Biology Chapter 3 Notes



Organic Chemistry


Organic Chemistry

  • the study of compounds that contain carbon regardless of origin.

  • because carbon can form four bonds, these building blocks can be used to make an inexhaustible variety of organic molecules.

  • the great diversity of organisms on the planet is due to the versatility of carbon.




Carbon

  • has 4 electrons in its outer shell - it can make up to four bonds.

  • framework of biological molecules consists primarily of carbon bonded to - Carbon, O, N, S, P, or H.

  • carbon only forms covalent bonds.

  • can form polar or nonpolar bonds.



Oxygen + Nitrogen

  • form polar bonds with carbon

  • hydrophilic and soluble in water.



Hydrocarbons

  • organic molecules consisting of only carbon and hydrogen.

  • many organic molecules (fats) have hydrocarbon components.

  • undergo reactions that release a large amount of energy.

  • nonpolar

  • only have C-C and C-H bonds.

  • hydrophobic and poorly soluble.






Functional Groups

  • components of organic molecules that are most commonly involved in chemical reactions.

  • the number and arrangement of functional groups give each molecules its unique properties.

  • Ex - amino group NH2NH_2 acts as a base.


Most Important Functional Groups in Chemistry of Life:

  • Hydroxyl group

  • Carbonyl group

  • Amino group

  • Sulfhydryl group

  • Phosphate group

  • Methyl group




Isomers

  • compounds with the same molecular formula but different structures and properties.


Structural Isomers

  • have different covalent arrangements of their atoms.


Cis-trans Isomers (Geometric Isomers)

  • have the same covalent bonds but differ in their spatial arrangements.


Enantiomers

  • isomers that are mirror images of each other.





Macromolecules

  • large polymers - known as macromolecules for their huge size.


Polymer

  • a long molecule consisting of many similar building blocks.


Monomers

  • the repeating units that serve as building blocks.






The Synthesis and Breakdown of Polymers


Dehydration Reaction

  • occurs when two monomers bond together through the loss of a water molecule.


Hydrolysis

  • polymers are disassembled to monomers.

  • essentially the reverse of dehydration reaction.





Carbohydrates

  • include sugars and polymers of sugars.

  • simplest carbohydrates = monosaccharides or simple sugars

  • carbohydrate macromolecules are polysaccharides; polymers composed of many sugar building blocks.

  • Cn(H2O)nC_{n}\left(H_2O\right)_{n}



Monosaccharides

  • simplest sugars

  • most common are 5 or 6 carbons.

  • Pentoses - Ribose (C5H10O5)\left(C_5H_{10}O_5\right), Deoxyribose (C5H10O4)\left(C_5H_{10}O_4\right)

  • Hexose - Glucose (C6H12O6)\left(C_6H_{12}O_6\right)

  • Serve as a major fuel for cells and as raw material for building blocks.



Disaccharides

  • composed of two monosaccharides.

  • joined by dehydration reaction - Glycosidic bond

  • broken apart by hydrolysis

  • Ex - sucrose, maltose, lactose





Polysaccharides

  • many monosaccharides linked in long polymers.

  • Energy Storage - Starch, Glycogen

  • Structural - Cellulose, Chitin



Storage Polysaccharides


Starch

  • storage polysaccharide of plants.

  • composed of glucose monomers.

  • plants store surplus starch as granules within chloroplasts and other plastids.


Glycogen

  • storage polysaccharide in animals.

  • stored mainly in liver and muscle cells.



Structural Polysaccharides


Cellulose

  • structural polysaccharide of plants.

  • most abundant organic compound on Earth.

  • composed of long chains (never branched) of glucose monomers.

  • parallel sheets of straight chains provide great strength to plant cell walls.

  • to digest cellulose, you need an enzyme that breaks the glycosidic bond between the glucose monomers - animals don’t produce this enzyme.



Chitin

  • structural polysaccharide in exoskeletons.





Nucleic Acids


  • responsible for the storage, expression, and transmission of genetic information


Two classes

  • Deoxyribonucleic acid (DNA) - stores genetic information encoded in the sequence of nucleotide monomers.

  • Ribonucleic acid (RNA) - decodes DNA into instructions for linking together a specific sequence of amino acids to form a polypeptide chain.



