Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
128 Cards in this Set
- Front
- Back
|
Ecology |
Interactions of an organism with other organisms in the environment |
|
|
Mutualism |
Both organisms benefit |
|
|
Commensionalism |
One benefits, one unaffected |
|
|
Predation/Parasitism |
One benefits, one harmed |
|
|
Neutralism |
Doesn't really exist in the real world. Neither orgainsm effected by presence of the other. |
|
|
Amensalism |
One harmed, one no effect |
|
|
Competition |
Both harmed Reduces the growth, survival, or reproduction Ex: ants and rodents that eat same seeds |
|
|
What are the two types of competition? |
1. Intra-specific = within the species (among members of the same species). 2. Inter-specifi = between species |
|
|
Who is the winner in competition? |
No winner. Only a loser and a bigger loser
|
|
|
What causes competition? |
Limiting resources. (Food, water, light, nesting space, pollinator) |
|
|
What happens when there is more intraspecific competition than interspecific? |
More species can coexist |
|
|
Competitive Exclusion Principle |
two species cannot live together in the same place at the same time if they are both limited by one or more of the same limiting resources. The superior competitor will always win |
|
|
Theory of Limiting Similarity |
species that are too similar (niche overlap too much) cannot coexist |
|
|
4 Resons so many different species survive in nature |
1. Resource partitioning 2. Temporal and spacial patchiness 3. Factors that keep populations small 4. Changes in environmental conditions
|
|
|
Resource partitioning |
inferior competitors for one resource may switch to another (less ideal) resources, lessening the competition |
|
|
Temporal and spacial pathchiness |
the best competitior may not always find the resources, or the inferior competitor may be able to use them for a time before found |
|
|
What are some factors that keep populations small? |
Predators, disease, weather |
|
|
In ecology lab, what can happen when you add 50 seeds (vs only 25)? |
Intraspecific competition between seeds of the same type. Limiting resources and space |
|
|
In ecology lab, what can happen when you add 25 seeds of a different type to a filled pot (vs. only the filled pot)? |
Interspecific competition. |
|
|
What are 2 important properties that distingish chemical processes as they occur in organisms? |
1. Chemical reactions are slower in living things 2. Chemical reactions proceed in steps |
|
|
Why are chemical reactions more slow in living things? |
Temperature, pressure that the organism lives in can affect reaction rate |
|
|
What are enzymes made of? |
They are proteins, so they are made of chains of amino acids that assemble into peptides. |
|
|
What is the catalytic region of the enzyme called? |
Active site (where the substrate binds, reaction takes place) |
|
|
Cofactors |
Usually metal ions. Must be present (along with enzyme and substrate) for the reaction to proceed at a rapid rate. Bind to and form part of the active site |
|
|
What are 3 common factors that affect enzyme (protein) conformation? |
1. Temperature 2. pH 3. Ionic composition of the solution |
|
|
Substrate |
The reactants of an enzyme-catalyzed reaction |
|
|
How do enzymes speed up chemical reactions? |
They lower the activation energy by increasing the number of interactions between the reactants |
|
|
Enzyme substrate complex |
When the reaction occurs |
|
|
2 reasons a low concentration of enzyme catalyze a reaction at a rapid rate? |
1. Enzyme is not consumed after one reaction 2. Breakdown of enzyme-substrate complex is extremely rapid |
|
|
Enzyme activity |
The rate of an enzyme catalyzed reaction per quantity of enzyme (rate per weight) |
|
|
How do you measure the rate of the reaction? |
Change in concentration of a reactant over a preiod of time. Measured as either substrate disappearance, or product formation over time |
|
|
5 things enzyme activity is affected by |
1. Concentration of enzyme 2. Concentration of Substrate 3. Concentrationof product 4. Conformation of the enzyme 5. Presence of inhibitors |
|
|
In general, rates of reactions increease with increases in... (2) |
1. Concentration of enzyme 2. Concentration of substrate |
|
|
Inhibitors |
