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Chapter 5 Notes

Macromolecules
- 4 types of large biological molecules:
- Carbohydrates
- Lipids
- Proteins
- Nucleic acids
- Polymer: long molecule consisting of many similar building blocks linked by
covalent bonds
- Monomers: the building blocks of polymers

Synthesis and Breakdown of Polymers


- Condensation reaction: 2 molecules are covalently bonded to each other through
the loss of a water molecule
- Specifically a dehydration reaction because the molecule lost a water
molecule
- One molecule provides hydroxyl group and the other one provides a
hydrogen with the help of enzymes
- Hydrolysis: (reverse of the dehydration reaction) bonds between
monomers are broken by the addition of water molecules

Carbohydrates
- Include sugars and the polymers of sugars
- Monosaccharides: simple sugars and main nutrients for cells (cellular
respiration)
- Most common: glucose (has a carbonyl group and multiple hydroxyl
groups)
- Disaccharides: 2 monosaccharides joined by a glycosidic linkage
- Glycosidic linkage: covalent bond formed between two monosaccharides
by a dehydration reaction
- Most common: sucrose

Polysaccharides
- a carbohydrate whose molecules consist of a number of sugar molecules bonded
together.

Storage Polysaccharides
- Starch: a storage polysaccharide of plants is made entirely of glucose monomers
- Stored in plastids (ex. chloroplasts)
- Helical shaped
- Animals store a polysaccharide called glycogen in liver and muscle cells
- Glycogen stores are depleted in a day unless the animal eats

Structural Polysaccharides
- Cellulose: major component of the tough walls that enclose plant cells (polymer
of glucose)
- Straight molecule and never branched
- When glucose forms a ring, the hydroxyl group attached to the number 1 carbon
is positioned either below or above the plane of the ring
- 2 types are called alpha and beta
- Enzymes that digest starch by hydrolyzing its alpha linkages are unable to
hydrolyze the beta linkages of cellulose because of the different shapes
- Humans can’t digest cellulose and just eliminate it in their feces
- Chitin: a structural polysaccharide used by arthropods (spiders, etc.) to build
their exoskeletons
- Leathery but hardens when it is encrusted with calcium carbonate

Lipids
- Don’t have polymers; grouped together because they have little to no affinity for
water (consist mostly of hydrocarbons)

Fats
- Constructed from 2 kinds of smaller molecules: glycerol and fatty acids
- Purpose: energy storage
- Fatty acid: long carbon skeleton, usually 16 or 18 carbon atoms in length
- At one end is a carboxyl group, makes it a fatty ​acid
- Fats separate from water because water molecules hydrogen bond to one another
and exclude fats
- Triacylglycerol: 3 fatty acids join to glycerol by an ester linkage
- Ester linkage: bond between the hydroxyl group and carboxyl group
- 3 types:
- Saturated fatty acid: if there are no double bonds between carbon atoms in
the chain, then as many hydrogen atoms as possible are bonded to the
carbon skeleton
- Animal fats
- Unsaturated fatty acid: has one of more double bonds, formed by the
removal of hydrogen atoms from the carbon skeleton
- Plant and fish fats
- Trans fat: ​ ​unsaturated fatty acid molecule​ that contains a ​trans double
bond​ between ​carbon atoms​, which makes the molecule kinked.
- Correlation between diets high in trans fats and diseases like
atherosclerosis and coronary heart disease.

Phospholipids
- Phospholipids: 2 fatty acids attached to glycerol rather than 3
- Hydrocarbon tails are hydrophobic but the hydrophobic head has an affinity for
water

Steroids
- Lipids containing a carbon skeleton of 4 fused rings
- Cholesterol: common component of animal cell membranes

Proteins
- Account for more than 50% of dry mass of cells
- Most important: enzymes
- Enzymatic proteins regulate metabolism by acting as catalysts
- Catalysts: chemical agents that speed up a reaction

Polypeptides
- Polypeptides: polymers of amino acids
- Protein: 1 or more polypeptides folded and coiled into specific conformations

