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Lecture

Summary of BIOL 112.pdf


Department
Biology
Course Code
BIOL 112
Professor
Joseph Dent

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BIOLOGY 112 (2010) - 1 C Aikins
2 - SMALL MOLECULES 2: BONDS ACIDS AND BASES
Ionic bond
Ionic bonds involve a complete transfer of one or more electrons
Ions are formed when an atom loses or gains electrons
Polar molecules tend to by hydrophilic
Nonpolar molecules are called hydrophobic
o They tend to aggregate with other nonpolar molecules in water (hydrophobic interaction)
Hydrophobic interaction
Water foreces nonpolar molecules to minimize their disruptive effects on the hydrogen-bonds in the water network
Van der Waals
Non polar molecules are also attracted to each other via relatively weak attractions van der Waals forces
(transient dipoles)
Bonds:
covalent bond (sharing electron pair)
>> hydrogen bonds (attraction of opposite charges)
> ionic bond (attraction of opposite charges)
> hydrophobic interaction (exclusion of nonpolar from water)
> van der Waals interaction (interaction do to fluctuating charges)
Molarity
A mole is the amount of a substance in grams whose weight is equal to its molecular weight (6.022142x10^23
molecules)
1 M = 1 mol/L
1 mol NaCl = 23+35.5 = 58.5 g
Acids and Bases
Acids release/donate H+ ions in solution
The carboxyl group (-COOH) is common in biological compounds. It functions as a weak acid because it
dissociates partially and reversibly
o –COOH -COO- + H+
Bases accept H+ in solution (release OH-)
The amino group (-NH2) is an important part of many biological compunds; it functions as a weak base by
partially and reversibly accepting H+
o NH2+ H+ -(NH3)+
pH is the measure of hydrogen ion concentration
o pH = -log10([H+])
o pH 7 = 1 x 10-7 M/L
Buffers
Buffers make the over all solution resistant to pH changes because they react with both added bases and acids
A solution of a weak acid and its conjugate base is a buffer
Buffers illustrate the law of mass action
Addition of reactants accelerates the reaction, while removal of products accelerates the reverse reaction
3 - BUFFERS AND LARGE MOLECULES 1: SUGARS
Functional groups – don’t need
Know carboxylic acids (carboxyl –COOH)
Amines (Amino –NH2)
Alcohols (Hydroxyl –OH)
Aldehydes (–CHO)
Keytones (Keto –CH–)

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Organic phosphates (Phosphate –PO4
2-)
Thiols (Sulfhydryl –SH)
Large molecules (macromolecules)
Proteins, nucleic acids, and carbohydrates are called macromolecules because they can form huge polymers
Macromolecules are made the same way in all living things and are present in all organisms in roughly the same
proportions
o Proteins > nucleic acids > carbohydrates> lipids
This biochemical unity allows organisms to acquire needed biochemical’s by eating other organisms
Creation/distruction of macromolecules
Know Polymerization
o Condensation –
H-monomer-OH + H-monomer-OH (enzyme) H-polymer-OH + H2O (1 per covalent
bond)
Know depolymerization
o Hydrolysis
H-polymer-OH + H2O H-monomer-OH + H-monomer-OH etc
Isomers
Isomers are molecules that have the same chemical formula but different arrangements of the atoms
Know structural isomers, and optical isomers
Sugars
Carbohydrates (sugars) act as energy storage and building blocks for other molecules (nucleic acids)
o Serve as structural components (wood)
o Attached to many membrane proteins and lipids and sometimes provided identity to cells (human blood
groups)
Three major categories
o Monosaccharides
o Disaccharides 2 monosaccharides
o Polysaccharides – 100s-1000s
General structure
General formula for a carbohydrate monomer is multiples of CH2O
o 1 carbonyl, several hydroxyl
Polymers are slightly different, as water is lost during condensation
Straight vs chain form – glucose
Exists as straight chain and ring, ring form predominate
α-glucose β-glucose exist in equilibrium
o α-glucose - 2-OH is trans H2OH
o β-glucose – 2-OH is cis H2OH
glycosidic linkages
Disaccharides
o maltose
straight chain
α-(14) link
o celloboise
ALWAYS straight
β-(14) link
o
polysaccharides

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o starch α-(14) links
amylose - unbranched
amylopectin – moderately branched (plants)
glycogen highly branched (animals)
o cellulose β-(14) link – always unbranched
4 - LARGE MOLECULES 2: NUCLEIC ACIDS AND LIPIDS
Nucleic acids
Roles for nucleic acids and nucleotides in organisms
o DNA contains info to make our genes
DNA is transcribed into RNA (ribonucleic acid) which is translated into proteins
Nucleotides have additional functions as signaling molecules and energy transducers
Nucleotides
The subunits of the nucleic acids
Consists of phosphate, sugar (5’ and 3’ position), bases (pyrimidine–purine, G–C, A–T [U in RNA])
the pentose sugars are different for DNA and RNA
o ribose (RNA) as in picture
o deoxyribose (DNA) with two Hs on the 2C
the bases are nitrogen-containing ring compounds
o pyramidines
o purines (extra ring)
the phosphates are normally joined to the 5C
o mono, di, tri phosphates store energy by having energy-rich bonds (breaking them releases energy)
o make nucleotide neg charged
Base pairing rule
Guanine-Cytosine
Adenine-Thymine
RNA/DNA differences
RNA
o usually single stranded
o sugarribose
o bases – A,C,G, Uracil
o (some have complex 3D structure, become catalytic (ribozymes))
DNA
o Usually double stranded
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