1.5 – biological chemistry. organic compounds – compounds containing c atoms bound to other...
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1.5 – Biological Chemistry
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Organic compounds – compounds containing C atoms bound to other elements• Main atoms found in the body: C, H, O, N
Functional group – a cluster of atoms that gives compounds specific chemical properties• Causes chemical reactions between organic
compounds
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Functional Group Structural Formula
Hydroxyl
Carboxyl
Amino
Sulfhydryl
Phosphate
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Biological Compounds
Macromolecules – large molecules sometimes composed of repeating subunits
There are 4 major classes:1. Carbohydrates2. Lipids3. Proteins4. Nucleic Acids
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Carbohydrates
Contain C, H, and O atoms in a 1:2:1 ratio (Ex. Glucose C6H12O6)
Used as sources of energy, building materials, and cell surface markers for cell-to-cell identification and communication
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Can be classified into 5 groups:
1. Monosaccharides – “simple sugars”• single chain of carbon atoms with hydroxyl
groups attached• identified by the carbonyl group and number
of carbons (pentose, hexose)• Ex. Ribose (DNA), glucose, fructose (fruit),
galactose (milk)
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2. Disaccharides – two simple sugars attached to one another• Glycosidic linkages – covalent bonds holding
monosaccharides to one another • Ex. Maltose (2 glucose), sucrose (glucose,
fructose), lactose (glucose, galactose)
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3. Polysaccharides – complex carbohydrates• Hundreds to thousands of monosaccharide
subunits held together by glycosidic bonds• Energy storage and structural support• Ex. Starch• Polymers – large molecules made of long
chains of repeating subunits• Monomers – the individual part of a polymer
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4. Cellulose – glucose polymer found in plant cell walls• Humans can’t digest it b/c of the bonds it has• Cellulose passes through the human digestive
system undigested– Helps waste pass through
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5. Chitin – modified form of cellulose that forms the tough exoskeleton of insects, fungi, and crustaceans • Used in contact lenses and stitches
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LipidsMade of C, H, O; hydrophobic – contain more non-polar O-H bonds
Used for storing energy, building membranes and other cell parts, and as chemical signalling molecules
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Can be divided into 4 types:1. Fats and OilsEnergy-storing molecules in living organisms; 1g fat = 9 calories
Animals convert excess carbohydrate into fat and store the fat molecules as droplets in the cells of adipose tissue
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Triglycerides – lipids containing 3 fatty acids attached to a single molecule of glycerol • Glycerol – 3-C alcohol containing a hydroxyl
group attached to each carbon• Fatty Acid – long H-C chains containing a
hydroxyl group (COOH) at each end
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Saturated triglyceride:• Has single bonds between carbons• Has the maximum number of hydrogens possible• Straight chains• Solid at room temp
– Ex. Butter
Unsaturated triglyceride: • Has double bonds between 2 or more carbons• Has less than the maximum number of H’s possible• Liquid at room temp• Monounsaturated – only 1 double bond• Polyunsaturated – more than 1 double bond
– Ex. Canola oil
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2. PhospholipidsGlycerol attached to 2 fatty acids (hydrophobic tails) and a highly polar phosphate group (hydrophilic head)
Found in cell membranes as the phospholipid bilayer – 2 layers with the phosphate heads on the outside and the fatty acid tails on the inside • Water can’t pass through the bilayer because
it’s mainly non-polar
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3. Sterols (steroids)• Compact hydrophobic molecules containing 4
fused hydrocarbon rings and many different functional groups. Ex. Cholesterol
4. Waxes• Long-chain FA’s linked to alcohols or carbon rings• Used for waterproof coatings on plants and
animal parts
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Proteins
Polymers of amino acids
Amino acids – a protein building block• Has a central C, amino group, carboxyl group, H atom, and
side chain (different)• 20 different amino acids – 20 different functional groups• Essential – body can’t make them; must get them from
food (8/20)• Nonessential – your body can make them (12/20)
Used as structural building blocks, functional molecules, enzymes, immunoglobins, transportation devices
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Peptide bond – bond between amino acids in a protein molecule
