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Case Study 1: Picture
Perfect
Summer Assignment 2014
Miss Albu AP Bio
Starch vs. Cellulose
(Structure & Function)
 Starch: storage carb (glucose monomers)
 Amylose: monomers joined by 1-4 linkages
 Amylopectin: branched polymer: 1-4 linkages AND 1-6
which give it slant and branch
 Cellulose:
 Structural: plant cell walls
 Glucose monomers but glycosidic linkages different from
starch (covalent btw two monomers). B configurations.
 Every glucose upside down in relation to others
 Can form hydrogen bonds with parallel cellulose molecules=
formation of STRONG fibers
Q
3
Hydrolytic Enzyme: Amylase
 Breaks apart starch by adding H2O molecule to break
1-4 glycosidic linkages.
 H atom added to one monomer and OH molecule to other
Q
5
Amylose vs. Amylopectin
 Amylose is made of glucose bound together in 1-4
glycosidic linkages.
 Amylopectin has these BUT also 1-6 glycosidic
linkages which are NOT broken down by amylase
 Amylopectin only partially degraded by amylase
Q
6
Amylase Cleaning Damage?
 Amylase has a specificity for a configuration (1-4
glycosidic linkages)
 Cellulose (cotton) consists of B linkages and therefore
NOT a substrate of Amylase.
7
IKI & Benedict’s
 Iodine Potassium Indicator (IKI) is a test for starch
 Benedict’s: for maltose
 Maltose alone: positive
 Starch & Amylase: positive b/c amylase broke down
starch into maltose
Why Iodine added to 1A & 3A? To test effectiveness of
iodine solution: iodine + amylase should not have led to blue
color
3/4
Removing Wallpaper
 Amylase breaks down the starch in wallpaper paste by
breaking down the 1-4 glycosidic linkages
 Because vinegar is an acid, it slightly hydrolyzes
starch, results only in small clear area
 H20 is solvent for potential removers (control). Alone
cannot break down starch as well as other products
1/2
Corn vs. Potato Granules
 Corn granules
 Smaller than potato granules, angluar, irregularly shaped
 Potatoes: smoother, sphere/oval shaped
 Most likely scraped off potatoes granules since described
as being 75um
1/2
Gelatinization
 Granules of starch swell up, break up, and disperse in
water
 surface: amylopectin & amylose molecules tightly
together (hydrogen bonding).
 H2O doesn’t easily penetrate granule
1) Water moves slowly though channels & forms H bonds with
amylose and amylopectin in center of granule
2) Bonding (H w/Amylose or Amylopectin) on adjacent
granules causes clumping
3) Amylose unbranched= can easily move through channels
more quickly than amylopectin
Heating past boiling point causes swollen granules to break into
fragments, and release all of starch molecules into water=
thinning of gravy
Cooking Problems
 Didn’t stir? Cornstarch granules swelled, amylose
molecules leaked out of center and adhered to each
other since you didn’t stir = GEL
 Overheating of potatoes: broke potato granules into
fragments: starch molecules dispersed in water=
potatoes thin and watery
Starches in Commercial
Prodcuts
 Cornstarch products: corn syrup
 Dent cornstarch 80% amylopectin, 20%amylose [low cost]
 Adhere to surfaces, form rigid layers as cooked
 Production of wallpaper paste (amylose-hydrogen bonds to
cellulose and hardens)
 Jelly bean outer coating
 Waxy cornstarch (amylopectin only): pours more easily [more
expensive]
 Hot chocolate mixes
 Modified waxy starches cross-linked with amylose or amylose
and amlyopectin (gravy & stew)
 Amylomaize: 70% amylose, 30% amylopectin: biodegradable
packaging
 Glues
 Dry starches (baby powder)
Industrial examples
 Instant Cheesecake Mix:
 C: Modified Waxy Starch
 Retains granular structure
 Produces more stable mixture with higher viscosity due to
cross-linking
Soup: Waxy (B). Needs to be poured easily (only
Amylopectin)
Batter & breading (adhere to chicken)
A) Dent because amylose is present enabling strach to stick
to chicken through hydrogen bonding
Case Study 2: Bean Brew
 Fermentation
 Glycolysis
 Enzyme Actions
 Osmosis
Enzyme- Substrate Complex
 Enzymes: proteins
 Contain groove= active site
 Area of enzyme that binds specific substrate
 When substrates are in active site, enzyme undergoes
conformational change
 Conformational change brings chemical groups of active site into
position to enhance their ability to catalyze reaction
 When reaction complete, resulting molecules released and
enzyme takes on previous conformation for next reaction
Q A1
Enzymes lower activation
energy & Speed up reaction
 Increases CHANCE of collisions
 Active site= template to help 2 or more reactants
become oriented favorably for reactions
 Stretch substrate molecules towards transition-state
conformation, stressing critical chemical bonds
(reduced free energy that must be absorbed for
transition state)
 Active site AAs can provide more favorable
environment (ex. pH) [Does not change pH]
Q
Breaking Down Macromolecules
1) Enzyme holds substrate so bond btw 2 building blocks
of macromolecule is exposed to H2O
2) Bond broken
3) Add H20 to bond giving H to one side and OH to other
In proteins: H added to amino side of bond and –
OH added to carboxyl side of bond
2
Isomers and Isomerase
 Isomerases facilitate transformation of one type of
isomer to another
 Isomer = compound with same molecular formula but
different structure (therefore diff properties)
3b
Aldolase p.162
 Cleaves sugar (fructose-1, 6-bisphosphate) molecule
into 2 diff 3-Carbon sugars:
 Glyceraldehyde-3-phosphate
 Dihydroxyacetone phosphate
With inhibitor this splitting wouldn’t occur  neither would
the subsequent reactions of glycolysis be likely to occur
Q
Osmosis
 Koji: breakdown of macromolecules into monomers
 Moromi: mixing koji w/water and lots of salt (brine)
Osmosis: movement of water
Higher salt concentration outside and lower water
concentration. Cell has lower salt and and higher water
compared to outside.
