The Structure and Function of Macromolecules

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Chapter 5

• The Structure and Function of Macromolecules

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Concept 5.1 Most macromolecules are polymers,
built from monomers

• A polymer is a long molecule consisting of many
  similar building blocks called monomers
• Three of the four classes of lifes organic
  molecules are polymers
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids

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Macromolecules

• Smaller organic molecules join together to form
  larger molecules
• macromolecules
• 4 major classes of macromolecules
• carbohydrates
• lipids
• proteins
• nucleic acids

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Polymers

• Long molecules built by linking repeating
  building blocks in a chain
• monomers
• building blocks
• repeated small units
• covalent bonds

Dehydration synthesis
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How to build a polymer
You gotta be open tobonding!

• Synthesis
• joins monomers by taking H2O out
• one monomer donates OH
• other monomer donates H
• together these form H2O
• requires energy enzymes

Dehydration synthesis
Condensation reaction
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How to break down a polymer

• Digestion
• use H2O to breakdown polymers
• reverse of dehydration synthesis
• cleave off one monomer at a time
• H2O is split into H and OH
• H OH attach to ends
• requires enzymes
• releases energy

Breaking upis hard to do!
Hydrolysis
Digestion
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Carbohydrates
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Carbohydrates

• Carbohydrates are composed of C, H, O carbo -
  hydr - ate
• CH2O
• (CH2O)x C6H12O6
• Function
• energy u energy storage
• raw materials u structural materials
• Monomer sugars
• ex sugars, starches, cellulose

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Concept 5.2 Carbohydrates serve as fuel and
building material

• Carbohydrates include sugars and the polymers of
  sugars
• The simplest carbohydrates are monosaccharides,
  or single sugars
• Carbohydrate macromolecules are polysaccharides,
  polymers composed of many sugar building blocks

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Sugars

• Most names for sugars end in -ose
• Classified by number of carbons
• 6C hexose (glucose)
• 5C pentose (ribose)
• 3C triose (glyceraldehyde)

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5
3
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Functional groups determine function
carbonyl
aldehyde
carbonyl
ketone
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Sugar structure
5C 6C sugars form rings in solution
Where do you find solutions? In cells!
Carbons are numbered
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Numbered carbons
C
6'
C
O
5'
C
C
1'
4'
energy stored in C-C bonds
C
C
2'
3'
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Simple complex sugars

• Monosaccharides
• simple 1 monomer sugars
• glucose
• Disaccharides
• 2 monomers
• sucrose
• Polysaccharides
• large polymers
• starch

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Building sugars

• Dehydration synthesis

monosaccharides
disaccharide
glucose
glucose
maltose
glycosidic linkage
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Building sugars

• Synthesis

monosaccharides
disaccharide
fructose
glucose
sucrose (table sugar)
Lets go to the videotape!
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Polysaccharides

• Polymers of sugars
• costs little energy to build
• easily reversible release energy
• Function
• energy storage
• starch (plants)
• glycogen (animals)
• structure building materials
• cellulose (plants)
• chitin (arthropods fungi)

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Linear vs. branched polysaccharides
starch (plant)
What doesbranching do?
energystorage
glycogen (animal)
Lets go to the videotape!
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Polysaccharide diversity

• Molecular structure determines function

in starch
in cellulose

• isomers of glucose
• structure determines function

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Digesting starch vs. cellulose
starcheasy todigest
cellulosehard todigest
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Cellulose

• Most abundant organic compound on Earth
• herbivores can digest cellulose
• most carnivores cannot digest cellulose
• thats why they eat meat to get their energy
  nutrients
• cellulose roughage

BIG DEAL!Who can liveon this stuff?!
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• Cow
• can digest cellulose well no need to eat other
  sugars
• Gorilla
• cant digest cellulose well must add another
  sugar source, like fruit to diet

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Helpful bacteria

• How can cows digest cellulose?
• bacteria live in their gut help digest
  cellulose-rich (grass) meals

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Lipids Fats Oils
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Concept 5.3 Lipids are a diverse group of
hydrophobic molecules

• Lipids are the one class of large biological
  molecules that do not form polymers
• The unifying feature of lipids is having little
  or no affinity for water
• Lipids are hydrophobic because?they consist
  mostly of hydrocarbons, which form nonpolar
  covalent bonds
• The most biologically important lipids are fats,
  phospholipids, and steroids

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• Lipids

energy storage
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Lipids

• Lipids are composed of C, H, O
• long hydrocarbon chain
• Diverse group
• fats
• phospholipids
• steroids
• Do not form polymers
• big molecules made of smaller subunits
• not a continuing chain

fat
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Fat subunits

• Structure
• glycerol (3C alcohol) fatty acid

• fatty acid long HC tail with COOH group at
  head

dehydration synthesis
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Building Fats

• Triacylglycerol
• 3 fatty acids linked to glycerol
• ester linkage between OH COOH

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Dehydration synthesis
dehydration synthesis
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Fats store energy
Why do humanslike fatty foods?

