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Flashcards in Biochemistry Deck (112):
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Organic molecule

Molecules containing Carbon

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Unique properties of Carbon

1) Tends to four form covalent bonds
2) Often forms double and triple bonds, particularly with othe carbon atoms
3) Catenates more often than any other atoms

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Catenate

Verb used to describe the action of atomically bonded chains

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Organic chemistry

The study of how carbon-containing molecules interact with other carbon-containing molecules

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Alkanes

Single bond hydrocarbon molecules

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Alkenes

Double bond hydrocarbon molecules

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Alkynes

Triple bond hydrocarbon molecules

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Hydrocarbons

Compounds that contain both carbon and hydrogen

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Structural formula

Formulas that show not only the number of atoms but the manner in which the atoms are arranged and bonded together

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Structural isomers

Molecules of the same chemical formula, but different arrangements

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Types of hydrocarbons

1) Aromatic hydrocarbons
2) aliphatic hydrocarbons (include alkanes, alkenes, alkynes)

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Stereoisomers

Molecules with the same conectivity but different spacial arrangements

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Connectivity

The types of bonds that hold the atoms together

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Spatial arrangement

The manner in which atoms are arranged in relation to one another

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Optical isomers

Type of stereisomer that is a mirror image of the natural molecule
(Also called enantiomers)

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Enantiomers

Type of stereisomer that is a mirror image of the natural molecule
(Also called optical isomers)

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Geometric isomers

A form of stereoisomers involving the orientation of functional groups in a molecule that contains bonds of incompatible rotating

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Chiral

The either molecule in a mirror isomer situation

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Dextrorotatory isomers

An optical isomer that rotates the polarization of light clockwise

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Levorotory isomer

An optical isomer that rotates the polarization of light counter-clockwise

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Racemic mixture

A mixture of both levorotatory and dextrorotary isomers that cancel each other out so that the polarized light is not rotated at all

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Saturated hydrocarbons

When a carbon or chain of carbons is bonded to as many hydrogens as it can be

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Unsaturated hydrocarbon

A hydrocarbon to which hydrogens could still bond

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Reaction of alkanes

Undergo substitution reactions in which one or more hydrogen atom is replaced by an atom or group of atoms

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Reactions with alkenes and alkynes

Always synthesis reaction, always breaks apart double or triple bonds or a single bond (the bond type of lowest potential energy)
Always visualize by drawing out the molecular geometry

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Polar reagents added to unsymetrical alkenes

The positive end (least electronegative) of the reagent adds to the carbon atom that has the most hydrogen atoms

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Aromatic hydrocarbons

Forms a 'nut shaped' hexagon of centrally bonded carbon atoms
With 3 double bonds and 3 single bonds
See book for specific notation

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Benzenes

An aromatic hydrocarbon in which only one carbon atom has been substituted.
Takes the form (substituent name)benzene

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Phenal group

The name of the long string of hydrocarbons used as the substituent in the carbon hexagon

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Di-substituted benzenes

Benzezne in which two hydrocarbons have been substituted

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Reactions of aromatic compounds

Given as the reaction between a benzene molecule and another compound

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Polycyclic aromatic compounds

Aromatic compounds in which individual rings are fused together

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Functional group

A characteristic atom or group of atoms that give the molecule certain qualities

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Alcohols

molecules containing a hydroxal group (OH-)
Bonded to the lowest carbon atom
End in '-ol' suffix

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Meth- prefix

1 hydrocarbon

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Eth- prefix

2 hydrocarbons

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Prop- prefix

Three hydrocarbons

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But- prefix

Four hydrocarbons

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Pent- prefix

Five hydrocarbons

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Hex- prefix

Six hydrocarbons

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Hept- prefix

Seven hydrocarbons

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Oct- prefix

Eight hydrocarbons

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Non- prefix

Nine hydrocarbons

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Dec- prefix

Ten hydrocarbons

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Alcohols

'-ol' suffix
One hydroxical group

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Ethers

'- Ether' suffix
Oxygen in the middle of a linear geometry
Hydrocarbons on either side

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Ketones

'-one' suffix
Carbon oxygen bond, between two hydrocarbons

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Carboxylic acids

End in 'acid'
Hydrocarbon bonded to a carbon/oxygen double bond with a hydroxyl group

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Esters

'-ate' suffix
Hydrocarbon bonded to a carbon oxygen double bond bonded to a oxygen-based-hydrocarbon

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Amines

Hydrocarbon-(NH2)
Ends in amine

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Aldehydes

'-al' suffix
Hydrocarbon bonded to carbon (carbon is double bonded to an oxygen, single bonded to a hydrogen

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Molecules of 1-4 hydrocarbons

Gas state at STP, used as fuel

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Molecules of 5-7 hydrocarbons

Low-boiling liquids at STP, solvents and gasoline

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Molecules with 6-18 hydrocarbons

