Keystone Review day 3

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Keystone Review day 3
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• Enzymes speed up the rate of chemical reactions
• Substrates molecules which react with enzymes
• Active site area on enzyme where substrate
  attaches.
• Active site may undergo a slight change in shape
  in order to fit with the substrate Induced fit
  model
• Enzymes can be reused
• Lower the amount of activation energy needed

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Animation How enzymes work
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Enzymatic reaction
Substrates are combined into a larger product
Substrate is broken down into smaller products
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• Temperature, pH, and concentration can all affect
  enzyme activity
• Temperature
• As the temperature rises, enzyme activity
  increases.
• If the temperature is too high, enzyme activity
  slows rapidly because the enzyme is denatured.
• When enzyme is denatured, its shape changes and
  it can no longer attach to the substrate.
• Each enzyme has an ideal temperature at which the
  rate of reaction is highest.

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• pH
• Each enzyme has an ideal pH at which the rate of
  reaction is highest.
• Change in pH can change the structure of the
  enzyme, and can eventually cause enzyme to
  denature.

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Rate of an enzymatic reaction as a function of
temperature and pH
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• Rates and concentration
• Reaction rate depends on the number of
  enzyme-substrate complexes that can be formed.
• When all available enzymes and active sites are
  filled, the rate of activity cannot increase
  further.

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• Overview of Cellular Respiration
• Makes ATP molecules
• Releases energy in 4 reactions
• Glycolysis ? Transition reaction ? Citric acid
  cycle (Krebs cycle) ? Electron transport system
• An aerobic process that requires O2
• If oxygen is not available (anaerobic),
  glycolysis is followed by fermentation

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The four phases of complete glucose breakdown
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• Structure of mitochondria
• Cristae are folds of inner membrane
• The matrix, the innermost compartment, which is
  filled with a gel-like fluid.

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Step 1. Glycolysis

• Inputs
• Glucose
• 2 NAD
• 2 ATP
• 4 ADP 2 P

• Outputs
• 2 pyruvate
• 2 NADH
• 2 ADP
• 2 ATP (net gain)

• Occurs outside the mitochondria
• No oxygen needed occurs in all organisms
• When no oxygen is available, glycolysis is
  followed by fermentation

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• Step 2 - Transition Reaction
• Requires oxygen (aerobic)
• Occurs in the matrix of the mitochondria

• Inputs
• 2 pyruvate
• 2 NAD

• Outputs
• 2 acetyl groups
• 2 CO2
• 2 NADH

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• Step 3 - Citric acid cycle
• Occurs in the matrix of the mitochondria.
• Requires oxygen (aerobic)

• Inputs
• 2 acetyl groups
• 6 NAD
• 2 FAD
• 2 ADP 2 P

• Outputs
• 4 CO2
• 6 NADH
• 2 FADH2
• 2 ATP

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• Step 4 - Electron Transport System (ETS)
• Requires oxygen (aerobic)
• Located in the cristae of mitochondria
• NADH and FADH2 carry electrons picked up during
  glycolysis, transition reaction, citric acid
  cycle and enter the ETS.
• The ETS consists of
• protein complexes that pump H
• mobile carriers that transport electrons
• ATP synthase complex - H flow through it, making
  ATP
• H flow through from high to low concentration
• For every 3 H that flow through, one ATP is made

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Accounting of energy yield per glucose molecule
breakdown
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• Fermentation
• Occurs when oxygen is not available.
• Follows glycolysis
• Occurs in anaerobic bacteria, fungus, human
  muscle cells.
• Produces alcohol CO2 or lactic acid
• Benefit produces ATP when no O2 is present and
  recycles NAD
• Drawback not very efficient lactic acid can
  damage muscle cells in humans

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• Photosynthesis
• Converts solar energy into the potential chemical
  energy of a carbohydrate in this way
• Solar energy carbon dioxide water ?
  carbohydrate oxygen
• Photosynthetic organisms include plants, algae,
  and certain bacteria.
• These organisms are called producers they
  synthesize organic molecules from raw materials.

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• Structure and Function of Chloroplasts
• Chloroplasts are the organelles that carry on
  photosynthesis.
• Mesophyll cells in the middle of a leaf house
  chloroplasts
• Mesophyll cells are protected from drying out by
  a waxy cuticle.
• Pores called stomata allow CO2 and O2 to enter
  the leaf.

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Mesophyll cells of a leaf
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Structure of Chloroplasts

• Bounded by a double membrane.
• The inner membrane encloses a large central space
  called the stroma that houses enzymes used to
  reduce CO2 to carbohydrate.
• A membranous system of thylakoids lies within the
  stroma some thylakoids are stacked into grana
  thylakoids contain chlorophyll and other
  pigments.
• Chlorophyll and other pigments absorb solar
  energy.

