Biochem Lab Finals

Complete reviewer for finals.

Fixed bed of large surface area; may be a porous or finely divided solid or a liquid that has been coated in a thin layer on an inert supporting material.

Stationary Phase

Fluid that moves through or over the surface of the stationary phase; may be liquid or gas.

Mobile Phase

Components must be in solution or vapor state; the relatively affinity of the solutes for each of the phases must be reversible.

Solute Mixture

In paper chromatography, ____________ is a post-run visualization reagent used to detect and locate amino acids and other primary and secondary amine containing compounds separated on the paper.

Ninhydrin

colored spots which allows scientists to see the locations of the separated components, as they are often colorless and invisible on the paper

Ruhemann's purple

Biological catalysts that increase the rate of chemical reactions taking place within living cells without themselves suffering any overall change.

Enzymes

Each enzyme is quite specific in character, acting on a particular substrate or substrates to produce a particular product or products.

True

The study of enzymes.

Enzymology

Non-protein group in an enzyme (prosthetic group) wherein an enzyme lacks catalytic activity.

Co-Factors

The inactive protein component of an enzyme.

Apoenzyme

Active enzyme

Holo-Enzyme

Some cofactors are only transiently associated with a given enzyme molecule, so that they function as cosubstrates.

True

Nonprotein organic compounds and many coenzymes are derived from vitamin precursors which are often essential components of the organism’s diet, thus giving rise to deficiency diseases when in inadequate supply.

Co-Enzymes

Enzymes + other substances such as vitamins or organic and inorganic substances

Co-Enzymes

Non-enzyme part of the Co-enzyme

Co-factor

inactive form of the enzyme

Zymogens/Proenzymes

Inactive form secreted by stomach linings.

Pepsinogen

Active form.

Pepsin

FAD

Flavine Adenine Dinucleotide

NAD

Nicotinamide Adenine Dinucleotide

FMN

Flavine Mononucleotide

FAD, NAD, FMN, are examples of…

Co-Enzymes

Involved in carbon dioxide fixation reactions and fatty acid synthesis.

Biotin

Coenzyme involved in the transfer of methyl groups; active in amino acid metabolism.

Vitamin B12

Other name for Vitamin B12

Cyanocobalamin

Needed for cellular and macrocellular syntheses.

Vitamin E

Coenzyme used in electron transport (naphthaquinones and quinones).

Vitamin K

Metal-ion activator

Inorganic Ions

Contains an apoenzyme and a metal ion cofactor

Metalloenzyme

Co-enzyme + apoenzyme

Holoenzyme

Metal ion activator + apoenzyme

Holoenzyme

All enzymes have an active site.

True

Location on the enzyme where a substrate is bound and catalysis occurs.

Active site

Is formed when a substrate and enzyme bond, resulting in conversion of substrate (S) to product (P)

Enzyme–substrate complex

States that the substrate has a shape that exactly fits the active site; implies that enzyme conformations are fixed or rigid but research proves otherwise.

Lock-and-Key Model

States that the conformation of the active site changes to accommodate an incoming substrate; active site has a shape that becomes complimentary to the substrate only after the substrate is bound.

Induced Fit Model

Increase in enzyme concentration will increase the concentration of ES in compliance with the reaction rate theory.

True

Rate of reaction is directly disproportional to enzyme concentration.

False

Initial rate of an enzyme-catalyzed reaction is unresponsive to increases in substrate concentration

False

Maximum rate

Vmax

Rates of enzyme-catalyzed reactions decrease with temperature.

False

Optimum temperature at which enzyme activity is highest

25°C to 40°C

Beyond this temperature, enzymes are vulnerable to denaturation.

True

Enzymes are most effective in a narrow pH range and less active at pH values lower or higher than the optimum pH (usually around 7).

True

Substances that decrease enzyme activity

Enzyme Inhibition

Consists of long-chained polynucleotides combined with one another through a phosphate diester linkage.

