General Biology 2 - Carbon in Life PDF

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________ and ________ are two fundamentalrequirements for organisms. Organisms also require water , minerals , andvitamins for the properfunctioning of their cells. Modes of nutrition are based on an organism’senergy and carbon source.What are the four nutritionalmodes?Can you Identify the photoauto...

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• ________ and ________ are two fundamental requirements for organisms. • Organisms also require water, minerals, and vitamins for the proper functioning of their cells. • Modes of nutrition are based on an organism’s energy and carbon source.

Can you Identify the photoautotrophs? chemoheterotrophs? How do each get their carbon?

What are the four nutritional modes?

What do we need a carbon for?

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• Living organisms consist mostly of carbon-based molecules. • Proteins, nucleic acids, carbohydrates, lipids are carbon-based molecules that distinguish living matter. • Carbon is unparalleled in its ability to form large, complex, and diverse molecules. 3

How many covalent bonds can each element make?

• Make up >95% of all matter found in organisms.

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• Biomolecules are molecules important in life. • Biomolecules include many organic molecules but also some inorganic molecules.

CO2 Carbon Dioxide

Large molecule Phospholipid

CH4N2O Urea

Macromolecules DNA

C6H12O6 Glucose

Supramolecular Complex Ribosome 5

• Term first used to describe molecules found in organisms. • Chemical definition: Carbonbased molecules. Urea (NH2)2CO Nitrogen waste product in the urine of mammals

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• Idea that: A. the production of organic molecules is governed by principles different from the principles of physics and chemistry observed in a lab. B. organic molecules are created by a vital force contained within an organism.

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• In 1828, Wöhler synthesized urea in a lab “without the use of kidneys, either man or dog.”

Friedrich Wöhler

• Supported that organic chemistry can be carried out in a lab and is governed by the principles of physics and chemistry.

Urea

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(c) Double bond position

(a) Length

Ethane

Propane

(b) Branching

Butane

1-Butene

2-Butene

(d) Presence of rings

2-Methylpropane (isobutane)

Cyclohexane

Benzene

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• Carbon-based molecules can form an almost limitless array of strong molecular skeletons that work in extreme and moderate environments. • Why? A. Carbon can form up to four ________ bonds because of its four ________ ________ . B. Carbon-carbon bonds are ________ .

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• Functional groups are H-, N-, O-, P-, and S-containing groups that are bonded to one of the carbon atoms of the skeleton. • In general, the carbon atoms in an organic molecule provide a skeleton that gives the molecule its overall shape. • Functional groups determine the chemical behaviors of a molecule: A. Chemical reactivity B. Interactions with other molecules

• The chemical behavior of a molecule determines its biological properties. 11

• The number and arrangement of functional groups give each molecule its unique chemical properties that result in unique biological properties. Estradiol Testosterone

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1.

Hydroxyl STRUCTURE (may be written HO—)

EXAMPLE

Ethanol

Alcohols (Their specific names usually end in -ol.)

NAME OF COMPOUND

• Is polar as a result of the electrons spending more time near the electronegative oxygen atom.

FUNCTIONAL PROPERTIES

• Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars.

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2.

Carbonyl STRUCTURE

Ketones if the carbonyl group is within a carbon skeleton

NAME OF COMPOUND

Aldehydes if the carbonyl group is at the end of the carbon skeleton

EXAMPLE

Acetone

Propanal

•  A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. •  Ketone and aldehyde groups are also found in sugars, giving rise to two major groups of sugars: ketoses (containing ketone groups) and aldoses (containing aldehyde groups).

FUNCTIONAL PROPERTIES

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3.

Carboxyl STRUCTURE

Carboxylic acids, or organic acids

NAME OF COMPOUND

EXAMPLE

• Acts as an acid; can

FUNCTIONAL PROPERTIES

H+

donate an because the covalent bond between oxygen and hydrogen is so polar:

Acetic acid Nonionized

Ionized

• Found in cells in the ionized form with a charge of 1– and called a carboxylate ion. 15

4.

Amino STRUCTURE

Amines

NAME OF COMPOUND

EXAMPLE

•

FUNCTIONAL PROPERTIES

Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms):

Glycine Nonionized

•

Ionized

Found in cells in the ionized form with a charge of 1+ +. 16

5.

Phosphate STRUCTURE

Organic phosphates

EXAMPLE

•

FUNCTIONAL Contributes negative charge to the molecule PROPERTIES of which it is a part (2– when at the end of a molecule, as at left; 1– when located internally in a chain of phosphates).

•

Molecules containing phosphate groups have the potential to react with water, releasing energy.

Glycerol phosphate

NAME OF COMPOUND

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6.

Sulfhydryl STRUCTURE

Thiols

NAME OF COMPOUND

•

FUNCTIONAL PROPERTIES

(may be written HS—) EXAMPLE

Two sulfhydryl groups can react, forming a covalent helps stabilize protein structure.

• Cysteine

Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be shaping it around curlers and then breaking and re-forming the cross-linking bonds. 18

7.

Methyl STRUCTURE

Methylated compounds

NAME OF COMPOUND

EXAMPLE

•

Addition of a methyl group FUNCTIONAL PROPERTIES to DNA, or to molecules bound to DNA, affects the expression of genes.

•

Arrangement of methyl groups in male and female sex hormones affects their shape and function.

5-Methyl cytidine

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• Different biomolecules leads to the diversity in cells in the body, individuals within populations, and species! • Structural diversity in biomolecules leads to functional diversity. • Structural diversity stems from: 1. _________________________ 2. _________________________ 20

C5H12 What is the structural formula?

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

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(a) Structural isomers

• Have different covalent arrangements of their atoms and different chemical properties (e.g. solubility, melting point, etc.).

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• Have identical bonding relationships, but the spatial positioning of the atoms differs.

(b) Cis-trans isomers

cis isomer: The two Xs are on the same side.

trans isomer: The two Xs are on opposite sides.

(c) Enantiomers CO2H

H CH3 L isomer

• Types:

CO2H

NH2

NH2

H CH3

• Can have similar chemical properties but different biological properties.

1. Cis-trans stereoisomers: have the same covalent bonds but differ in spatial arrangements.

D isomer

2. Enantiomers: are isomers that are mirror images of each other. 23

Drug

Condition

Ibuprofen

Pain; inflammation

Albuterol

Effective Isomer

Ineffective Isomer

S-Ibuprofen

R-Ibuprofen

R-Albuterol

S-Albuterol

Asthma

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1. Can you identify one of each? 2. How do each differ? 3. What determines whether one type of bond is formed vs. another?

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What are polymers? Example? What are monomers? Example? What type of reaction makes polymers? Breaks them down?

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Reaction

Reaction

One of these reactions requires an input of energy. Which one? 27

What is the name of a digestive enzyme that can break down starch?

Small intestine

Hydrolytic enzymes breakdown polymers and other molecules into smaller components.

Blood vessel Excess glucose is stored as glycogen in liver and muscle. Digestion

Absorption

Starch à Glucose Excess fatty acids are used to build fats and stored in adipose tissue.

Fats à Fatty acids

Proteins à Amino acids

2. Building Amino acids are transported into all cells where they are used to build proteins. Other organic molecules can be used as to build. 3. Energy Use

Absorption of nutrients occurs along the length of the small intestine.

Glucose or Fatty Acids

A portion of absorbed glucose and fatty acids are used to supply energy needs for cells.

ATP 28...