Amino Acid Monomers


- Amino acids: organic molecules possessing both carboxyl groups and amino
groups
- R group (AKA side chain) differs with each amino acid
- Polar side chain = hydrophilic
- Non-polar side chain = hydrophobic

Amino Acid Polymers


- Peptide bond: when 2 amino acids are positioned so the carboxyl group of one is
adjacent to the amino group of the other, an enzyme can cause them to join by
catalyzing a dehydration reaction, with the removal of a water molecule
- Repeated over and over it becomes a polypeptide
- Amino end: N-terminus; Carboxyl end: C-terminus
- Frederick Sanger: used protein-digesting enzymes to break polypeptides at
specific places rather than completely hydrolyzing the chains to amino acids
- Chromatography: cleaves the polypeptides into fragments
- Used chemical methods to determine the order of amino acids

4 Levels of Protein Structure


- Primary structure: a protein's unique sequence of amino acids
- Secondary structure: segments in the polypeptide chains of proteins the
repeatedly coil or fold in patterns that contribute to the overall conformation
- Ex. 𝛼 helix, 𝛽 pleated sheet
- Tertiary structure: the overall shape of a polypeptide resulting from interactions
between the side chain of various amino acids
- Hydrophobic interactions: water molecules exclude non-polar substances
as they form hydrogen bonds with each other and the hydrophilic parts of
the protein
- Disulfide bridges: ​a covalent bond derived from two thiol groups.
- Quaternary structure: the overall protein structure that occurs when a protein
consists of two or more polypeptide chains

Sickle Cell Disease


- Caused by substitution of valine amino acid for a normal one (glutamic acid)
- Angular cells clog tiny blood vessels, impeding blood flow

Protein Conformation
- Three dimensional shape determined and maintained by interactions responsible
for secondary and tertiary structures
- Denaturation: if the pH, salt concentration, etc. are altered, the protein may
unravel and lose its original conformation
- Happens if they transfer from an aqueous environment to an organic
solvent
- When a test tube solution has been altered by heat or chemicals it returns
to its functional shape after the denaturing agent is removed

Protein Folding Problem


- Chaperonins: protein molecules that assist in the folding of other proteins
- Keep the polypeptide separated from “bad influences: in the cytoplasm
- X-ray crystallography: determines a protein's 3-D structure

Nucleic Acids
- DNA and RNA
- DNA: provides directions for its own replication and for RNA synthesis
- RNA: controls protein synthesis (ex. messenger RNA)
- Gene: the amino acid sequence of a polypeptide is programmed by a unit of
inheritance
- Polynucleotides: nucleic acids are macromolecules that exist as polymers
- Nucleotides: the polynucleotide consists of monomers

Nucleotide Monomers
- 2 parts:
- Nitrogenous base (2 types)
- Pyrimidine: has a six-membered ring of carbon and nitrogen atoms
- Thymine, Cytosine, Uracil
- Purines: larger, with 6 membered ring fused to 5 membered ring
- Adenine, guanine
- Sugar
- Sugar is numbered so the sugar atoms have a prime (‘) to
distinguish them (second carbon sugar is 2’)
- The carbon that extends from the ring is called 5’ carbon

Nucleotide Polymers
- Adjacent nucleotides are joined by covalent bonds called phosphodiester linkages
between hydroxyl group on the 3’ of one nucleotide and the phosphate on the 5’
carbon of the next
- The linear order of bases specifies the amino acid sequence of the protein which
decides the 3-D conformation and functionality of the cell

DNA Double Helix


- 2 polynucleotides (AKA strands) that spiral around an imaginary axis
- Watson and Crick proposed the structure in 1953
- Anti-parallel: two sugar-phosphate backbone run in opposite 5’ -> 3’ directions
from each other and the nitrogenous bases are paired on the inside of the helix
- The strands are held by hydrogen bonds in the paired bases and the van
der Waals interactions between the stacked bases
- Pairing: (strands are complementary)
- A and T
- G and C