Outside is hypertonic (higher solute concentration
compared to inside) Therefore water will move from high
to low concentration. Cell will shrivel.
1
Fermentation
 Facultative Anaerobes
or microbes that are
always anaerobes
(produce ATP in
absence of O2)
1) Fermentation:
glycolysis produces
ATP.
2) Fermentation cycle
continues when
pyruvate is reduced
by NADH
3) Without NAD+
fermentation will stop
3 Q
Lactic Acid Fermentation &
Alcohol Fermentation
Pyruvate (3H) reduced by NADH
to lactate (5H)
Pyruvate (3H) converted to
acetylaldehyde (3H). Acetylaldehyde
(3H) reduced to ethanol (6H).
Lactate oxidized: gives e-’s to NAD+
Ethanol oxidized: gives e-’s to NAD+
Lactic Acid Fermentation
Alcohol Fermentation
Q 4
Removing alcohol
 Because high alcohol levels would not be reached, the yeast would not be
killed with increasing levels and so sugar would decrease.
 The yeast populations would increase until it reached the limit imposed by
its food source and then decrease
 Open bottle? Airborne aerobes would start breaking down grape sugar
through citric acid cycle and oxidative phosphorylation
Higher Alcohol Tolerance
 Yeast (cultivated) tolerates alcohol at a higher rate (~9.5%) before its
populations begin to decline. Wild yeast populations begin to decline at
about 4% alcohol
 More alcohol produced, the greater the number of yeast cells present. Day
3.25: Cultivated cells 10x10^6 vs. wild 6x10^6
To boil or not to boil
 Shorter distances in Asia: filtered & barrels
 Longer distance: spoiled so boiled
 Kills majority of organisms
Barrel vs. Airtight
- Airtight: prevents additional microbes from entering
- Remains aerobes die once sealed
- Barrel: microbes can enter during shipping and commence
cellular respiration=spoil
Pasteurization: only 60C which kills most microorganisms and
preserve taste
Case Study 3: Donor’s
Dilemma
 WNV transmission
 Mutations in WNV
 Life cycles of WNV and HIV
 Using RT-PCR to test ford WNV in blood donations
 Using genomics to track spread of WNV
Transmission
 Reservoir host: High viral titer: bird
 Incidental host: Lower titer: donor must be exposed to
virus recently and be viremic to pass on (high number
of viral particles: Humans
 Titers usually not high enough that if bitten by mosquito
could be passed on to others
 Vector: Mosquito- transmit to animals fed on
Comparing nucleotide
sequences
 Examining sequence for noticeable differences in length
 Comparing sequence nucleotide by nucleotide
 Translating sequences from codon to amino acid
Sequence 5 from Uganda (yr unknown): most different w/o
changing overall length of sequence
Sequence 3 (Senegal, 1979): Most changed- 38
nucleotides and within that 8 substitutions. (12 nucleotides
missing= 1 deletion
Codon (nucleotide triplets) to AA
 2: no mutation no change
 3) 5 changes in AA: 4 AA were lost in deletion. AA #13 is Lys rather than Gln
 4) 1 change Pro instead of Ser
 5) 2 changes: AA #9 is Ser instead of Asn. #12
 6) 1 change: #14
Percent point mutations does not tell you exactly how many AA substitutions will
occur but might indicate trends (more point mutations higher likelihood of AA
substitutions. Due to redundancy of the genetic code, several different
codon sequences code for the same AA.
