Bio Lab Investigation Exam

what is science?

science is a process of discovery that allows us to connect isolated facts into a coherent and comprehensive understanding of our world and the universe

why is science important?

Scientific knowledge can improve the quality of life at many different levels

what are some limits of science?

• doesn’t make moral judgments

• doesn’t make aesthetic judgments

• decisions about the applications

• conclusion about the supernatural

what is an experiment?

a procedure carried out to make a discovery, test and hypothesis or demonstrate a known fact

what is discrimination when referring to a experiment?

an experiment should be able to clearly discriminate between different hypothesis

what is replication when referring to an experiment?

experiments must be repeated enough times for the results to be analyzed statistically

what is controls when referring to the experiment?

normal biological variation, research bias, and environmental variation are all factors that can skew results; therefor, scientific control groups provide a reliable baseline to compare the results with

positive control

this group is expected to have result that shows that the procedure is working and capable of producing results

negative control

this control makes sure that non confounding variable has affected the results

what is accuracy in experiment measurement?

how close a measurement is to the true value

what is precision in experiment measurement?

how close repeated measurement are to each other

what are the steps in the scientific method?

1. observations of a phenomenon

2. parking questions

3. forming a hypothesis

4. a prediction

5. conducting experiments

6. conclusion

hypothesis

is a proposed explanation for a observed phenomenon, not a guess, must be testable, not and if… then statement

when making a hypothesis, consider:

• testability

• parsimony

• scope

• fruitfulness

• conservation

null hypothesis

assumes no relationship between the independent and dependent variables

alternative hypothesis

proposes that the observation are the result of a real effect

primary structure

an amino acid sequence that gives a protein its genetic information it codes for

secondary structure

a protein’s structure is its ability to form hydrogen bonds between the amine hydrogen and carboxyl oxygen atoms contained in the backbone of the peptide

tertiary structure

each unique polypeptide folds up into a uniquely 3D shape by virtue of interactions between amino acids and interactions in environment

reactions that stabilize tertiary and quaternary structures

• ionic bond

• disulfide bridge

• hydrophobic interactions

• van der waals

• hydrogen bonds

quaternary structure

associations between separate polypeptides that the environment factors have an effect in (pH and temp)

proteins functions

• catalytic activity

• structural support

• storage

• transport

• cellular communications

• movement

• defense against foreign substance

solution

homogeneous mixture composed of two or more substances

solvent

substance that makes up most of the solution

solute

what the solvent dissolves

concentration

refers to the amount of solute per unit of solution

spectrophotometry

a method of assessing concentrations of solutes, which takes advantages of the light-absorbing properties

spectrophotometer

instrument that lets you make such a measurement of light absorbance

Beer’s law

states that absorbance is directly proportional to the solute concentration

enzymes

catalysts used to speed up the rate of the reaction by binding temporarily to the potential reactants

amylase

an enzyme that catalyze the hydrolysis of starch into sugars

three categories of amylase

• alpha

• beta

• gamma

alpha amylase

found in some animals, plants, fungi and some bacteria. present in saliva and aids in the digestion process of starchy foods

beta amylase

mostly found in bacteria, fungi, and plants

gamma amylase

is found in animals and some bacteria

reaction

a process in which chemical bonds are made or broken

rate calculating

mg starch reduced/ time

when are enzymes are saturated

when they reach the V max

standard deviation

measure of how dispersed the data is in relation to the mean

standard error

allows for two samples sets to be compared

t-test

statistical test used to determine whether there is a different between two independent groups

what are some aspects of scientific investigation?

• science is empirical

• it exposes wrong explanations

• advances through disproof

• “the pursuit of ignorance”

inductive reasoning

is logically uncertain: if the assertions are true, the conclusion may follow

deductive reasoning

is logically definite: if the assertions are true, the conclusion must follow

what is the process of science?

1. observations are made about phenomenon

2. these observations spark questions

3. a testable hypothesis is formed to explain observations

4. a prediction is developed based on hypothesis

5. hypothesis is tested by conducting experiments

6. based on data collected, a conclusion about the hypothesis is drawn

principle of parsimony/ Occam’s razor

states that the simplest explanations are the ones that are usually correct

scientific theories

well-confirmed explanation brough together via inductive reasoning

what are termites?

