AP Biology

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AP Biology

Organic Molecules

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Isomers

• Isomers: same molecular formula, different 3- D shape.

• Structural: look at definition: Glucose and Fructose

Glucose: Fructose:

Both Images: Public Domain, Wikimedia Commons

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Isomer, 2

• Geometrical: different arrangements around a double bond: cis and trans

Image: Public Domain, Wikimedia Commons

• Stereoisomers/Enatiomers: mirror images

usually deal with a central chiral carbon. Right and left handed (Thalidomide).

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Carbon Backbone

• C bonds with other C.

• Can form Hydrocarbons: C and H

• Image: Public Domain, Wikimedia Commons

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Functional Groups

• Combination of SPONCH elements that are involved in chem rxns, behave in a

characteristic way, and attached to a carbon

backbone.

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Examples of common Fxnal Groups

Formula Group Name Significance

R-OH Hydroxyl (Alcohol) Polar: water soluble. Forms H bonds

R-NH₂ Amino Weak Base (accepts H+)

R-COOH Carboxylic Acid Weak Acid (H+ donor)

R-SH Sulfyhdral Forms disulfide bridges in proteins R-H₂PO₄ Phosphate Acidic (loses 2 H+)

R-CH₃ Methyl Nonpolar, hydrophobic

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Monomers/Polymers

• Monomers are basic units

• Add monomers together and you get a polymer

• Condensation/Dehydration/Synthesis: add monomers with release of water

• Hydrolytic cleavage/Hydrolysis: add water to

break apart polymers

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Synthesis/Condensation/Dehydration/Hydrol ysis Reaction

Image: Public Domain, Wikimedia Commons:

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4 types of Org Mol

• 1) Carbohydrates: CHO

• 2) Lipids

• 3) Nucleic Acids

• 4) Proteins

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CHO

• Composed of C, H and O.

• C(H

₂

O)

_n

: empirical formula.

• Monomer: Monosaccharide

• Main Mono: Glucose (end in –ose)

• Two forms: Alpha and Beta

• Difference?

• Alpha:

• Beta:

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Alpha and Beta Glucose

Alpha Glucose:

Beta Glucose:

Both images: Public Domain, Wikimedia Commons

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Disaccharides

• Put two monosaccharides together by

synthesis reaction and you get a disaccharide.

• Form an alpha glycosidic bond (in this case).

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Polysaccharides

• Add many monos together and you will eventually end up with a polysaccharide.

There are two main groups:

• Ones made with Alpha glycosidic bonds

• Ones made with Beta glycosidic bonds.

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Alpha Glycosidic Bonds

• Starch: How plants store energy

– Amylose

– Amylopectin

• Glycogen: How animals store energy

Image: Boumphreyfr, 5/20/09, Wikimedia Commons

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Beta Glycosidic Bonds

AKA: Structural Polysaccharides

• Cellulose: plant cell walls. Most abundant org mol on earth. Can’t break it down.

• Pectin and Carrageenan: algae, food thickeners.

• Chitin: make component of arthropod

exoskeletons.

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CHO Fxn

• 1) Energy: broken down first. 4 Kcal/gram

• 2) Structure: plants

• 3) Energy storage: starch and glycogen

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Lipids

• Diverse

• Based on solubility…not structures: All Hydrophobic

• Hydrophobic: Water fearing

• Hydrophilic: Water loving

• Amphipathic: Both hydrophobic and hydrophilic

• Types: Triglycerides, phospholipids,

glycolipids/glycoprotein, steroids and waxes

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Triglycerides

• Types: fats and oils

• Glycerol and 3 fatty acids and synthesis rxn

http://science.halleyhosting.com/sci/ibbio/chem/notes/chpt3/triglyceride.htm

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Fatty Acids

• 3 types based on the saturation of H.

• Saturated: animals produce

• Unsaturated: plants produce

• Polyunsaturated:

• Hydrogenated/Transfat?

Image: http://www.aafp.org/afp/2009/0815/p345.html

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Triglyceride Fxns

• 1) Energy: 9 Kcal/gram

• 2) Storage of excess energy: Adipose cells

• 3) Insulation

• 4) Floatation

• 5) Padding

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Phospholipid

• 2 FA, 1 Phosphate and Glycerol

• Synthesis rxn

• Amphipathic

Image: OpenStax, 5/18/16, Wikimedia Commons

• Main component of cell membrane

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Glycolipid/Glycoprotein

• CHO and Lipid

• 1 CHO (oligosacc)/protein, 2 FA and 1 Glycerol (synthesis)

• Found in cell membrane… receptor

Image: https://2012books.lardbucket.org/books/introduction-to-chemistry-general-organic-and-biological/s20-03-membranes-and-membrane-lipids.html

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Steroid

• Not structurally similar to other lipids: 4 linked C rings.

• All formed from cholesterol

• Cholesterol (bad rap): vit D, steroids, cell membrane…

Images: Public Domain, Wikimedia Commons

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Wax

• 1 FA and 1 Alcohol chail

• Fxn: decrease H2O loss. Found on insects,

plants: fruits, petals, leaves….

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Nucleic Acids

• Largest organic molecule

• Two types: DNA and RNA

• Basic Unit: RNA: nucleotide DNA: Deoxynucletoide

• Both are made up of:

– Pentose Sugar: ribose and deoxyribose – Phosphate

– Nitrogen base:

• Double Ring/Purines: Adenine and Guanine

• Single Ring/Pyrimadines: Cytosine, Thymine and Uracil

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Components of Nucleic Acids

Phosphate:

Sugar: Ribose and Deoxyribose:

Images: Public Domain, Wikimedia Commons

Nitrogenous bases:

Images: Mrbean427, 12/5/08, Wikimedia Commons

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Nucleotide/Deoxynucleotide

• Nucleotide:

• Deoxynucleotide:

Image: http://faculty.ccbcmd.edu/~gkaiser/SoftChalk%20BIOL%20230/

Molecular%20Genetics%20Review/DNA/DNA_print.html

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NA Fxns

• DNA: contains the code for all of organisms proteins.