Polypeptide – a short chain of amino acids
Protein Synthesis – amino acids get joined together to make a protein• As the amino acid chain grows, it folds (due to
attraction/repulsion forces)• If the protein doesn’t fold properly, it won’t
work properly (won’t fold properly due to a change in just one amino acid)
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A protein has 4 structures:
1. Primary – the sequence of amino acids in the polypeptide
2. Secondary – the way that the polypeptide is shaped (α-helix, β-sheets)
3. Tertiary – the way that the polypeptide is folded
4. Quaternary – 2 or more polypeptides attached together (making a functional protein)
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Protein DenaturationA change in the 3D shape of a protein• Caused by high temperatures (>40 deg) or
acidic, basic, or salty environments
Causes the protein to not work properly due to bent or broken peptide bonds
Will return to its normal shape once it is out of the harsh environment, as long as the peptide bonds aren’t broken
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Fever above 39 degrees can denature enzymes in the brain leading to seizures or death
Curing meats with lots of salt, or picking preserves food by denaturing the enzymes in bacteria that causes food to go bad
Heat denatures proteins in hair so people can curl or straighten it
Coagulation – permanent change in a protein’s shape due to the breaking of bonds between amino acids
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Nucleic Acids
Stores hereditary information that determines structural and functional characteristics
Nucleic acids are made of strands of nucleotides
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Nucleotides are made of 3 components:1. A 5-C sugar (ribose in RNA, deoxyribose in
DNA)2. A phosphate group3. A nitrogenous base
• There are 4 types of nitrogenous bases: adenine (A), guanine (G), cytosine (C), thymine (T)
• A and G are purines• T and C are pyrimidines
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Deoxyribonucleic Acid – double-stranded
Ribonucleic Acid – single-straned
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DNA
• The sugars and phosphate groups for the backbone of the DNA or RNA
• The sugars and phosphates join together through a phosphodiester bond and the nitrogenous-bases face each other forming a “double helix”
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A complimentary strand of DNA is made such that the N-bases bind as follows: A with TC with G
• A binds with T because 2 hydrogen bonds can form between them
• G binds with C because 3 hydrogen bonds can form between them
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RNA• Single strand of NTs (mRNA and tRNA)• Contains uracil U, instead of thymine T• Codes for protein
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The Central Dogma
DNA → RNA → protein
All of the features of our body are made of protein, which is coded for by DNA
Gene – a sequence of nucleotide bases in DNA• Each gene codes for 1 protein → 1 gene, 1 protein hypothesis
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TranscriptionA section of DNA that codes for the protein to be made is unwound and unzipped, exposing the N-bases
Nucleotides come together and form a “complimentary” strand to the DNA• This strand is called messenger RNA (mRNA) and
has uracil (U) binding to A (no T)
The mRNA strand detaches from the DNA → single strand → leaves the nucleus, goes to the cytoplasm, and the ribosome subunits bind to it
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TranslationThe ribosome that is attached to the mRNA moves over a sequence of 3 nucleotides → codon• A codon codes for a certain amino acid
When the ribosome is over the codon, it sends a signal to the complimentary tRNA codon (anticodon) to bind to the mRNA codon• The tRNA will be holding the proper amino acid, coded for by
the mRNA
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• Once the tRNA and amino acid are in place, the ribosome moves over to the next codon
• The complimentary tRNA comes in and holds the aa in place and a peptide bond is formed between the 1st and 2nd amino acid
• Once the bond is formed, the first tRNA goes to get another amino acid in case it is needed again
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• This process keeps happening until a chain of amino acids is formed
• Once the chain is formed, the ribosome subunits fall off the mRNA and the mRNA is recycled
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• Depending on the sequence of amino acids, the protein will fold in certain ways, attaining its secondary and tertiary structure, and will bind to other proteins, attaining its quaternary structure– Then, the protein is functional
• The structure of the protein is important → change the structure, change the function
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Homework
• Pg. 35 # 1, 2, 5-13