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Chloroplast structure
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• Pigments (chlorophylls and carotenoids) found
  within photosynthesizing cells, are capable of
  absorbing various portions of visible light.
• Both chlorophyll a and chlorophyll b absorb
  violet, blue, and red light best.
• Carotenoids absorb light in the violet-blue-green
  range and reflect yellow or orange
• Leaves appear green because green light is
  reflected and only minimally absorbed.

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In the fall when the pigment chlorophyll breaks
down, the remaining pigment (carotenoids) become
unmasked, reflecting the colors like orange and
yellow
Video why leaves turn colors in the fall
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Two Sets of Reactions

• Photosynthesis is divided into two sets of
  reactions, as implied by the term
  photosynthesis
• Photo refers to the light-dependent (needs
  light) reactions that capture energy from the sun
  
• Photosystem II
• Photosystem I
• Synthesis refers to the light-independent (does
  not need light) reactions that produce
  carbohydrate (glucose).
• Calvin Cycle

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Light-Dependent Reactions

• Light energy is absorbed by chlorophyll
  molecules.
• ATP, NADPH, and oxygen are produced.
• Water is split to produce oxygen, hydrogen ions,
  and electrons
• Photosystem II occurs first
• Photosystem I occurs second
• Both occur within the thylakoid membranes inside
  the chloroplast

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LIGHT-DEPENDENT REACTION
Requires Light and Water
WHAT IT DOES
WHERE IT HAPPENS
SPLITS H2O
Leaf
Creates ATP and NADPH For Calvin Cycle
Chloroplasts
Inside Thylakoids
Forms O2 as a byproduct
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Light-Independent Reactions

• The light-independent reactions do not need light
• Reactions make up the Calvin cycle.
• Carbon dioxide (CO2) is taken up by the plant
  (from the atmosphere)
• ATP and NADPH (made from the light dependant
  reactions) add phosphates and electrons to CO2,
  and convert it to glyceraldehyde 3- phosphate, or
  G3P
• G3P is a type of sugar which a plant can easily
  convert to glucose. This glucose can then be
  used as a source of stored energy for the plant

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Calvin cycle (dark reactions)
Requires ATP, NADPH, and CO2
WHAT IT DOES
WHERE IT HAPPENS
Produces High Energy Sugars
Leaf
Combines CO2, ATP and NADPH
Chloroplasts
In the Stroma (Thick Fluid inside Chloroplast)
Forms a 6 carbon sugar (Glucose)
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Overview of Photosynthesis
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Photosynthesis Vs. Cellular Respiration
Overall equation for photosynthesis is
Overall equation for cellular respiration is
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• Evolution the process by which species change
  over time
• Charles Darwin famous for observations made at
  the Galapagos Islands came up with theory of
  natural selection to explain how evolution
  occurs.
• Artificial selection - Breeders selected
  individuals with desired traits to breed the next
  generation

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• Populations become modified through natural
  selection
• Natural selection - the process by which
  individuals that are better adapted to their
  environment survive and reproduce more
  successfully than less well-adapted individuals
  do
• Fitness reproductive success

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• Natural selection involves the following
• Overproduction more offspring are produced than
  can possibly survive
• Variation differences within a population
• Selection having a particular trait may make an
  individual more likely to survive
• Adaptation those selected traits improve
  survival and become more common in a population

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• Patterns of natural selection
• Stabilizing selection average form of a trait
  is favored extreme forms of a trait are
  eliminated.
• Directional selection one extreme form of a
  trait is favored.
• Disruptive selection both extremes of a trait
  are favored over an average form of a trait.

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Stabilizing selection
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Directional selection
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Disruptive selection
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• Adaptations vs. Variations
• Variations differences that exist within a
  population that may have no effect on fitness
• Ex length of your thumb
• Adaptations a variation that all members of a
  population have inherited because that trait
  improves fitness
• Ex an opposable thumb

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• Evidence for evolution
• Fossils traces of organisms that lived in the
  past
• Ex shells, bones, teeth, imprints
• Tell us things such as age, habitat, diet,
  lifestyle of organisms.
• Biogeography - the study of the locations of
  organisms around the world
• Darwin saw similarities of organisms on different
  continents but similar environments
• Differences in organisms due to geographic
  separation

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Emu (Australia)
Ostrich (Africa)
Rhea (South America)
Similar animals from different continents
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Continental drift
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• Anatomy
• Developmental biology the more similar the
  embryos are at certain stages of development, the
  more closely related they are thought to be.

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• Homologous structures characteristics that are
  similar in two or more species and that have been
  inherited from a common ancestor of those species
• Ex frog, lizard, bird, whale, cat, bat, and
  human forelimbs

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• Analogous structures - used for the same purpose
  but are not due to a common ancestor
• Ex bird wing insect wing

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• Vestigial structures structures that have no
  function in the living organism but may have been
  used by its ancestors.
• Ex human appendix,
• python leg bones

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• Biochemistry comparisons of DNA or amino acid
  sequences in proteins
• The more similar the genes and proteins are, the
  more closely related organisms are thought to be
• Ex Hemoglobin to carry oxygen is identical in
  humans and chimpanzees.