Chemicals that decrease the rate of an enzymatic reaction |
|
|
Percent Inhibition |
Percent drop in enzyme activity in the presence of an inhibitor |
|
|
Equation for percent inhibition |
(rate without inhibitor) - (rate with inhibitor) _____________________________________________ (rate without inhibitor) |
|
|
Percent inhibition may be changed by... (2) |
1. Addition of substrate 2. Addition of enzyme |
|
|
Competitive Inhibitors |
Molecular structures resemble that of the substrate. Bind to the active site, block substrate from doing so temporarily. |
|
|
The rate of a reaction in the presence of a competitive inhibitor depends on... (2) |
1. Concentration of inhibitor 2. Concentration of substrate NOT concentration of enzyme |
|
|
During competitive inhibition, as substrate concentrations increase, percent inhibition __________. |
decreases. In competitive inhibition, percent inhibition depends on substrate concentration. |
|
|
Noncompetitive inhibitors |
Do not bind to active site. Reduce the ability of the enzyme to bind to the substrate |
|
|
3 ways a noncompetitive inhibitor can affect enzyme activity |
1. Remove a necessary cofactor 2. Bind to enzyme (not at active site) and reduce the "flexibility" of the enzyme 3. Change the shape of enzyme |
|
|
Non competitive inhibition depends on... (2) |
1. Concentration of enzyme 2. Concentration of inhibitor NOT substrate concentration |
|
|
Which type of inhibitors have a percent inhibition that remains constant? |
Non competitive |
|
|
2 other names for Polyphenol Oxidase |
1. Tyrosinase 2. Catechol oxidase |
|
|
What are the tubers of a potato? |
The asexual reproductive structures of the potato. Parent plant stores resources in tubers, which can allow for sprouting |
|
|
What is the product of a polyphenol oxidase catalyzed reaction with catechol? |
Orthoquinone |
|
|
3 ways a potato can protect the starch near its surface |
1. Mechanical barriers (skin) 2. Production of distasteful chemicals 3. Ability to seal off bruising on the surface |
|
|
Why do potatos produce orthoquinone? |
It is toxic to a variety of microbes and insect |
|
|
How might potatoes adapt to maximize individual fitess in their environment? |
Regulation of polyphenoloxidase activity in response to predators |
|
|
On the surface, polyphenol oxidase is responsible for... (2) |
1. Darkening that occurs when freshly peeled potatoes or fruit stand in air 2. Tanning of skin in response to sunlight |
|
|
What actually happens to catechol in the enzyme catalyzed reaction? |
It becomes oxidized. Oxygen is consumed by catechol to produce benzoquinone, which then condenses to orthoquinone |
|
|
What is an example of a secondary metabolite, and what do senconday metabolites do? |
1. Orthoquinone 2. Important only for interactions between the plant and other organisms. Sometimes can produce odors, flavors, and pigments. |
|
|
Homogenate |
suspension of broken cells that contain enzyme |
|
|
In our homogenization, after centrifugion what are contained in the two layers? |
1. Top layer = supernatant = enzyme 2. Bottom layer (heavier particles) = solid pellet = unruptured cells, cell walls, large organelles |
|
|
Spectrophotometric methods depend on... |
mathematical relationship between concentration of a substance and the amount of light it absorbs |
|
|
When using the spectrophotometer, the rate of the reaction is shown by.. |
the slope of the line formed when results are plotted against time |
|
|
Serial dilution |
continuously creating solutions that are diltued to half the concentration of the solution before it |
|
|
Absorbance Units (AU) |
the amount of light absrobed at a particular wavelength, which is in turn proportional to the number of colored molecules presencce |
|
|
Potassium arsenite |
potential noncompetitive inhibitor. Reacts with sulfhydryl groups in protein and disrupts three dimensional structure. |
|
|
Para-hydrobenzoic acid |
potential competitive inhibitor. Mimics chemical structure of the substrate (catechol) |
|
|
Chleating agent |
compounds that bind tightly to metal ions. (Metal ions are usually cofactors) |
|
|
phenolthiourea (PTU) |
reacts with copper, will steal copper cofactor from active site of enzyme |
|
|
potassium cyanide |