• insect in order Isoptera

• help recycle dead wood

• colonies be up to 12 million

• consists of 3 castes

termites workers

• wingless, sterile and blind

• males and females

• clear bodies

termite soldiers

• wingless, sterile and blind

• males and females

• only one that has like hrons

termites reproductives / alates or swarmers

have wings to find a mate and once they do they drop their wings

genotoxic

ability of chemical to damage genetic information may lead to mutations, which may lead to cancer

mutation

a change in the sequence of DNA

serial dilutions

used to reduce the concentration of a sample

what is a lawn in a serial dilution?

uncontrolled growth

what are the colonies in a serial dilution?

many piles of bacterial cells originating from one cell

CFU

colonies forming units= # of colonies X reciprocal of dilution factor/ volume plated in mL

culture media

contains all the elements that most bacterial need for growth. used for the general cultivation and maintenance of bacteria

minimal media

a defined media that has just enough ingredients to support growth. used to select for or against certain microorganisms

selective media

contains or lacks a specific component that is needed to survive in the media used to separate microorganisms from others (LB with ampicillin and HIS-media)

differential or indictor media

distinguishes one microorganism from another growing on the same medium. uses biochemical characteristics of microorganisms as an indictor of their presence (blood agar, eosin methylene blue, mannitol salt agar)

point mutations

chemical changes in just one base pair of gene

frameshift

the insertion or deletion of nucleotides into a DNA sequences un numbers that are not multiples of three, disrupting the normal reading frame of the genetic code

Ames test

a test for gene mutation, measures the ability of a chemical to induce back mutations (reversions) of an auxotroph to its original state

what does the Ames test detect?

• detects frame shifts and base substitutions

• the greater number of revenant colonies, the more mutagenic the test substance must be

• positive results indicate the chemical is mutagenic

Salmonella typhimurium

genetically modified to be significantly less virulent, pathogenic bacteria, auxotrophic for histidine, will be added to medium with a small amount of histidine: which allows it to complete several rounds of replication until it runs out

phototroph

wild type, can make its own nutrients, able to grow on minimal media

auxotroph

mutant, can not produce essential nutrients, can only grow on minimal media

what is the purpose of the histamine in the top agar?

to allow for a few DNA replication cycles to occur, allowing for the compound to introduce mutations

how does bacteria grow?

binary fission

how to know if it is genotoxic?

• reversion frequency

• if reversion frequency is similar to the negative control= not genotoxic

• if the test product is 5 times higher than the negative control= genotoxic

reversion frequency

number of revertant colonies per mL / total number o CFU per ml of overnight culture

what are some limitations of genotoxic/ Ames test?

• rate of mutagenicity is not the same in all organisms

• sometimes the actual compound is not mutagenic but the metabolites are

• thus a positive test in the ames test is subject to further testing before being labeled as carcinogenic

what are the sources of DNA in a cell?

chromosomal and extrachronosonal

chromosomal DNA

• contains essential genes

• double stranded

• linear or circular

• found in nucleus or neculoids

extrachromosomal

plasmids- circular, double stranded, contain non-essential benefits genes for the cell, like antibiotic resistance

isolation process/ Polymerase Chain Reaction (PCR)

• template: bacterial DNA

• nucleotides are just commercially available

• cofactors: maganism ions are necessary for the functioning for the enzymes

• Thermal cycler: programmed to alter the temperature o the reaction ever few mins to allow DNA denaturation and synthesis

• buffers: provide appropriate pH and cofactors needed

what are the processes of PCR?

1. denaturation

2. annealing

3. extension

denaturation

heating up DNA strands to make them separate

annealing

primer binds to the strand specific for hisG gene

Extension

Taq polymerase synthesizes a new strand of DNA

what does the % of agarose do in the gel electrophoresis?

determines the separate resolution; a higher percentage of agarose will resolve smaller DNA molecules and vice versa

what does the loading dye do in the gel electrophoresis?

provides weight and monitors the migration of the sample

what does the SB buffer do in the gel electrophoresis?

• low conductivity buffer which allows gels to be ran at higher voltages to speed the process up without compromising resolution

• without the buffer, DNA can lose its negative charge

what does the agarose gel do in the gel electrophoresis?

stabilize medium used for the electrophoretic separation of nucleic acids

electrophoresis

movement of charged particles in solution under influence of an electric field

BLAST

basic local alignment search tool, a computer program that aligns sequences based on similarity

true reversion

reversion by removal of the original insertion

second-site reversion

reversion by removal of another base

steps for mark and recapture

1. catch and mark a random sample (M)

   1. number marked represents some fraction of the total population (N)

2. set the animals free to re-mix

3. catch and count another random sample (C) and determine how many of them are recaptured animals (R)

standard deviation

a measure of the dispersion the data exhibit around the mean

biodiversity

is the level of variety that exists in a biological system usually refers to variety o species

biological insurance

when one component fails, others will take its place

higher production leads to higher biodiversity lead to greater complexity=

greater stability and resiliency

two measures of species biodiversity

1. species richness- number of different species

2. species evenness- degrees o similarity in the relative abundance o those species

biodiversity index

attempts to quantity biodiversity according to a scale

Shannon-Wiener Index H

indicates degree of uncertainty inherent in predicting what the species of a given individual picked at random from a community is like to be

statistics

field of math that involves using sample measurement to accurately infer truths about the larger population they came from

descriptive statistics

quantify the likely true population characterizes based in the observed sample characteristics and sample size