Download Nerve activates contraction

The Structure and Function of
Macromolecules
Chapter 5
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
Building & Breaking Polymers:
http://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
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
HYDROLYSIS…it
breaks bonds between
monomers by adding
water molecules.
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
CARBOHYDRATES
Fuel & Building Material
http://bcs.whfreeman.com/thelifewire/content/chp03/0302002.html
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 1:2:1 ratio (CnH2nOn)
• Has carbonyl group (C=O) and multiple hydroxyl
groups (-OH)
• Size of carbon skeleton determines category
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.
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
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!
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)
Examples of Disaccharide Synthesis
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.
Storage Polysaccharides –
Starch and Glycogen
• STARCH AND GLYCOGEN are
storage
polysaccharides.
– Starch: storage for plants
– Glycogen: storage for
animals
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
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.
Structural Polysaccharides
• Cellulose and Chitin are structural
polysaccharides:
– Cellulose: found in cell wall of PLANTS
– Chitin: found in cell wall of FUNGI
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)
Arrangement of Cellulose in Plant Cell Walls
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
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
Chitin, a structural polysaccharide: exoskeleton and
surgical thread
LIPIDS
Energy Storage
Lipids
http://bcs.whfreeman.com/thelifewire/content/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 C—H bonds!
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
“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 Hbonds to another water and excludes the fats
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
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
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.
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
Saturated and Unsaturated Fats and Fatty Acids: Butter and Oil
UNSATURATED
SATURATED
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
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
The structure of a phospholipid
Two structures formed by Self-assembly of Phospholipids
in Aqueous Environments
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
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)…
NUCLEIC ACIDS
Polymers of Information
NUCLEIC ACIDS
http://bcs.whfreeman.com/thelifewire/content/chp03/0302002.html
POLYMERS OF INFORMATION – BUILDING BLOCKS OF DNA & RNA
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)
Two Categories of Nitrogenous
Bases
• Pyrimidines and
Purines:
– Pyrimidines:
smaller, have a sixmembered ring of
carbon and nitrogen
atoms (C , U, T)
– Purines: larger, have
a six- and a fivemembered ring fused
together (A, G)
NUCLEIC ACIDS consist of: phosphate group, pentose sugar, nitrogenous base
Nucleic Acids
• Exist as 2 types : DNA and RNA
*DNA --
synthesis
*RNA --
*double stranded (entire code)
*sugar is deoxyribose
*never leaves nucleus
*bases are A,T,C,G
*involved in replication and protein
*single stranded (partial code)
*sugar is ribose
*mobile – nucleus and cytoplasm
*bases are A,U,C,G
*involved in Protein Synthesis
Summary of Flow of Genetic Info
• DNA

RNA
transcription

protein
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)
DNA→RNA→Protein: A Diagrammatic Overview of Information Flow in a Cell
PROTEINS
Structural | Storage | Transport | Catalysts
Proteins
http://bcs.whfreeman.com/thelifewire/content/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
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
• 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.
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)
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.
Protein’s 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!
Lysozyme
Four Levels of Protein Structure
1. Primary Structure: unique sequence of amino
acids (long chain)
2. 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
3. Tertiary Structure: superimposed on
secondary structure; irregular contortions from
interactions between side chains
4. Quaternary Structure: the overall protein
structure that results from the aggregation of
the polypeptide subunits
The Primary Structure of a Protein
This is the unique amino acid
sequence…notice carboxyl
end and amino end!
These are held together by
PEPTIDE bonds!!!
The Secondary Structure of a Protein
Alpha Helix & Beta Pleated Sheet
BOTH PATTERNS HERE
DEPEND ON HYDROGEN
BONDING BETWEEN C=O
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!
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
Examples of Interactions Contributing
to the Tertiary Structure of a Protein
Quaternary Structure
• Quaternary Structure: the overall protein
structure that results from the aggregation
of the polypeptide subunits
– Ex. collagen – structural
– Ex. hemoglobin – globular
The Quaternary Structure of Proteins
Review: The Four Levels of Protein Structure
https://mywebspace.wisc.edu/jonovic/web/proteins.html
See FIGURE 5.24 IN TEXT!
X-ray Crystallography – Figure 5.27
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 protein’s 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!
Denaturation and Renaturation of a Protein
Denatured proteins can often renature when environmental
conditions improve!
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)
A Chaperonin in Action