Comparing Viral Lifecycles:
WNV & HIV
 Both enter cell after interaction of envelope glycoproteins w
host plasma membrane
 Both contain ssRNA: WNV genomic RNA serves as mRNA
upon entry
 WNV transcribe complementary RNA strand as template to
produce more RNA(does not involve nucleus of host cell)
 HIV uses reverse transcriptase to transcribe RNA DNA and
second complementary DNA strand to be incorporated into
host’s DNA.
When a person is infection with HIV host cells retain provirus in
their own genome. Immune system cannot detect HIV in host cell
and provirus cannot be removed from body as foreign. At any
time provirus can produce more viral mRNA and new HIV
particles.
RT-PCR
 Primers: needed for PCR bc DNA polymerases can
add nucleotides only to preexisting strands of nucleic
acids. In cells, the preexisting strands (primers) are
RNA. In PCR, the synthetic single-stranded DNA is
used as a primer
 Only those cDNAs that have sequences matching a
particular primer would be the target of interest
How did WNV arrive in NYC?
 Unlikely that a human traveler brought WNV: human
viral titer is too low to enable mosquito to pick up and
pass on
 More likely: infected bird, migrating sea gull or
agricultural pet trade
 Mosquito would not survive on a boat trip
Map Confusion
Spread of virus
 Spread seems to be strongly related to geographic
location: over time proximity to source seems to be
most important factor
 Colorado: more efficient vectors






increased populations of reservoir hosts
most species of reservoir hosts
human lifestyles in Colorado vs. NY
outdoor summer activities in Colorado
difference in climate and rainfall patterns
better eradication measures for vector populations in NY.
Increased breeding sites (swamps) for vector
Case Study 4: Tree Thinking
 Preparing Cladograms using observable characters
 Using bioinformatics and DNA testing as forensic
methods to detect illegal whale products
 Comparing unknown sequences to a database of know
cetacean sequences
 Comparing trees prepared using morphological and
molecular characters
 Considering the biological impacts and ethics of
whaling
Cladograms
 Do not imply chronology
 Cladograms allow you to group taxa by shared characters in a
concise format
 Look at relationships between taxa by reorganizing table as
cladogram (generate hypotheses about relatedness)
 Shared Primitive characters: homologous traits that are
common to larger taxonomic groups: flowers found in all
angiosperms
 Shared Derived Characters: homologous traits that are limited
to particular taxa; flowered with united petals found in
angiosperms
 Depending on taxa included in cladogram: same character
could be considered primitive in 1 cladogram and derived in
another
Biotechnology: Systematics
 Whale meat or not? DNA extraction, PCR, sequencing
of samples. Sequences aligned to compare with other
sequences
 Systematics: Analytical approach to understanding the
diversity and relationships of organisms, alive and
extinct.
 Study of evolutionary relationships among different
groups of organisms based on multiple characteristics,
expressed as phylogenetic trees
It is important to have an expert do the identification: then
database of sequences more valid. Systematists look at
many characters in making an identification NOT just
sequence of DNA expressed or not expressed
Genomic Comparison
 mtDNA (mitochondrial DNA):
 highly conserved (retained with few differences among
species)
 Known differences in hypervariable subsections of region
used to distinguish among cetacean species
Used PCR to amplify target mtDNA sequence
Phylogenetic trees
 Based on analysis of multiple characteristics for
multiple taxa
 Implies chronological sequences of divergence
(branching)
Divergent Evolution
 Use of hypervariable mtDNA vs. hemoglobin gene
 Hypervariable: changes relatively frequently (good
molecular marker for recent events: change over short
period of time)
 50-65 million yrs relatively short for evolutionary
measures
 Hemoglobin (slow to change/highly conserved): much
known about REGULAR rate of change and therefore
molecular marker used to compare changes in taxa
over longer periods of time
Weakness in methodology
 Tiny fragment of mtDNA
 Question systematics experts
Defend:
* Tiny piece of DNA but experts used multiple
morphological characters which lends weight to validity of
inferences regarding genetic similarity
Ungulates: Hoofed Mammals
 Odd-toed (Perissodactyla): zebra, horses, rhinos
 Even-toed (Cetartiodactyla): deer, sheep, pigs, cows
 Differences: fusiform body shape, no adult hair, limbs
for swimming, hold breathe
 Characteristics in early whale fossils to support eventoed common ancestor? Hind limbs w/even toes,
hooves
Case 5: Back t the Bay
 Animal Behavior
 Alternatives for control of gulls
 Population dynamics
 Link between human population and health of bays
 Human interactions with natural ecosystems
 Use of bird calls as deterrent
 Species specificity of calls
Dead gulls
 Presence of dead gulls provides visual stimulus (signal) that
accompanies acoustic signal- they respond by leaving the
area where it appears gulls are dying
 Suggests that gulls are capable of learning, or processing
information and distinguishing between a false alarm and
the real thing
 Associative learning & negative reinforcement: Associative
learning occurs as gulls acquired the ability to associate one
feature (death of species members) with a second (alarm
calls/danger). This is an example of negative reinforcement
(increases behavior) specifically active avoidance of noxious
stimuli
Design an experiment
 Hypothesis: The age of the bird affects how it will
respond to a distress call. If the response is learned,
younger birds will have fewer appropriate responses
than older birds.
