Unit 3 Macromolecules, Enzymes, and ATP

Mrs. Stahl AP Biology

Organic chemistry is the study of carbon compounds

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Organic chemistry is the study of compounds

that contain carbon Organic compounds range from simple molecules such as methane- CH4 to colossal ones like proteins.

Most organic compounds contain hydrogen atoms in addition to carbon atoms

• • Percentages of the major elements are pretty consistent from one organism to another, however they can be utilized in many different ways.

Different species of organisms and individuals within the same species are distinguished by their differences in organic molecules (DNA, enzymes, etc).

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How did it all begin?

Scientists wanted to learn how to purify and improve substances such as food, medicine and fabrics, which are all obtained from living things.

1800’s- Chemists were making things in the lab by combining elements under the right conditions.

They believed that artificial synthesis (recreating molecules) in the lab was impossible.

Vitalism was the belief that organic compounds could only arise in living organisms.

Vitalism was disproved when chemists were able to synthesize organic compounds

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Example

1928- urea was accidentally created in a lab by a German chemist, Friedrich Wohler He was trying to make an inorganic salt called ammonium cyanate by mixing ammonium and cyanate ions but made urea instead. Urea is an organic compound that is found in the urine of mammals.

Scientists (Vitalists) were not convinced because the cyanate was extracted from animal blood. Vitalism crumbled after several decades of synthesizing complex organic compounds. Thoughts shifted from vitalism to mechanism.

Mechanism- physical and chemical laws govern all natural phenomena. Redefined organic chemistry as the study of carbon compounds, regardless of origin.

Stanley Miller’s Synthesis

• • • His synthesis of organic compounds related to evolution Miller tested whether complex organic molecules could arise spontaneously under conditions thought to have existed on early Earth (abiotic factors). Experiments support the idea that abiotic synthesis of organic compounds, perhaps near volcanoes, could have been a stage in the origin of life 1953- set up a closed system to simulate conditions thought to have existed on early Earth.

The Experiment

• • • • • 1. Water mixture in “sea” flask was heated; vapor entered atmosphere flask. 2. “Atmosphere” flask contained a mix of hydrogen gas, methane, ammonia, and water vapor 3. Sparks were discharged to mimic lightning 4. Condenser cooled the “atmosphere,” “raining” water and any dissolved molecules down into the sea flask 5. Material cycled through the apparatus and Miller periodically collected samples and analyzed them

Water vapor CH 4 “Atmosphere” Electrode Cooled “rain” containing organic molecules Condenser Cold water H 2 ” O “sea Sample for chemical analysis

Results

• • Miller was able to identify a variety of organic molecules such as formaldehyde, hydrogen cyanide, and complex amino acids and hydrocarbons.

Organic molecules may have been synthesized abiotically on early Earth.

Carbon: The Backbone of Life

• • • • Living organisms consist mostly of carbon-based compounds Carbon is unparalleled in its ability to form large, complex, and varied molecules Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon atoms bonded to one another and to other elements (H, O, N, S, and P).

Carbon enters the planet through plants photosynthesis. Plants take CO2 from the atmosphere and transforms it into usable forms of energy – glucose (C6H12 O6) and O2, which are passed along to animals through the process of cellular respiration.

CARBON!!!

Carbon can form up to four covalent bonds!

Carbon can bond to four other atoms or groups of atoms, making a large variety of molecules possible.

• • The electron configuration of carbon gives it covalent compatibility with many different elements The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the building code for the architecture of living molecules

• Carbon atoms can partner with atoms other than hydrogen; for example: – Carbon dioxide: CO 2 – Urea: CO(NH 2 ) 2

Molecular Diversity Arising from Variation in Carbon Skeletons

• • Carbon chains form the skeletons of most organic molecules Carbon chains vary in length and shape

(a) Length Ethane (b) Branching Propane (c) Double bond position 1-Butene (d) Presence of rings 2-Butene Butane 2-Methylpropane (isobutane) Cyclohexane Benzene

Animation: Carbon Skeletons

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Hydrocarbons

Hydrocarbons are organic molecules consisting of only carbon and hydrogen. Very common on Earth.

Attached to carbon skeleton wherever electrons are available for covalent bonding Many organic molecules, such as fats, have hydrocarbon components that serve as stored fuel for animals Hydrocarbons can undergo reactions that release a large amount of energy Major components of petroleum. Petroleum is called a fossil fuel because it is partially made up of decomposed remains that lived millions of years ago.