• Long HC chain
• polar or non-polar?
• hydrophilic or hydrophobic?
• Function
• energy storage
• very rich
• 2x carbohydrates
• cushion organs
• insulates body
• think whale blubber!

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Saturated fats

• All C bonded to H
• No CC double bonds
• long, straight chain
• most animal fats
• solid at room temp.
• contributes to cardiovascular disease
  (atherosclerosis) plaque deposits

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Stearic acid
Saturated fat and fatty acid.
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Unsaturated fats

• CC double bonds in the fatty acids
• plant fish fats
• vegetable oils
• liquid at room temperature
• the kinks made by doublebonded C prevent the
  molecules from packing tightly together

mono-unsaturated? poly-unsaturated?
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Oleic acid
cis double bond causes bending
Unsaturated fat and fatty acid.
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Saturated vs. unsaturated
saturated
unsaturated
?
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Phospholipids

• Structure
• glycerol 2 fatty acids PO4
• PO4 negatively charged

Its just like apenguin A head at one end a
tail at the other!
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Phospholipids

• Hydrophobic or hydrophilic?
• fatty acid tails hydrophobic
• PO4 hydrophilic head
• dual personality

It likes water also pushes it away!
interaction with H2O is complex very important!
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Phospholipids in water

• Hydrophilic heads attracted to H2O
• Hydrophobic tails hide from H2O
• can self-assemble into bubbles
• bubble micelle
• can also form bilayer
• early evolutionary stage of cell?

bilayer
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Why is this important?

• Phospholipids create a barrier in water
• define outside vs. inside
• cell membranes

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Phospholipids cells

• Phospholipids of cell membrane
• double layer bilayer
• hydrophilic heads on outside
• in contact with aqueous solution outside of cell
  and inside of cell
• hydrophobic tails on inside
• form core
• forms barrier between cell external environment

Tell themabout soap!
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Steroids

• ex cholesterol, sex hormones
• 4 fused C rings
• different steroids created by attaching different
  functional groups to rings

cholesterol
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Cholesterol

• Important cell component
• animal cell membranes
• precursor of all other steroids
• including vertebrate sex hormones
• high levels in blood may contribute to
  cardiovascular disease

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Cholesterol
Important component of cell membrane

• helps keep cell membranes fluid flexible

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From Cholesterol ? Sex Hormones

• What a big difference a few atoms can make!

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Proteins
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Concept 5.4 Proteins have many structures,
resulting in a wide range of functions

• Proteins account for more than 50 of the dry
  mass of most cells
• Protein functions include structural support,
  storage, transport, cellular communications,
  movement, and defense against foreign substances

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• Proteins

Multipurposemolecules
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Proteins

• Most structurally functionally diverse group of
  biomolecules
• Function
• involved in almost everything
• enzymes (pepsin, polymerase, etc.)
• structure (keratin, collagen)
• carriers transport (membrane channels)
• receptors binding (defense antibodies)
• contraction (actin myosin)
• signaling (hormones insulin)
• storage (bean seed proteins)

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Proteins

• Structure
• monomer amino acids
• 20 different amino acids
• polymer polypeptide
• protein can be one or more polypeptide chains
  folded bonded together
• large complex molecules
• complex 3-D shape

hemoglobin
growthhormones
Rubisco
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Amino acids

• Structure
• central carbon
• amino group
• carboxyl group (acid)
• R group (side chain)
• variable group
• confers unique chemical properties of the amino
  acid

R
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Nonpolar amino acids
Why are these nonpolar hydrophobic?
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Polar amino acids
Why are these polar hydrophillic?
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Ionizing in cellular waters
H donors
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Ionizing in cellular waters
H acceptors
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Sulfur containing amino acids

• Form disulfide bridges
• cross links betweens sulfurs in amino acids

H-S S-H
You wonderedwhy permssmelled like rotten eggs?
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Building proteins

• Peptide bonds
• linking NH2 of one amino acid to COOH of another
• CN bond

dehydration synthesis
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Building proteins

• Polypeptide chains
• N-terminus NH2 end
• C-terminus COOH end
• repeated sequence (N-C-C) is the polypeptide
  backbone
• can only grow in one direction

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Protein structure function

• Function depends on structure
• 3-D structure
• twisted, folded, coiled into unique shape

pepsin
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4 Levels of Protein Structure

• The primary structure of a protein is its unique
  sequence of amino acids
• Secondary structure, found in most proteins,
  consists of coils and folds in the polypeptide
  chain
• Tertiary structure is determined by interactions
  among various side chains (R groups)
• Quaternary structure results when a protein
  consists of multiple polypeptide chains

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Primary (1) structure

• Order of amino acids in chain
• amino acid sequence determined by gene (DNA)
• slight change in amino acid sequence can affect
  proteins structure its function
• even just one amino acid change can make all the
  difference!