Nucleic Acids

Nucleic acids sequence are always specified as 5’ → 3’

True

Found in all cells which participate in storage, transmission, and translation of genetic information.

Macromolecules

2 Types of Nucleic Acids:

RNA, DNA

Responsible for using the genetic information encoded to produce the thousands of proteins found in living organisms.

RNA

Stores genetic information.

DNA

DNA, molecules of heredity.

Deoxyribonucleic acid

RNA, protein synthesis.

Ribonucleic acid

DNA + Histone

Chromatin Complex

Found in the nucleus of cells as a double-stranded chain of nucleotides that resemble a ladder that has been twisted into a helix; highly twisted polymer.

DNA

It is a right-handed double helix that protects the DNA during extreme condition such as desiccation. Protein binding also removes the solvent from DNA.

A-DNA

This is the most common DNA conformation and is a right-handed helix. Majority of DNA has this conformation under normal physiological conditions.

B-DNA

Is a left-handed DNA where the double helix winds to the left in a zig-zag pattern. It is found ahead of the start site of a gene and hence is believed to play some role in the gene regulation.

Z-DNA

Discovered the Z-DNA.

Andres Wang and Alexander Rich

Swiss biologist who discovered DNA.

Johannes Friedrich Miescher

DNA was discovered in…

1869

The double helix structure of a DNA molecule was later discovered through the experimental data by…

James Watson and Francis Crick

A biochemist who discovered that the number of nitrogenous bases in the DNA was present in equal quantities.

A=T C=G

Erwin Chargaff

• The DNA of any cell from any organism should have a 1:1 ratio of purine and pyrimidine bases.

• To make exact copies of itself in the process of replication.

• To transfer the genetic information to m-RNA in the process of transcription.

Chargaff’s Rule

DNA that constitutes the total genetic information content of an organism.

Genome

The segments of the DNA that can be translated.

Gene

DNA segment that do not convey code for genetic information.

Introns

DNA segments that convey genetic information

Exons

Single chain of nucleotides.

RNA

• Made in the nucleus of the cell as a component to a DNA strand.

• Serves as cytoplasmic messenger of genes and carrier of genetic information for protein synthesis.

• U=A; G=C

Messenger RNA

• Comprise 70-80% of the total cell RNA (most abundant).

• Bind the m-RNA and a specific enzyme for protein synthesis.

Ribosomal RNA

• 10-15% of the total RNA content of the cell (second most abundant).

• Carry specific amino acids to the ribosomes and decodes the genetic information in mRNA in terms of proper amino acid sequence.

Transfer RNA

Composition of Nucleic Acids:

carbon, hydrogen, oxygen, nitrogen, phosphorous

15-16%

Nitrogen

9-10%

Phosphorous

Nitrogenous – Base

Both

Isolated from the hydrolysates of nucleic acid (one ring).

Pyrimidine

Occurring in nature which are metabolic products in animals (two rings).

Purine

• Are derivatives of purines and pyrimidines that have a sugar linked to a ring nitrogen of a purine or pyrimidine.

• Nitrogenous base + sugar

Nucleosides

Common Nucleosides of RNA

Pyrimidine and Purine

Functional subunits of nucleic acids that are formed when 1 or more phosphate groups is attached to the 5′carbon.

Nucleotides

Is a chemical test that detects the presence of pentoses.

Bial’s Test

Each DNA strand has a sugar-phosphate chain backbone, with a nitrogenous base attached to each sugar that is indicated by the number of rings.

Test for Purine Base

The color of the final solution indicates the concentration of reducing sugar in the sample, with hotter colors indicating higher concentrations.

Benedict’s Test

A positive result for inorganic phosphate in a test is indicated by the formation of a bright yellow precipitate of ammonium phosphomolybdate.

Test for Inorganic Phosphate

bluish-green or bluish precipitate

Bial’s Test

presence of white salt precipitation

Test for Purine Base

Blue to blue-green or yellow-green

Negative

Yellowish to bright yellow

Moderate positive

Bright orange

Very strong positive