reacts with both copper and iron, will steal both copper and iron from active site of enzyme |
|
|
Why can salt concentration affect reaction rate? |
ions in solution destabalize ionic bonds that hold the enzyme in its probper conformation |
|
|
In a simple (nonenzye) chemical reaction, when you double reactants, what happens to reaction rate? |
double reaction rate |
|
|
In an enzyme catalyzed reaction, when you double reactants, does reaction rate double? |
Not necessarily. Reaction rate depends on substrate AND enzyme concentrations (whichever is limiting) |
|
|
What does negative free energy indicate? -deltaG |
energy is released in the reaction. products are lower in energy than reactants were. Most enzyme catalyzed reactions have -deltaG |
|
|
Vmax |
maximum rate of the reaction. enzyme is saturated with reactant |
|
|
Km |
substrate concentration at which reaction rate is half of maximum. measure of affinity of the enzyme for the substrate |
|
|
What 3 things will cause Km to vary? |
1. temperature 2. pH 3. presence of inhibitors |
|
|
The lower the Km, the more likely an enzyme.. (2) |
is operating at its Vmax has a strong affinity for the substrate |
|
|
What happens to Vmax during competitive inhibition (vs without competitive inhibition)? |
stays constant |
|
|
What happens to Km during competitive inhibition (vs without competitive inhibition)? |
Km will be higher, because it takes more substrate to get same rate of product formation (or, to get same amount of active sites filled with substrate) |
|
|
What happens to Vmax during noncompetitive inhibition (vs without noncompetitive inhibition)? |
Vmax decreases, because there are less active sites that can hold substrate, because changes in the enzyme's shape alter the active site |
|
|
What happens to Km during noncompetitive inhibition (vs without noncompetitive inhibition)? |
May or may not change. Depends if substrate binding is affected. |
|
|
During _________inhibition, inhibitior is equally effective at all substrate concentrations. |
noncompetitive |
|
|
Which kinds of inhibitors can be reversible or irreversible? |
noncompetitive |
|
|
If % inhibition at high substrate is greater than % inhibition at low substrate, then inhibitor is.... |
competitive |
|
|
If % inhibition at high substrate is = % inhibition at low substrate, then inhibitor is... |
noncompetitive |
|
|
Ethylenediaminetetraacetic acid (EDTA) |
reacts with iron or copper cofactors (if present) |
|
|
Citric Acid |
reacts with iron or copper cofactors (if present) |
|
|
What are the two plasmids we used? |
pGLO and pGEM-3Z |
|
|
Gene |
a length of DNA that codes for a biologically useful product. a subset of a chromosome. product is usually a protein but can be RNA |
|
|
Plasmid |
extra-chromosomal genetic elements. double stranded circular DNA. replicate without chromosomal control (allows for amplification). carry nonessential genes. can be natural or engineered. cause cells to be resistant to antibiotics. |
|
|
what is an ori? |
origin of replication, a region of plasmid DNA where proteins bind to initiate DNA replication (needed to make more copies of the plasmid in cells) |
|
|
what does pGLO carry? |
3 genes and an ori 1. GFP 2. araC 3. Bla |
|
|
what is Bla? |
beta-lactamase, an enzyme that breaks down ampicillin and makes plasmid-bearing cells antibiotic resistant |
|
|
what is araC? |
a regulatory protein, links GFP expression to presence of arabinose |
|
|
what is GPF? |
green fluorescent protein, the gene we are trying to clone |
|
|
what do araC genes produce? |
araBAD |
|
|
what do araBAD genes do? |
metabolize arabinose (sugar) |
|
|
what causes araC activation? |
araBAD genes, which have metabolized arabinose Note: araBAD genes are regulated by araC |
|
|
what turns on GFP production? |
metabolized arabinose |
|
|
what are the steps of PCR? |
1. Denaturation with heat 2. Annealing cooling 3. Extension |
|
|
Why do we heat DNA during PCR? (95 degrees C) |
heat briefly separates DNA strands Note: DNA polymerase must be heat resistant (taq) |
|
|
4 things needed for PCR |
1. DNA template (pGLO) 2. Synthetic primers (upsteam and downstream from GFP gene) 3. Heat resistant DNA polymerase 4. Nucleoside triphosphates
|
|
|
Why do we cool and annealate during PCR? |