lysozyme enzyme in tears mucus that kills
bacteria
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Sickle cell anemia
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Secondary (2) structure

• Local folding
• folding along short sections of polypeptide
• interaction between adjacent amino acids
• H bonds between R groups
• ?-helix
• ?-pleated sheet

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Secondary (2) structure
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Tertiary (3) structure

• Whole molecule folding
• determined by interactions between R groups
• hydrophobic interactions
• effect of water in cell
• anchored by disulfide bridges(H ionic bonds)

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Quaternary (4) structure

• More than one polypeptide chain joined together
• only then is it a functional protein
• hydrophobic interactions

collagen skin tendons
hemoglobin
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Protein structure (review)
R groups hydrophobic interactions, disulfide
bridges
3
1
2
4
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Denature a protein

• Unfolding a protein
• disrupt 3 structure
• pH ? salt ? temperature
• unravels or denatures protein
• disrupts H bonds, ionic bonds disulfide
  bridges
• destroys functionality
• Some proteins can return to their functional
  shape after denaturation, many cannot

In Biology,size doesnt matter, SHAPE matters!
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What Determines Protein Conformation?

• In addition to primary structure, physical and
  chemical conditions can affect conformation
• Alternations in pH, salt concentration,
  temperature, or other environmental factors can
  cause a protein to unravel
• This loss of a proteins native conformation is
  called denaturation
• A denatured protein is biologically inactive

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Chaperonin proteins

• Guide protein folding
• provide shelter for folding polypeptides
• keep the new protein segregated from cytoplasmic
  influences

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Protein models

• Protein structure visualized by
• X-ray crystallography
• extrapolating from amino acid sequence
• computer modelling

lysozyme
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Enzymes

• Enzymes are a type of protein that acts as a
  catalyst, speeding up chemical reactions
• Enzymes can perform their functions repeatedly,
  functioning as workhorses that carry out the
  processes of life

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HELIXHELIX
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Concept 5.5 Nucleic acids store and transmit
hereditary information

• The amino acid sequence of a polypeptide is
  programmed by a unit of inheritance called a gene
• Genes are made of DNA, a nucleic acid

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• Nucleic Acids

Informationstorage
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Nucleic Acids

• Function
• store transmit hereditary information
• Examples
• RNA (ribonucleic acid)
• DNA (deoxyribonucleic acid)
• Structure
• monomers nucleotides

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Nucleotides

• 3 parts
• nitrogen base (C-N ring)
• pentose sugar (5C)
• ribose in RNA
• deoxyribose in DNA
• phosphate (PO4) group

Are nucleic acidscharged molecules?
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RNA DNA

• RNA
• single nucleotide chain
• DNA
• double nucleotide chain
• N bases bond in pairs across chains
• spiraled in a double helix
• double helix 1st proposed as structure of DNA in
  1953 by James Watson Francis Crick (just
  celebrated 50th anniversary in 2003!)

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Types of nucleotides

• 2 types of nucleotides
• different nitrogen bases
• purines
• double ring N base
• adenine (A)
• guanine (G)
• pyrimidines
• single ring N base
• cytosine (C)
• thymine (T)
• uracil (U)

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Building the polymer
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Nucleic polymer

• Backbone
• sugar to PO4 bond
• phosphodiester bond
• new base added to sugar of previous base
• polymer grows in one direction
• N bases hang off the sugar-phosphate backbone

Dangling bases?Why is this important?
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Pairing of nucleotides

• Nucleotides bond between DNA strands
• H bonds
• purine pyrimidine
• A T
• 2 H bonds
• G C
• 3 H bonds

Matching bases?Why is this important?
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Information polymer

• Function
• series of bases encodes information
• like the letters of a book
• stored information is passed from parent to
  offspring
• need to copy accurately
• stored information genes
• genetic information

Passing on information?Why is this important?
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DNA molecule

• Double helix
• H bonds between bases join the 2 strands
• A T
• C G

H bonds?Why is this important?
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Copying DNA

• Replication
• 2 strands of DNA helix are complementary
• have one, can build other
• have one, can rebuild the whole

Matching halves?Why is this a good system?
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When does a cell copy DNA?

• When in the life of a cell does DNA have to be
  copied?
• cell reproduction
• mitosis
• gamete production
• meiosis

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DNA replication

• It has not escaped our notice that the specific
  pairing we have postulated immediately suggests a
  possible copying mechanism for the genetic
  material.
• James Watson
• Francis Crick
• 1953

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Watson and Crick and others
1953 1962
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Maurice Wilkins and
1953 1962
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Rosalind Franklin (1920-1958)
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Interesting note

• Ratio of A-TG-C affects stability of DNA
  molecule
• 2 H bonds vs. 3 H bonds
• biotech procedures
• more G-C need higher T to separate strands
• high T organisms
• many G-C
• parasites
• many A-T (dont know why)

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Another interesting note

• ATPAdenosine triphosphate

• modified nucleotide
• adenine (AMP) Pi Pi