 Results: Younger birds should show statistically
significant differences in response to distressed calls
from older birds (moved away from source of calls).
Case 6: Corn under
Construction
 genetic engineering of crops
 Planting Bt corn vs. non-Bt corn
 Corn growth and reproduction
 Consideration of the role of biotechnology in agriculture
 Spread of pollen/hybrid crops
 Pesticide application vs. genetic engineering
Staminate= male, Carpellate=
female
Reproduction/Problems
 Pollen grains from tassels (staminate) of one corn plant
are carried by the wind to mature silks. Pollen that
lands on a silk is germinated immediately and produces
a pollen tubs that grows down length of the silk. Silks
from the base are the first to emerge from husk
followed by those closer to EAR TIP
Growth Problems
 A: Depending on when the irrigation system broke, the silks
towards top could have been pollinated but not successfully
developed into kernels (abortion) due to lack of water
(STRESS) or water availability. Perhaps a limited amt. of
time for pollen to be available before silks at tip matured &
emerged from husks
 B: Silks exposed from husks and most likely not resistant to
beetles thus fed on silks with could not be fertilized to
produce kernels. Silk clippings by beetles feedings on
exposed parts of silk.
Analyzing Shot holes
 When ECB caterpillars first emerge, corn is in early
stage of growth: whorl stage (Leaves tightly wrapped
around each other.
 THEN stem elongates and they separate
 1 or 2 feeding simultaneously= tunneling of holes in a row
through several leaves, subsequent elongation of leaves
causes this to look like independent events
Case 7: Galloper’s Gut
 Structure & Function of selected mammalian digestive
systems
 Nutrition for horses
 Over-crowding of grazing animals
 Reproduction barriers
 Horse Evolution
Horse, Human, Cow
 Cow has a 4-chambered stomach that includes rumen,
reticulum, omasum, abomasum (RUMINANT). Horses
& humans have a single-chambered stomach
(MONOGASTRIC).
 Cows: almost all digestion occurs in stomach (large
populations of microbes thrive).
 Horse: small stomach therefore much more digestion
must occur after food has left stomach
 Humans: stomach, small intestine & large intestine ALL
have about the same capacity
Microbes
 Cow: 2 chambers of stomach (rumen & reticulum)
 Small cecum (also fermenters)
 Horse: Cecum & large intestine, no stomach
compartments with microbes
 Human: microbes assist digestion in large intestine
Stomach Function & Cellulose
 Cow: two contain microbes to digest cellulose, 2
chambers remove water & secrete enzymes
 Horse & human: secretes enzymes to break down food
but cellulose not broken down in stomach of either
Grazers & Omnivores
 Horse & Cow: long digestive systems adapted for diet
of plant material
 Highly concentrated microbes along tract help breakdown
cellulose
 Human: digestion in stomach and small intestine, very
little digestible material remains when it reaches large
intestine
Small Intestine Function
 Further digestion of all macromolecules (carbs, lipids,
nucleic acids)
 Facilitated by enzymes from pancreas
 Bile added to guide fat digestions
 Nutrients absorbed from small intestine wall into
bloodstream and lymph
Horse Evolution
 The tree (in text 24.24) shows many branching points
and many extinct taxa. It is not a single branch from
Hyracotherium to Equus. Contradicts the impression
that one equid taxon died out as the next taxon
emerged. The only living taxon of this tree is the genus
Equus, which includes horses, donkeys, and zebras.
Ecology
 Community: assemblage of populations of different
species living close together for potential interactions
 Ecosystem: all organisms in a given area and ABIOTIC
factors with which they interact. One or more
communities and their environment
 Food Chain: Pathway along which food energy is
transferred from trophic level to trophic level beginning
with producers
Food Web vs. Food Chain
 Food Web: consists of all the food chains in an
ecosystem
 Important to highlight that each living organism is involved
in MULTIPLE food chains
 If 1 organism affected (predation/pollution) will not only
affect next trophic level but MULTIPLE chains
ENERGY LOST through trophic levels (10% from one to
next). Biomass decrease, numbers decrease.
Nitrogen: needed for AAs and
nitrogenous bases
1) bacteria in soil fixate nitrogen from atmosphere (N2) into useable form
for plants (NO3-, nitrates)
2) Primary consumers eat plants and secondary consumers eat primary
consumers
3) Denitrifying bacteria convert nitrogen from dead matter in soil into
atmospheric nitrogen