Liquid state at STP
gasolines

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Molecules with 12-24 hydrocarbons

Liquid at STP
Used as jet fuel, and portable-stove fuel

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Molecules with 18-50 hydrocarbons

High-boiling liquids at STP
Diesel fuel, lubricants, heating oil

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Molecules with over 50 hydrocarbons

Solids at STP
Petroleum jelly, paraffin wax

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Suffix '-yne'

Hydrocarbons with a triple bond between carbon atoms

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Suffix '-ene'

Hydrocarbons with a double bond between carbon atoms

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Suffix '-yl'

Refers to the hydrocarbon group bonded to the main hydrocarbon
Prefix indicates number of individual hydrocarbons within that structure

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Methyl group

A -CH3 bonded to a hydrocarbon

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Family (Organic)

Molecules with the same functional group

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Iso- prefix

Used when a methyl group is bonded to the first carbon in 'CHCH3'

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-ane suffix

Used when hydrocarbons are bonded together by single bonds

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Geometric isomerism

A type of isomerism in which the natural molecule is rotated on one side or the other from the center

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Alcohol mixed acids

Forms a substitution reaction
Breaks alcohol into a halogenated hydrocarbon and water vapor

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Halogenated hydrocarbon

Hydrocarbon bonded to a halogen gas

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Dehydration of alcohols

In the presence of a catalyst, alcohols break down into a complex hydrocarbon and water vapor

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Oxidation of alcohols

Alcohols loose a hydrogen, forming a aldehyde

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Reduction of alcohol

Looses on oxygen to form an Alkane

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Oxidation of alkane

Alkanes gain oxygen forming an alcohol

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Reduction of aldehyde

Gains an H+, forming an alcohol

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Reduction of carboxylic acid

Looses an oxygen to form an aldehyde

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Alcohols reaction with metal

Release Hydrogen and bonds to the metal

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Carbonyl Group

Double bond between carbon and oxygen, bonded to a hydrocarbon

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Condensation reaction

Two or more organic compounds join, often giving off water vapor

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Amines

'-amine' suffix
Organic compound containing N
Act as weak bases

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Polymers

Long chains of repeating hydrocarbons

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Monomers

Each unit in a polymer chain

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Addition polymer

A polymer in which the monomers link together without loosing any atoms

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Dimer

Any reaction between two monomers

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Condensation polymers

Polymers that eliminate certain atoms when they come together

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Lipids

Chemical components of a cell that are in insolubile when mixed with non-polar solvents

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Fatty acid

A lipid, carboxylic acid with a hydrogen tail

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Saturated fatty acid

Hydrocarbon chain that has no double bonds

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Triglycerides

Triesters composed of glycerol with three fatty acids

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Saturated fat

A triglyceride in which the fatty acids are saturated
Tend to be solid at room temperature

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Phosopholipids

Lipids of the same basic structure as triglycerides except that only one fatty acid groups is replaced with a polar phosphate group
One part is hydrophilic the other is hydrophobic

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Glycoplipids

Lipids of similar structures and properties as phospholipids, but in which the nonpolar end is composed of one fatty acid chain, and one hydrocarbon chain

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Hydrophilic

A molecule with a strong affinity for water

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Steroids

Lipids with a four-ring structure

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Lipid bilayer

A double layered structure that results from non-polar parts of a phospholipid or glycolipid interacting with all non-aqueauos environments, with the polar end interacts with the remaining aqueous envirnoments

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Carbohydrates

Polyhydroxy aldehydes that give 4 energy units from their bonds

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Monosaccharides

"One sugar" the simplest form of carbohydrate
(Six carbons)

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Hexose

Six carbon sugar

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Aldose

A simple sugar with an aldehyde group

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Ketose

A sugar that is a ketone

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'-ose' suffix

Means the molecule can be broken down for energy
An isomer C6H12O6

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Polycaccharide

A long chainlike molecule composed of many monosacharite units bonded together
Type of complex carbohydrates

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Cellulose

Glucose units bonded by glycosidic linkages
Most abundant organic substance on earth
Not digested by humans

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Starch

Two slightly different polysacharides, amylose and amylopectin
Soft, plyable substance

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Glycogen

Amylopectin, but with a longer chain

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Amino acids

A carbon atom bonded to four different groups, an amine group, a hydocarbon group, a carboxylic acid, and a hydrogen atom

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Side chain

The hydrocarbon chain that makes the amino acid

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Structural protein

Compose structures within living organisms

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Enzymes

Catalyze and control biochemical reactions

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Hormones

Chemicals that regulate metabolic processes

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Transport proteins

Transport substances from one place to another

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Storage proteins

Transport substances from one place to another

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Contractile and motile proteins

Mediate motion and muscle contraction

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Protective proteins

Protect and defend cells

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Proteins

Long chains of amino acids