Hydrocarbon Fun Facts

• • • • NONPOLAR- do they dissolve in water?

Hydrophobic Have the potential to release a lot of energy through reactions The gas in your car is made up of them

Nucleus Fat droplets 10 μ m (a) Part of a human adipose cell (b) A fat molecule

Functional Groups

• • • • Carbon and Hydrogen have similar electronegativities with evenly distributed electrons that is why they are nonpolar.

There are other biological molecules in cells that contain other atoms with different electronegativities that are partially positive and negative, making them polar. These groups can be referred to as the C-H core group where other molecules known as functional groups can attach to. -OH is a common functional group, aka hydroxyl group

• The seven functional groups that are most important in the chemistry of life – Hydroxyl group – Carbonyl group – Carboxyl group – Amino group – Sulfhydryl group – Phosphate group – Methyl group

Chemical Group Hydroxyl group ( —OH) Compound Name Alcohol Carbonyl group ( C

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O) Carboxyl group ( Amino group ( —COOH) —NH 2 ) Ketone Aldehyde Carboxylic acid, or organic acid Acetone Acetic acid Amine Glycine Sulfhydryl group ( —SH) Thiol Examples Ethanol Propanal Cysteine Phosphate group ( —OPO 3 2− ) Organic phosphate Glycerol phosphate Methyl group ( —CH 3 ) Methylated compound 5-Methyl cytosine

Isomers

• Isomers are compounds with the same molecular formula but different structures and properties – Structural isomers have different covalent arrangements of their atoms (carbon skeleton). Example-glucose – Stereoisomers (Cis-trans isomers / Geometric Isomers- )- have the same carbon skeleton but differ in how the groups are attached / three dimensional shape in space.

• Enantiomers are isomers that are mirror images of each other

Enantiomers

• • Chiral molecule- molecule that has mirror image versions and typically occurs when carbon is bound to four different molecules.

Think of them as left handed and right handed. Just as your right hand won’t fit into a left handed glove, the molecules working in the cell can tell the difference between the two versions by shape. One is typically active, while the other is inactive.

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Enantiomers are really important in the pharmaceutical industry because two enantiomers of a drug may not be equally effective and can sometimes have harmful effects.

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Example: Thalidomide was a drug prescribed for 1000s of pregnant women in the late 50's, early 60's. This drug was a mixture of two enantiomers: one that would reduce morning sickness, and the other caused severe birth defects such as shortened arms and legs, blindness, deafness, heart problems, and brain damage ( http://www.bbc.com/news/uk-england-23500853 ).

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The differing effects of enantiomers in the body demonstrate that organisms are sensitive to even the most subtle variations in molecular structure and design.

(a) Structural isomers Pentane (b) Cis-trans isomers 2-methyl butane cis isomer: The two Xs are on the same side.

(c) Enantiomers CO 2 H trans isomer: The two Xs are on opposite sides.

CO 2 H H C CH 3 L isomer NH 2 NH 2 C CH 3 D isomer H

Animation: Isomers

Figure 4.7a

(a) Structural isomers Pentane 2-methyl butane

Figure 4.7b

(b) Cis-trans isomers cis isomer: The two Xs are on the same side.

trans isomer: The two Xs are on opposite sides.

Figure 4.7c

(c) Enantiomers CO 2 H CO 2 H H C CH 3 L isomer NH 2 NH 2 C CH 3 D isomer H

The Molecules of Life

• • • All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids Macromolecules are large molecules and are complex Large biological molecules have unique properties that arise from the orderly arrangement of their atoms

Figure 5.1

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Macromolecules are polymers, built from monomers

A polymer is a long molecule consisting of many similar building blocks The repeating units that serve as building blocks are called monomers Three of the four classes of life ’ s organic molecules are polymers – Carbohydrates – Proteins – Nucleic acids

The Synthesis and Breakdown of Polymers

• • • Enzymes are specialized macromolecules that speed up chemical reactions such as those that make or break down polymers A dehydration reaction occurs when two monomers bond together through the loss of a water molecule Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction

Understanding Dehydration Synthesis and Hydrolysis

• See the board and copy into your notes 

Where do we get proteins from?

• • Amino Acids Ex- We eat a steak-> goes into our digestive system where hydrolysis occurs and the protein is broken down into amino acids-> weave it back together to form a polymer so that it can make a protein and functions can be carried out.