Bio 198 final

What are the different levels of protein structure? How does this relate to an enzyme and its ability to function?

Primary - sequence of amino acids

Secondary - alpha helices & beta sheets

Tertiary - full 3D shape of polypeptide

Quaternary - multiple polypeptides interacting

• function depends on shape of the active site. if structure changes, substrate won’t bind properly = loss of function

Understand the relationship between enzymes, substrates, and products

Enzyme binds a specific substrate at active site → forming enzyme-substrate complex → lowering activation energy (Ea) → substrate converted to products → products released → enzyme not consumed

What was the purpose of each of the reagents used in the experiment (Figure 5.1, lab #5)

Hydrogen Peroxide → substrate for peroxidase

Peroxidase → enzyme

Guaiacol → indicator (turns brown when oxidized → used to measure rate via absorbance)

pH buffer → keeps pH constant

water → adjusts volume/control variable

What are some environmental factors that can affect the structure of protein (enzyme)?

temperature

pH

substrate concentration

enzyme concentration

What does it mean if an enzyme is denatured? If the rate is low, does it always mean the enzyme was denatured? Why or why not?

denaturation - enzyme loses its 3D shape = no longer functions

low rate does not equal denature

• could be due to non optimum conditions (low substrate concentration, low temperature, incorrect pH)

Why is peroxidase important to living organisms?

breaks down hydrogen peroxide → protects cells from oxidative damage

How was the rate of the enzyme calculated in these experiments (lab 5)?

measured absorbance at 500 nm/time

What happened to the rate of peroxidase at different temperatures? Why?

rate increases with temperature due to more collisions

peaks at optimum temperature (around 37C)

decreases sharply at high temps (denaturation)

What happened to the rate of peroxidase when other conditions were varied? Why?

enzyme activity varies w/ pH

• optimal pH = highest rate

• too acidic or basic:

  • alters charge of amino acids

  • lowers rate

  • disrupts active site

• from data:

  • highest activity near neutral-ish pH

  • lower at extremes

What is the overall equation for cellular respiration?

C6H12O6 + 6O2 → 6H2O + 6CO2 + ~36 ATP

glucose is broken down using oxygen

Which organisms did you test? Why did we specifically test germinating peas for a plant example?

• Germinating peas (plants)

  • actively growing = high metabolic activity

  • undergoing rapid cell division

• Superworms (animals)

  • used to compare plant vs animal respiration

• germinating peas used bc higher respiration rate, no leaves = not photosynthesizing

What did you measure in order to determine the rate of respiration in these organisms?How were the rates calculated?

• measured CO2 concentration (ppm)/time

• used CO2 gas sensor

• rate = slope of CO2 vs time = CO2/time

  • then M.A.R. (mass adjusted rate) = rate/mass of organisms

Which gas was measured in the experiment? Was this gas produced or consumed in cellular respiration?

• measured CO2

• CO2 is produced during cellular respiration, comes from breakdown of glucose in Krebs cycle

How does the activity level of an organism correspond to the rate of cellular respiration?

• higher activity → higher respiration rate

  • more ATP needed → faster glucose breakdown

• lower activity → lower respiration rate

Know how to calculate the mass adjusted respiration rate(M.A.R.)of CO2 production and understand whyit was important to adjust for the massof the organisms.What are the units associated with M.A.R. for this lab

• Formula: M.A.R. = respiration rate/mass

• units: ppm/s/g

• why adjust for mass:

  • allows fair comparison between organisms of different sizes

  • bigger organisms naturally produce more CO2

What is the overall equation for photosynthesis?How do photosynthesis and cellular respiration relate to each other?

• 6CO2 + 6H2O + light → C6H12O6 + 6O2

• photosynthesis:

  • uses CO2 + H2O

  • produces glucose + O2

• Cellular respiration:

  • uses glucose + O2

  • produces CO2 + H2O

What organism did you test?How did you (experimentally) measure the rate of photosynthesis and cellular respiration for this organism?How did you calculate the rate of photosynthesisand cellular respiration?

• Organism: algae beads (Scenedesmus obliquus)

• measured: CO2 levels using pH indicator/absorbance at 550 nm

• rate calculation: slope of absorbance vs time (absorbance/time)

How does the pH of the CO2indicator solution correspond to photosynthesis/cellular respiration and the production or consumption of CO2?

• more CO2: more carbonic acid → lower pH

• less CO2: less acid → higher pH

• photosynthesis consumed CO2 (pH inc); respiration produces CO2 (pH dec)

What happened to the rate of CO2 consumption or production in the dark and in the light? Why?What did this column graph look like?

• light condition:

  • photosynthesis > respiration

  • CO2 decreases

  • pH increases

  • Absorbance changes in direction showing less CO2

• dark condition:

  • only respiration occurs

  • CO2 increases

  • pH decreases

  • absorbance reflects more CO2

• Graph:

  • light → downward CO2 trend/upward pH trend

  • dark → upward CO2 trend/downward pH trend

What happened to the rate of CO2consumption or production when other conditions were varied? Why? (Table 7.4)What did these column graphs look like?