to allow primers to form hydrogen bonds with the template strands of ss-DNA |
|
|
What happens during extension in PCR? |
allow polymerase to extend primers, nucleotides added to 3' end of primers (72 degrees C) |
|
|
what instrument allows PCR to be repeated 25-30 times, resulting in a billion fold increase in source DNA? |
thermocycler |
|
|
during transformation, what are the component cells? |
HB101 cells |
|
|
what are the vectors during genetic engineering? |
plasmids |
|
|
what does genetic engineering require? |
enyzmes to cut and paste, and a carrying vector for cloned DNA |
|
|
what are the purposes of genetic engineering? |
study the gene, move and join pieces of DNA, purification of protein, altercation of organisms. allows scientists to multiply, modify, and move genes |
|
|
what are restriction endonucleases? |
Bacterial proteins which bind DNA at a specific site and cleave a phosphodiester bond between nucleotides
|
|
|
what is the natural function of restriction endonucleases/emzymes? |
defense against bacteriophages |
|
|
what is the natrual function of DNA ligase? |
Normally joins Okazaki fragments during DNA replication |
|
|
why are we using DNA ligase? |
to join two restriction fragments (recreates phosphodiester bonds) |
|
|
what is a vector? |
things with an ori/YAC (replication controller) allows amplification of template DNA ex) plasmid, disabled virus |
|
|
what is recombinant DNA |
the DNA we create after genetic engineering |
|
|
if you place DNA in an electrode, it will move towards the _________ charged end, because it is ____________charged. |
1. positive 2. negatively |
|
|
What type of fragments move faster during DNA electrophoresis? |
smaller. rate is related to size/length |
|
|
what is DNA stained with in electrophoresis? |
ethidium bromide (EtBr) |
|
|
which restriction enzyme do we cut our DNA with? |
XBaI (cuts plasmid vector) |
|
|
during "cleaning" why do we heat shock? |
to prevent the restriction enzymes from cutting, allowing the ligase to take over |
|
|
what are the 6 steps of cloning? |
1. isolate DNA of interest, amplify 2. cut source DNA and plasmid vector with restriction enzyme 3. run digests on gel to confirm siize and concentration 4. mix source and vector, ligate 5. transform recombinant plasmids into bacteria 6. select for desired phenotype |
|
|
what are two resistances plasmids can contain genes for? |
ampicillin or tetracycline resistance |
|
|
what do polymerases do? |
assemble nucleotides to strands of severed DNA |
|
|
what is a primer? |
something that binds to a specific location on the severed DNA. This is where polymerase will begin to add nucleotides. |
|
|
we substitute helicase for heat in PCR. What does helicase normally do? |
severs strands of DNA |
|
|
what are 3 advantages of PCR? |
1. ability to amplify tiny amounts of DNA 2. ability to amplify a particular region of source DNA defined by primers chosen 3. speed |
|
|
why do we use restriction enzymes? |
to cut our very long lengths of DNA into much smaller ones - small enough that they can bind to a plasmid. Leaves the DNA with staggered ends that can have new nucleotides add |
|
|
XbaI cuts on the ___' side of a DNA strand |
3 |
|
|
what is DNA transformation? |
when new DNA is taken up by bacteria, then the bacteria begin showing new phenotypes |
|
|
which 2 chemicals can alter the permeability of a cell membrane? |
MgCl2 and CaCl2 |
|
|
during screening of our product, how will we know if we were successful in moving gfp? |
our successful products will glow |
|
|
which 2 steps of genetic engineering can be inefficient? |
1. restriction/ligation process - few of the millions of pieces of cut DNA will come together to form the desired plasmid 2. transformation - only a fraction of the cells exposed to the ligation mixture will take up and DNA |
|
|
how do we screen for cells that have in fact taken up the desired plasmid after the ligation mixture? |
use a cloning vector (our plasmid pGEM) that can survive where other cells cannot. pGEM carries a gene that is resistant to ampicillin. So if we allow our products to live on ampicillin, only the cells that have taken up our plasmid (pGEM) will exist PLUS they should glow green (if they have taken the gfp gene from our template DNA) |
