Chapter 4: Carbon & the Molecular Diversity of Life

5-Methylcytosine

A modified cytosine with addition of methyl group, affecting gene expression and hormone function.

Abiotic synthesis

Formation of organic molecules without the involvement of living organisms.

Acetic Acid

An organic acid that gives vinegar its sour taste. example of a carboxyl group.

Acetone

simplest ketone

Alcohol

A molecule containing a hydroxyl group.

Aldehyde

A molecule with a carbonyl group at the end of a carbon skeleton.

Aldoses

Sugars with aldehyde groups

Amine

A molecule containing an amino group.

Amino acid

A molecule containing both an amino group and a carboxyl group.

Amino group

-NH2 group, acts as a base, found in amines and amino acids.

Asymmetric carbon

A carbon atom bonded to four different atoms or groups.

ATP

Adenosine triphosphate, an energy-carrying molecule.

Biological activity

The ability of a molecule to interact with biological systems.

Carbon

Element with four valence electrons, forming diverse molecules.

Carbon Dioxide Structural Formula

O=C=O. Considered inorganic due to simplicity and lack of hydrogen.

Carbon skeleton

The chain of carbon atoms forming the backbone of an organic molecule.

Carbon Skeleton Arrangement

Can be straight, branched, or arranged in closed rings.

Carbon Skeleton Varying Methods

length, branching, double bond position, presence of rings

Carbonyl group

C=O group, found in aldehydes and ketones.

Carboxyl group

-COOH group, acts as an acid because covalent bond between oxygen and hydrogen is polar, found in carboxylic acids.

Carboxylic acid (organic acid)

A molecule containing a carboxyl group.

Charge

Functional groups can carry a negative or positive charge.

Cis Isomer

Arrangement with both Xs on the same side of a double bond.

Cis-trans isomer

Covalent bond to the same atoms, differ in spatial arrangement due to inflexibility of double bonds

Cysteine

A sulfur-containing amino acid with a sulfhydryl group (-SH).

Double bond

A covalent bond involving four shared electrons between two atoms.

Enantiomer

Isomers that are mirror images of each other.

Energy

ATP releases energy when its phosphate bonds react with water.

Ethanol

An alcohol, has hydroxyl group

Functional group

Chemical groups directly involved in chemical reactions.

Functional group properties

Shape, charge, and polarity determine chemical reactivity.

Geometric isomer

Another name for cis-trans isomer.

Glycerol Phosphate

A molecule that takes part in many important chemical reactions in cells, has phosphate group

Glycine

An amino acid. It is the simplest amino acid, has amino group

How do fats use hydrocarbons?

Fats have long hydrocarbon tails attached to a nonhydrocarbon component.

How do hydrocarbons work in carbon skeletons?

Atoms of hydrogen are attached to the carbon skeleton wherever electrons are available for covalent bonding, can undergo reactions that release a relatively large amount of energy

Hydrocarbon

Long chains of only carbon and hydrogen atoms.

Hydrophilic

Water-loving; polar or charged groups that dissolve in water.

Hydrophobic

Water-fearing; nonpolar molecules that do not dissolve in water.

Hydroxyl group

-OH group, Polar due to electronegative oxygen Forms hydrogen bonds with water Helps dissolve compounds such as sugars

If each carbon has two different atoms attached to it, then how many different cis-trans isomers are possible?

Two different cis-trans isomers are possible.

Isomer

Compounds with the same molecular formula but different structures and properties

Ketone

A molecule with a carbonyl group within a carbon skeleton.

Ketoses

sugars with ketone groups

Methyl group

-CH3 group, affects gene expression when bonded to DNA or to proteins that bind to DNA Affects shape and function of male and female gender hormones

Methylated compound

compound modified by the addition of a methyl group.

Methylated DNA

Methyl groups affect gene expression when bonded to DNA.

Molecular diversity

Arises from carbon's ability to form four bonds and create varied skeletons.

Nonpolar covalent bond

A covalent bond where electrons are shared equally.

Organic chemistry

The study of organic compounds, key to life

Organic compound

Any compound containing carbon.

Organic phosphate

A molecule containing a phosphate group.

Out of the 7, which ones are hydrophilic and thus increase the solubility of organic compounds in water?

All of them except Methyl and Sulfhydryl are this or basically Hydroxyl, carbonyl, carboxyl, amino, and phosphate groups are hydrophilic and increase solubility in water.

Out of the 7, which ones are ionized at normal cellular pH?

Carboxyl and amino groups are ionized at normal cellular pH.

Pharmaceutical industry

Industry where enantiomers' specific biological activity is crucial.

Phosphate group

-OPO₃²⁻ group, important in ATP, Contributes 1- when inside chain of phosphates and 2- when at the end Gives molecule ability to react with water, releasing energy

Plane

Atoms joined by a double bond lie in the same plane.

Polar covalent bond

A covalent bond where electrons are shared unequally.

Propanol

an alcohol, example of aldose

Properties of Enantiomers

Differ in shape due to presence of asymmetric carbon Usually, only one isomer is biologically active because only that form can bind to specific molecules in an organism

Protein structure

Stabilized by sulfhydryl group cross-links.

Rotation

Free rotation occurs around single bonds, not double bonds.

Single bond

A covalent bond involving two shared electrons between two atoms.

Single Bonds in Cis-Trans Isomers

Single bonds allow free rotation without changing the compound, double bonds don't permit this rotation

Solubility

Hydrophilic groups increase solubility in water.

Stanley Miller's experiment

Showed organic molecules could form abiotically on early Earth, amino acids were produced at end of his experiment

Structural isomer

Isomers that differ in the covalent arrangement of their atoms, Increase as size of skeleton increases May also differ in the location of double bonds

Sulfhydryl group

-SH group. two —SH groups can react, forming a "cross-link" that helps stabilize protein structure

Tetrahedral shape

Arrangement of bonds around a carbon atom with four single bonds.

Thiol

A molecule containing a sulfhydryl group.

Trans Isomer

Arrangement with atoms on opposite sides of a double bond.

Valence

The number of covalent bonds an atom can form.

What are the seven most important chemical groups in biological processes? (I'm referring to them as the 7 in the future questions)

Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl.

What do the valences of carbon usually bond with?|

arbon's valences usually bond with hydrogen, oxygen, and nitrogen.

What does the arrangement of four hybrid orbitals cause bonds to angle into?

The corners of an imaginary tetrahedron, approximately 109.5° are the bond angles in the orbitals formed by four single bonds in carbon

What is the asymmetric carbon attached to in enantiomers?

Attached to four different atoms or groups of atoms.

Which chemical group out of the 7 isn't chemically reactive?

The methyl group (-CH3) is not chemically reactive.