• variables tested:

  • light intensity

  • light color (wavelength)

  • distance from light

  • temperature

• effects:

  • higher light intensity = higher photosynthesis rate

  • lower light = slower rate

  • different wavelengths

    • red & blue & white → highest photosyntheis

    • green → (reflected, not absorbed)

Know how to interpret an absorbance spectrum. Which colors of light are the best /worst for photosynthesis and why?(Figure 7.2)

• pigments absorb specific wavelengths:

  • chlorophyll a/b → absorb blue & red

  • reflect green

• best wavelengths:

  • blue (~450 nm)

  • red (~650-700 nm)

• worst:

  • green (~500-550 nm)

Be able to identify the different pigments (by name) that you observed using chromatography.Know which pigments are polar/nonpolar(and why/how do you know?)

• chlorophyll a → blue-green

  • polar (stayed lower)

• chlorophyll b → yellow-green

  • most polar

• xanthophyll → yellow

  • slightly polar

• carotene → orange

  • non polar (travel farther)

• reason:

  • chromatography separates based on polarity

  • nonpolar dissolves in solvent → moves farther

Know how to measure & calculate Rf

• formula: Rf = (distance pigment traveled/distance solvent traveled)

• range: between 0 & 1

• highest Rf = less polar

• lower Rf = more polar

Understand DNA replication, transcription and translation

Be able to apply the Watson-Crick complementary base-pairing rules for DNA replication and transcription

What are nucleic acids, nucleotides, bases, amino acids, and what are the relationships between these terms?

Understand how to use a codon chart for translation of mRNA to amino acids

What is RFLP? Why is it used

What is a restriction enzyme? How do RFLPs and restriction enzymes relate to each others?

How does agarose gel electrophoresis work?

Know how to interpret a gel that has undergone a restriction enzyme digest and electrophoresis (understand how DNA travels based on charge and size of fragment)

Understand how to solve sickle cell problems with Punnett squares

What is an ELISA, and what does ELISA stand for? Why is it used? What are some common applications of an ELISA test?

How does an ELISA work (what are the different components involved?)

What is the purpose of using positive and negative controlsin an ELISA test?

Why did we run the tests in triplicate?

What is an antigen? What is an antibody? How do they relate to each other and to an ELISA?

Why is there a primary and a secondary antibody? What is the purpose of each in an ELISA?

What is the purpose of the substrate in an ELISA test?

How are enzymes important to ELISA’s?

Understand how ABO & Rh blood typing work

What blood type is a universal donor? What blood type is a universal acceptor?

Understand how to solve blood typing problems with Punnett squares

Explain what '“optimum” means. Do all enzymes have the same optimum pH and temperature?

• condition where enzyme works fastest

• No, each enzyme has its own specific optimum pH & temperature

Why was a 10 minute incubation allowed for the temperature experiment?

• to let enzyme & substrate reach same temperature

• ensure accurate & consistent results

• prevents temp. fluctuations

What would the optimum pH for pepsin, an enzyme that breaks down protein in your stomach? Why?

• around pH 1-2 bc its adapted to function best in low pH conditions

An organism lives in a hot spring. What effect will placing it in cool water have on its enzymes? Do you think it will live? Why or why not?

• enzyme activity would slow down a lot & organism likely won’t survive bc metabolic processes would be too slow & reduce enzyme function

Why do you think you feel tired and lethargic when you have a high fever?

• high temp. disrupts enzyme function

• energy is used to fight infection

• body processes become less efficient

Germinating seeds are not mobile, and yet are producing CO2 gas as a result of aerobic cellular respiration. What cellular processes are they undergoing that require them to carry out aerobic cellular respiration?

• cell division

• protein synthesis

• growth & development

• breaking down stored nutrients

What is the anatomical structure through which CO2 is diffusing in the super worms? Is this the same structure used by terrestrial vertebrates? What about aquatic organisms?

• SW: diffuse through spiracles

• terrestrial vertebrates: use lungs

• aquatic organisms: use gills

Summarize the results of your inquiry experiment

• SW had higher CO2 production than GP

• both organisms showed increased CO2 production in experimental conditions

• SW had high variability

Other than the Calvin Cycle, what physiological process does a plant continue to perform, even when it is in the dark?

cellular respiration

Explain why lights for house plants are never green

• plants mainly absorb red & blue wavelengths for photosynthesis & chlorophyll reflects green light

How does cellular respiration impact the observed rate of photosynthesis? Is your calculated rate of photosynthesis accurate? Why or why not?

• cellular respiration uses O2 & releases CO2 which affects O2 produced during photosynthesis so calculated rate is not fully accurate for photosynthesis

The current pH of the ocean is 8.1. For the past 300 million years, the pH was 8.2. Consider what you just learned about algae and how the chemistry of the pH indicator used in these experiments. Hypothesize why oceans are at their current pH level.

• oceans are at their current pH level bc there’s more CO2 in the atmosphere that gets into the oceans which makes H2CO3 (carbonic acid) & algae can’t remove CO2 as fast

Think about how ocean pH is changing and why. How might this affect organisms that live in the ocean?

• coral reefs become unstable as it can affect survival, growth & reproduction

• can disrupt food chains & ecosystems

• may make it difficult for organisms to maintain hard structure-like shells