Components of Nucleic Acids


  • Monomers → Nucleotides

  • made up of phosphate group, a five-carbon sugar (either ribose of deoxyribose), and a single or double ring of carbon and nitrogen atoms known as a base.

  • Nucleotides - linked into a polymer by a sugar-phosphate backbone.



Deoxyribonucleic Acid (DNA)

  • encodes information for amino acid sequence of protein - sequence of bases.

  • double helix- 2 polynucleotide strands connected by hydrogen bonds.

  • Base - Pairing Rules → A + T, C+G



RNA

  • single-stranded

  • the sugar is ribose

  • uses uracil (U) instead of thymine (T)

  • Several forms → messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA)




Proteins


  • nearly every function of living things depends on proteins


Functions

  • speeding up chemical reactions

  • defense

  • storage

  • transport

  • cellular communication

  • movement

  • structural support


  • Life would not be possible without enzymes - chemical agents that selectively speed up chemical reactions without being consumed in the reaction (so it can be used repeatedly)

  • Proteins account for more than 50% of the dry mass of most cells.

  • Humans produce tens of thousands of different proteins each with their own specific structure and therefore function


Amino Acids

  • building blocks of proteins.

  • 20 different amino acids.

  • common structure with variable sidechains that determines structure + function.




Polypeptide Formation

  • amino acids joined by dehydration reaction.

  • Carboxyl + amino forms peptide bond.


Polypeptides

  • polymers of amino acids.

  • broken down by hydrolysis.


Protein

  • a biologically functional molecule made up of one or more polypeptides each folded and coiled into a specific 3-D structure.




Protein Structure and Function


  • Protein structure and function is determined by the sequence of the amino acids in a polypeptide.

  • Proteins structure = determines how it functions.

  • Ensuring that a protein has its correct/appropriate shape is critical for it to function correctly.




Levels of Protein Structure





Primary Structure

  • unique sequence of amino acids.

  • determined by inherited genetic information.



Secondary Structure

  • consists of coils and folds in the polypeptide chain.

  • chemical and physical interactions cause protein folding.

  • a helices and B pleated sheets - key determinants of proteins characteristics.



Tertiary Structure

  • determined by interactions among various side chains (R-groups).

  • folding gives protein complex 3D shape.

  • the final level of structure for a single polypeptide chain.



Quaternary Structure

  • results when a protein consists of multiple polypeptide chains.

  • made up of two or more polypeptides.

  • protein subunits - individual polypeptide chains.

  • proteins can be formed from several copies of the same polypeptide.

  • multimeric - composed from different polypeptides.

  • Ex - Hemoglobin



Sickle-Cell Disease

  • an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin.

  • slight change in primary structure can affect a protein’s structure and ability to function.

  • the abnormal hemoglobin molecules cause the red blood cells to aggregate into chains and to deform into a sickle shape.




Lipids



  • composed predominantly of hydrogen and carbon atoms

  • nonpolar - insoluble in water.

  • include: fats, oils, phospholipids, steroids, waxes, and even some vitamins

  • comprise about 40% of the organic matter in the average human body.



Fats

  • known as triglycerides or triacylglycerols

  • formed by bonding glycerol to 3 fatty acids.

  • joined by dehydration; broken apart by hydrolysis.




Fatty Acids


Saturated

  • all carbons linked by single bonds.

  • straight, linear structure.

  • solid at room temperature.


Unsaturated

  • contain one or more double bonds

  • liquid at room temperature (oils)


Monounsaturated fatty acids: contain one double bond (C=C)

  • double bond adds a kink.

  • olive oil.


Polyunsaturated: contain 2 or more C=C bonds.

  • canola oil.





Function of Fats

  • energy storage

  • fatty acid tails - hydrocarbons

  • Hydrocarbons - contain a lot of energy that can be released by chemical reactions.

  • fats contain twice the energy as the same mass of polysaccharide.

  • Mammals store their long-term food reserves as fats in adipose tissue - serves as a cushion around vital organs as well as insulation under the skin.



Phospholipids

  • formed from glycerol. two fatty acids, and a phosphate group.

  • amphipathic molecules.

  • Phosphate head → polar/hydrophilic

  • Fatty acid tail → nonpolar/hydrophobic




Steroids

  • four interconnected rings of carbon atoms.

  • insoluble in water.

  • tiny differences in structure can lead to profoundly different specific biological properties.