Chemistry - Carbon Compounds, Macromolecules - The Structure of Molecules Determines the Function
Latin
• Amphi – dual;
• Hydro - water
• Saccar – sweet; saccharide
amphipathic
• Iso - equal
• Sulf – sulfur; sulf-hydryl
• Carb – carbon;
• Lip – fat; lipids
bond
carbohydrate
• Macro – large;
• Poly – many; polypeptide
• De – remove; dehydration
macromolecules
• Oligo – few;
• Di – two - disaccharide
• Micro – small; microscope
oligosaccharides
• Glyco – sweet;
• Mono – one;
• Tri – three; triphosphate
glycoprotein
monosaccharide
Terms
• Amino acid
• Chitin
• Cholesterol
• Dehydration synthesis
• Disaccharide
• DNA
• Functional group
• Glycogen
• Hydrolysis
• Hydrophilic
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Hydrophobic
Isomer
Lipid
Monomer
Monosaccharide
Oligosaccharide
Nucleic acid
Nucleotide
Phospholipid
Peptide bond
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Polymer
Protein
RNA
Saturated fat
Starch
Steroid
Triglyceride
Unsaturated fat
College Board Objectives:
4.A.1 – The subcomponents of biological molecules and their sequence determine the properties of that molecule.
 Structure and function of polymers are derived from the way their monomers are assembled
 Nucleic acids, biological information is encoded in sequences of nucleotides.
o Nucleotide structure.
o DNA and RNA differ in structure, structural differences create different functions.
 Proteins, the specific order of amino acids in a polypeptide is primary structure; Overall shape of the protein also involves
secondary, tertiary and quarternary structure. The R group of an amino acid determines tertiary structure and can be
categorized by chemical properties (hydrophobic, hydrophilic, and ionic), and the interactions of these R groups determine
structure and function of that region of the protein.
 Lipids are mostly nonpolar; Phospholipids have both polar regions that interact with other polar molecules (water), and with
nonpolar regions; differences in saturation of fatty acids also determines the structure and function of lipids.
 Carbohydrates are composed of sugar molecules whose structures and bonding with each other by dehydration synthesis
determines the properties and functions of the molecules. Ex. cellulose, vs starch vs chitin vs glycogen
 Directionality influences structure and function of the polymer.
o Nucleic acids have ends, (the 3’ and 5’ carbons of the sugar) that determine the direction in which complementary
nucleotides are added during replication and the direction in which translation occurs (from 5’ to 3’).
o Proteins have amino (NH2) and carboxyl (COOH) ends, and are a linear sequence of amino acids connected by
peptide bonds by dehydration synthesis between amino and carboxyl groups of adjacent monomers.
o The nature of the bonding between carbohydrate subunits determines their relative orientation in the carbohydrate,
which then determines the secondary structure of the carbohydrate.
4.B.1 – Interactions between molecules affect their structure and function
 Change in the structure of a molecule may result in a change in the function of the system.
 The shape of enzymes’ active sites determines the function of the enzyme
o The substrate must fit into the enzyme’s active site.
 The interaction of cofactors and coenzymes with some enzymes causes a structural change that alters the activity rate of the
enzyme. The enzyme may only become active when all the appropriate cofactors or coenzymes are present and bind to the
appropriate sites on the enzyme.
 Other (inhibitor) molecules and the environment can enhance or inhibit enzyme activity.
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Molecules can bind reversibly or irreversibly to the active or allosteric sites.
The change in function of an enzyme can be interpreted from data regarding the concentration of product or substrate as a
function of time. These representations demonstrate the relationship between an enzyme’s activity, the disappearance of
substrate, and/or presence of a competitive inhibitor
4.C.1 – Variation in molecular units provides cells with a wider range of functions
 Variations within types of molecules provide cells and organisms with a wider range of functions.
Ex. Phospholipids, types of hemoglobin, MHC, chlorophylls, antibodies.
Notes:
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Importance of Carbon
 carbon has 4 valence electrons – bonds 4 times (single or double), which gives C a huge variety of
shapes/functions (rings, branches)
 Functional groups (groups of atoms) have chemical properties that may be part of the molecule which
provides even more variety to carbon compounds
• functional groups - OH, NH2, COOH, SH, CH3 (nonpolar)
Polymers – a long chain of monomers assembled by dehydration synthesis (polymerization)
Dehydration synthesis – process of linking small molecules to form a polymer by removing water and using enzymes
Hydrolysis – process of breaking down polymers by adding water and using enzymes
4 Polymers in biology: carbohydrates, lipids, proteins, nucleic acids
– Carbohydrate - Carbon + water - Basic formula: CH2O(n)
– Monomers – (monosaccharides) Glucose, fructose, galactose, ribose, deoxyribose
• ‘Simple sugars’; end in _____
• Glucose - C6H12O6******Function of glucose __________________
• Disaccharides: - two monosaccharides
– Maltose - glucose + glucose
– Sucrose - glucose + fructose
– Lactose - glucose + galactose
– Formula of three glucose molecules?