• RNA: helps with protein synthesis

• Cell’s energy currency (ATP)

• Helps with hormone reactions (cAMP)

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Proteins

• Large and complex. We are a giant collection of protein and protein products.

• Monomer: amino acids (AA):

Image: User:Ppfk, 6/25/05, Wikimedia Commons

• 4 groups: Amine, carboxyl (acid), H and R group.

Different for each AA.

• Synthesis rxn. Form peptide bonds. 2 AA:

dipeptide, 3 AA: tripeptide, many AA: polypeptide

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Synthesis Reaction

• https://cnx.org/contents/uxP-2V9n@4/Amines-and-Amides

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Protein Shape

• Shape = Fxn

• Δ shape, Δ fxn.

• How does a protein get their shape (Conformation)?

• 4 levels (steps) to protein conformation.

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Primary Level

• AA sequence.

• Determined by DNA

• Δ NA, Δ AA sequence, Δ fxn.

• http://chemistry.tutorvista.com/biochemistry/structure-of-proteins.html

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Secondary Level

• You have AA chain. It will start to fold and coil…start forming a shape.

• H bonds between the AA of the polypeptide backbone…NOT BETWEEN R GROUPS.

• Small R groups: Beta pleated sheets

• Large R groups: Alpha helix

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Secondary Level

• http://www.mhhe.com/biosci/ap/ap_prep/chemH5.html

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Tertiary Level

• The AA chain folds even more. This folding provides a shape.

• R groups interact:

– H bonds between polar R groups.

– Ionic bonds: Acids and Bases

– Hydrophobic Interaction: nonpolar R groups

– Disulfide Bridges: Cysteines.

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Tertiary Level

• https://celestemohan.wordpress.com/2013/02/25/tertiary-level-of-protein-structure/

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Quaternary Level

• A protein may be made up of more than one polypeptide chain. These chains must fit

together. R groups on each chain will form

bonds: hydrophobic interactions, ionic, H

bonds and disulfide bridges

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Quaternary Level

• http://momentumhealth.net/?uid=70874

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Shape

• How can we affect fxn by Δing shape?

• Sickle cell anemia:

Image: Keith Chambers, 5/31/11, Wikimedia Commons

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Primary Level

• https://thestrangeandspectacularworldofbiochemistry.wordpress.com/tag/sickle-cell-anemia/

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Protein Shape

• http://helicase.pbworks.com/w/page/17605711/Sickle%20Cell%20Anemia

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Sickle Cell Consequences

• https://www.nhlbi.nih.gov/health/health-topics/topics/sca

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Denature

• Δ protein shape = Denaturing the protein

• How can you denature the protein? Break H bonds.

• How?

– Decrease pH – Increase Heat

– Add free radicals

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Types of Proteins

• Binding/Transport Proteins: bind to and carry

– Hemoglobin

• Structural Proteins: Support and shape

– Collagen: connective tissue, up to 25% of body mass.

– Elastin – Keratin:

• Hormones: coordinate activities, maintains

homeostasis.

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Types of Proteins

• Receptor Proteins: on cell membranes. Receive Ligands.

• Defense: Antibodies.

• Enzymes:

– Decrease the activation energy of rxns.

– Act. E: amount of E needed for a rxn.

– You need rxns to live. Mol need to move and bump into each other to react. To increase movement, you increase E (temp). However, you increase temp too much, you

denature proteins.

Image Credit: https://en.wikibooks.org/wiki/Biochemistry/Catalysis

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Enzyme shape

• Enz have a specific shape (determined by 4 levels of protein conformation).

• Active site: groove or depression on the

enzyme that allows substrates (mol) to enter.

• Active site: shape is important!

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Enzymes

• Enzymes provide a place for rxns to occur.

• They have a specific shape that will allow specific mol (substrates) to enter and react.

• Catalysts.

• Lock and Key: old

• Induced Fit Model: new

• Enzyme, substrate, enzyme substrate complex,

enzyme product complex, enzyme and product.

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Enzyme/Substrate Reaction

• http://www.ducksters.com/science/biology/enzymes.php

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Enzyme/Substrate Reaction

• http://ejdio.weebly.com/enzymes.html

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Enzyme Kinetics

• What affects enzyme rate?

• Temperature: initially, increase and the rate of reaction increases (mol move faster). At about 40

^o

C, H vibrate too much, break H bonds,

denature, rxn stops.

• Time: initially [Sub] is high, rxn is fast. Over time [sub] decreases, rxn rate decreases. Due to

increase in [prod]. Prod enters active site and

prevents sub from entering…Negative Feedback.

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Enzyme Kinetics, 2

• Decrease pH: increase [H+].

– Each enz has an optimal pH.

• Free (Hydroxyl) radicals: increase [OH-]

– Produced normally in prod of E.

– Superoxide dismutase

– Antioxidants

Image: Smokey Joe, 8/21/15, Wikimedia Commons

• Cofactors/coenzymes: in active site, provides

shape. Vitamins and minerals.

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Enzyme Kinetics, 3

• Allosteric control:

– Secondary site on some enz: allosteric site.

– Mol bind and change the shape of protein (active site). Stops rxn.

– Usually a product of a multistep rxn.

– https://www.boundless.com/biology/textbooks/boundless-biology-textbook/metabolism-6/enzymes-72/control-of-metabolism-through-enzyme-regulation-351- 11577/

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