

• Tertiary structure superimposed on secondary
  structure irregular contortions from
  interactions between side chains (R-groups) of
  amino acids
• nonpolar side chains end up in clusters at the
  core of a protein caused by the action of water
  molecules which exclude nonpolar substances
• hydrophobic interaction
• van der Waals interactions, H-bonds, and ionic
  bonds all add together to stabilize tertiary
  structure
• may also have disulfide bridges form when amino
  acids with 2 sulfhydryl groups are brought
  together these bonds are much stronger than the
  weaker interactions mentioned above

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Examples of Interactions Contributing to the
Tertiary Structure of a Protein
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Quaternary Structure

• Quaternary Structure the overall protein
  structure that results from the aggregation of
  the polypeptide subunits
• Ex. collagen structural
• Ex. hemoglobin globular

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The Quaternary Structure of Proteins
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Review The Four Levels of Protein
Structurehttps//mywebspace.wisc.edu/jonovic/web/
proteins.htmlSee FIGURE 5.24 IN TEXT!
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X-ray Crystallography Figure 5.27
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What determines Protein configuration?

• Polypeptide chain of given amino acid sequence
  can spontaneously arrange into 3-D shape
• Configuration also depends on physical and
  chemical conditions of proteins environment
• if pH, salt , temp, etc. are altered, protein
  may unravel and lose native conformation
• DENATURATION

• Denatured proteins are biologically inactive!
• Anything that disrupts protein bonding can
  denature a protein!

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Denaturation and Renaturation of a Protein
Denatured proteins can often renature when
environmental conditions improve!
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Protein-Folding Problem

• HOW proteins fold is not always clear may be
  several intermediate states on the way to stable
  conformation, but there are a few ways to track,
  though
• chaperonins protein molecules that assist the
  proper folding of other proteins.
• computer simulations Blue Gene, a
  supercomputer able to generate the 3-D structure
  of any protein starting from its aa sequence
  (medical uses)

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A Chaperonin in Action