• Polysaccharides - Long chain of monosaccharides
– Type of monosaccharide and placement creates variation/function***
– Starch (amylose, amylopectin) = plant store glucose
– Glycogen = animals store glucose
– Cellulose = plant cell walls
– Chitin = exoskeleton of arthropods, some fungi
Carbohydrates: Function
– Energy; stored energy - ex. ______________, _______________
– Structure – __________________, __________________________
– Cell-to-cell communication, identification (glycoproteins, glycolipids)
• Antigens/antibodies
– Lipids - Insoluble in water - basic formula: C50H70O6
– Three types: Triglycerides, phospholipids, steroids
• Triglycerides - fats, oils, waxes
• Fatty acids - hydrocarbon chain (Hydrophobic)
• Saturated – ____
• Unsaturated – ___
Types of triglycerides (fats)
Saturated
• Unsaturated
– No double bonds
• Double bond(s)
– Saturated
• Unsaturated
– Solids @ (200)
• Liquids @ (200)
– Animal fats - Bacon grease, lard, butter
• Plant fats (oil) - Corn, peanut, olive oils
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• Hydrocarbon chains are high in energy but more difficult to breakdown
Phospholipids - Glycerol + 2 fatty acids + phosphate group (polar)
• Most of the cell membrane
• ‘Head’ end is polar (term?)
• ‘tail’ end is non-polar (term?)
• Amphipathic
• Function of cell membrane?
• Micelle - first prokaryotes evolved when phospholipids formed micelles in water (?)
Steroids - 4 fused carbon rings + functional group(s)
• Insoluble in _________
• Ex. Cholesterol
• Between fatty acids tails of phospholipids
• Helps to moderate the effects of extreme temperatures
• Arrangement of functional groups is critical
Proteins
Many shapes = many functions (‘first place’)
Polymers of amino acid, Linked by peptide bonds
Proteins = folded, shaped polypeptides
Amino Acids
• 2 carbon skeleton
• _____ group
• ________ group
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__ atom
• Side group (R group)
Peptide bonds – formed by ____________________________________?
• Polypeptide - ?
• ___________________________ shape – 3d shape that enables a protein to function
• Folding and twisting of the amino acids
• _______________________________ – change of shape
• Protein no longer works
• What would denature a protein___________________________________?
• Four levels of protein structure:******
• Primary - Sequence of amino acids
• Ex. Alanine, alanine, guanine, tyrosine, glycine, etc.
• Determined by genetic code
• ‘goof’ in sequence can have harmful or lethal effects
• Secondary - Folds or twists created by H-bonding in the carbon backbone; not the R group
• 2 types: both may be in a protein
• Alpha - helix
• Beta - pleated sheet
• Tertiary - Irregular contortions caused by bonding of R groups:
• Ionic, hydrogen, disulfide bridges (covalent)
• Hydrophobic interaction - nonpolar portions line up away from water
• Quaternary - Multiple polypeptides combine into one giant protein
• Hemoglobin (heme + globin)
• Polypeptides are NOT proteins
• Need to be folded into conformational shape
• Other groups may be added (lipids – lipoproteins, sugars - glycoproteins
• Denaturation - alteration of conformational shape
• Caused by:
• pH, salinity, organic solvents (alcohols, carbon tetrachloride, acetone, etc.), heat,
inorganic chemicals that dissolve bonds (HCl)
• Some change shape to function
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• Receptor(?), contractile (?), transport (?)
Nucleic Acids
• DNA, RNA
• Polymers of nucleotides
• Nucleotide:
• Simple sugar (ribose or deoxyribose)
• Nitrogenous base
• Phosphate group (PO4)
• Nitrogenous bases are complimentary
• A-T, C-G; Hydrogen bonds
• Sugar-phosphate backbone
Big Idea – Evolution life - evolved from non-living chemical reactions
– 4 steps:
• Abiotic synthesis of small organic molecules (amino acids, nitrogenous bases)
• Miller-Urey – simple amino acids could form spontaneously from raw materials and energy
found in early earth conditions
• Methane, ammonia, CO2, N2 and H2 gases, heat, lightning.
• Joining of small molecules into macromolecules
• Formation of Polymers from Monomers - RNA nucleotides and amino acids will spontaneously
polymerize when solutions of amino acids are dripped onto hot sands or clays (life may have
evolved in clayey soils?)
• The origin of self-replicating molecules that stores a code?
• Origin of Self-Replicating Molecules (RNA?)
• Formation of protocells (phospholipids – micelles)
• Formation of Protocell
• Phospholipids spontaneously form micelles in water
• Protobiont - ‘1st Life’?