Transcript 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 2. Lipids 3. Proteins 4. Nucleic Acids
Building & Breaking Polymers:
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• How do monomers link up to form polymers?
– Condensation reaction synthesis ): (specifically, dehydration • 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 monosaccharides – made up of linked • 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
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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 1:2:1 ratio (C n H 2n O n ) • 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 (C 12 H 22 O 11 ) – Sucrose – Lactose – glucose and fructose joined (C 12 H 22 O 11 ) – glucose and galactose joined (C 12 H 22 O 11 )
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
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• 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
between cells within and • 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 H bonds to another water and excludes the fats
The Synthesis and Structure of a Fat, or Triglycerol
• One glycerol & 3 fatty acid molecules • One H 2 O 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 ( hardening of arteries)!
saturated) • THESE ARE THE BAD ONES!!! – they can cause atherosclerosis (plaque develop, get less flow of blood, – 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
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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 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)
NUCLEIC ACIDS consist of: phosphate group, pentose sugar, nitrogenous base
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
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)
DNA →RNA→Protein: A Diagrammatic Overview of Information Flow in a Cell
PROTEINS
Structural | Storage | Transport | Catalysts
Proteins
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• 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:
acids (long chain) unique sequence of amino
2. Secondary Structure:
• the polypeptide backbone 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
3. Tertiary Structure:
superimposed on secondary structure; irregular contortions from interactions between side chains
4. Quaternary Structure:
structure that results from the aggregation of the polypeptide subunits the overall protein
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
more regions of the – two or 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
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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)