Terminology and Concepts in Experimental Biology and Molecular Biology, Quizzes of Cellular and Molecular Biology

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Manipulated Variable

The variable that is changed by the scientist in an experiment. TERM 2

Dependent Variable

DEFINITION 2 The variable that is measured in an experiment. TERM 3

Controlled Variable

DEFINITION 3 The variable that is kept constant during an experiment and is sometimes used as a tool for comparison. TERM 4

Positive Control

DEFINITION 4 An experiment whose result is already known to be positive.For example:In a PCR detection test it would typically be the amplification of a sample known to yield the correct result. TERM 5

Negative Control

DEFINITION 5 Experiment done with a mock sample that should normally yield a negative result.For example:Running a PCR reaction with water as a template.

Quantitative Assays

Actually measure the amount of substance in a sample. TERM 7

Qualitative Assays

DEFINITION 7 Detect the presenceof substance in a sample. Simply - is it there or not? TERM 8

SDS-page Assay

DEFINITION 8 Test for protein fingerprinting - profile of proteins present in a sample at a given time TERM 9

Biuret's Test

DEFINITION 9 Test for detection of proteins. TERM 10

Sudan III Test

DEFINITION 10 Test for detection of fats (lipids).

Iodine Test

Test for detection of starch (a carbohydrate) TERM 12

Benedict's Test

DEFINITION 12 Test for detection of reducing sugars (carbohydrates) TERM 13

Purpose of Laemmli Buffer

DEFINITION 13 Stabilization of the pH value within SDS-PAGE gels and electrophoresis buffers. TERM 14

Electrophoresis Marker Lane

DEFINITION 14 Used for separating molecule sizes in gel wells. Also used for showing band lengths of DNA fragments. TERM 15

Smaller vs. Larger Molecule Migration in SDS-

PAGE

DEFINITION 15 Smaller molecules move more quickly through the pores of the electrophoresis gel than the larger molecules and thus travel farther down the marker lanes.

Percent Commonality

Equation

%C = (# protein bands in common) total # of protein bands in 2 samples - # protein bands in common above result multiplied by 100 TERM 17

Nomenclature for

Spectrophotometry

DEFINITION 17 A - absorbanceOD - optical densityL - wavelength TERM 18

A(max)

DEFINITION 18 Wavelength most efficiently absorbed by the compound in question. TERM 19

Beer's Law

DEFINITION 19 This law states that the absorbance of a substance is directly proportional to its concentration insolution. A = lc = the extinction coefficient of the substance, has units of M1 * cm1 (this is a constant, unique foreach substance) l = the sample path length measured in centimeters (i.e., the width of the cuvettealmost always 1cm) c = the molar concentration of the solution (you must express concentration in terms of molarity) TERM 20

CiVi = CfVf

DEFINITION 20 CiVi = CfVfWhere:Ci = initial concentration of sample you want to diluteVi = initial volume of sample usedVd = volume of diluentCf = final concentration of diluted sampleVf = final (total)volume in the tubeVf = Vd + Vi(See Appendix D for more information)

"X"

Solutions

The working concentration of a reagent or buffer is by definition "1X". So if a concentration is labeled as "10X" then that means that the reagent or buffer concentration is at ten times the working concentration. TERM 22

Enzymes

DEFINITION 22 _____ are affected by certain environmental conditions including temperature and pH levels.At optimal pH levels they form the 3D conformation that allows for efficient substrate binding and catalysis. Otherwise they will denature and lose efficiency.At optimal temperature levels they react faster. TERM 23

Signal Transduction

DEFINITION 23 ___________ occurs when an extracellular signaling molecule activates a cell surface receptor. TERM 24

Four Stages of Signal Transduction

DEFINITION 24

1. Signaling molecule activates its receptor2) The receptor carries the signal into the cell3) The signal travels through the cell and interacts with other receptors4) The receptors activate the responses within the cell and exhibit the signal's results TERM 25

Ligand

DEFINITION 25 Signal triggering molecule that binds to a site on a target protein.

G-protein couple receptors and Tyrosine

Kinases

These play large roles in Signal Transduction by carrying signals through the process._____________ are inactive until bonded with a ligand and then pass the signal from the ligand through the signal transduction pathway._____________ form dimers to help transfer the signal through the pathway. TERM 27

Kinase Cascades

DEFINITION 27 These are pathways of many connected intracellular signals.The multiple steps in these amplify the original signal.This also allows for different responses depending on the absence of presence of targeting proteins. TERM 28

Second Messengers

DEFINITION 28 ________ _________ are molecules that relay signals from receptors on the cell surface to target molecules inside the cell, in the cytoplasm or nucleus. Some examples include: cyclic AMP (derived from adenosine triphosphate) and IP3 (soluble and diffuses through the cell) TERM 29

PCR

DEFINITION 29 ________ ____________ ___________is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.It can be used to transfer PGlo+ to new cells and generate colonies that exhibit the characteristics of PGlo+ (they will glow under black light). TERM 30

Three Steps of a PCR Cycle

DEFINITION 30 Denaturation: occurs at 95C,the hydrogen bond between the twocomplementary strands melt, unraveling the DNA molecule and exposing the nucleotide bases. Annealing: occurs at 57Callowing binding (annealing) of the primers to their complementary targets on the DNA template Elongation: occurs at 72C,Taq will bind to each DNA strand and extend from the priming sites (add nucleotides tosynthesize a complementary strand of the targeted DNA).

Taq polymerase

This is used instead of a normal DNA polymerase because it can withstand high temperatures after being collected from a Hot Spring. TERM 32

Lateral Transfer of Genes

DEFINITION 32 This occurs when genes are incorporated from one organism by another that is NOT the offspring of that organism.In contrast with Vertical transfer which is the incorporation of genes from an ancestor.Type of this used in lab - TERM 33

Plasmids

DEFINITION 33 DNA material that is not connected with the actual DNA chromosomes. These can also replicate by themselves and are often useful in lateral transfer of genes. Bacterial organisms often have these, but some eukaryotic organisms have also shown them. TERM 34

Reasons for adding Loading Dye

DEFINITION 34

1. Allows you to visual your samples2) Makes it easier to get the sample into the well and not let it float away3) Serves as a dye-front to determine when you need to stop the electrophoresis process (you can see when the dye gets to the positive end of the gel and thus you need not go further)