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• Gene pool total of all the genes of all the
  individuals in a population
• If the frequency of genes in a population
  changes, evolution has occurred
• Microevolution refers to evolution as a change
  in genes within populations
• Macroevolution refers to the appearance of new
  species over time
• Species a group of organisms that are closely
  related and that can mate and produce fertile
  offspring

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• Processes of microevolution
• Natural selection some are better suited to
  survive and reproduce than others
• Migration movement of individuals into, out of,
  or between populations
• http//nortonbooks.com/college/biology/animations/
  ch17a01.htm
• Mate choice mates are limited, or selecting a
  mate based on appearance or behavior
• Mutation changes genes within population
• Genetic drift random events cause only certain
  individuals to survive and reproduce

genetic drift animation
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• Examples of genetic drift
• Founder effect - Founding member of Amish
  population had recessive allele for rare kind of
  dwarfism - of Amish with this allele higher
  than in general population
• Random death of certain color animals results in
  only one color reproducing next generation

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• Macroevolution occurs when one population is
  isolated from another population
• Mutations occur
• Result in successful traits
• Mutation spreads through population
• Population changes over time

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• Patterns of macroevolution
• Convergent evolution
• Coevolution
• Adaptive radiation
• Extinction if all members of a species die off
  or fail to reproduce, the species is said to be
  extinct
• Gradualism
• Punctuated equilibrium

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• Convergent evolution species living in similar
  environments should evolve similar adaptations

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• Coevolution change of two or more species in
  close association with each other
• Ex predator prey, parasite host, insects and
  plants they pollinate

Other examples
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• Adaptive radiation - an evolutionary pattern in
  which many species evolve from a single ancestral
  species
• Tends to happen when a new species enters an
  environment that contains few other species
• Ex several species of finches on the Galapagos
  Islands - each one has a different way of life.

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The Galapagos finches
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• Gradualism suggests that change is slow and
  steady large-scale changes require many
  small-scale changes over a period of time.
• Punctuated equilibrium suggests that a period
  of no change is interrupted by period of rapid
  change species is stable, then environmental
  changes create new pressures, causing new species
  to suddenly appear

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Gradualism versus punctuated equilibrium
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• An ecosystem contains
• Biotic (living) components
• Populations of organisms
• Abiotic (nonliving) components
• Inorganic nutrients, water, temperature, and
  wind.
• Levels of ecological organization
• Largest ? smallest
• Biosphere
• Biome
• Ecosystem
• Community
• Population
• Organism

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• Levels of ecological organization
• Organism a living thing capable of carrying on
  the processes of life
• Population a group of organisms of the same
  species that live in a specific area
• Community a group of several species that live
  together and interact in a particular area
• Ecosystem A community of organisms and their
  abiotic components
• Biome A large region characterized by a
  specific climate and certain types of plant
  animal communities
• Biosphere all of the ecosystems of the earth

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Biotic Components of an Ecosystem
Autotrophs are producers that produce food for
themselves and for consumers. Most are
photosynthetic organisms but some chemosynthetic
bacteria are autotrophs. Heterotrophs are
consumers that take in preformed food.
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Consumers may be Herbivores animals that eat
plants, Carnivores animals that eat other
animals, Omnivores, such as humans, that eat
plants and animals, or Decomposers, bacteria and
fungi, that break down dead organic
waste. Detritus is partially decomposed organic
matter in the soil and water beetles,
earthworms, and termites are detritus feeders.
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Primary consumer an organism that gets its
energy from plants (producers) Secondary
consumer a consumer that gets its energy from
primary consumers Tertiary consumer carnivores
that eat other carnivores a top-level consumer,
which is usually the top predator in the food
chain
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Food chains vs. food webs A food chain is
diagram that link organisms together by who eats
whom starts with plant life and ends with an
animal. Most food chains have no more than 4 or
5 links Ex tree ? giraffe ? lion Most
animals are part of more than 1 food chain eat
more than 1 kind of food in order to meet their
food and energy requirements. These
interconnected food chains form a food web.
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Food chain
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Forest food webs
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Ecological Pyramids
The shortness of food chains can be attributed to
the loss of energy between trophic
levels. Generally, only about 10 of the energy
in one trophic level is available to the next
trophic level. This relationship explains why so
few carnivores can be supported in a food web.
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Ecological pyramid
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• Biotic interactions
• Predation - an interaction between two organisms
  in which one organism kills and feeds on the
  other organism
• Parasitism a relationship between two species
  in which one organism benefits while the other is
  harmed
• Symbiosis a relationship in which two species
  live in close association with one another ex
  mutualism and commensalism
• Mutualism both species benefit
• Commensalism one species benefits while the
  other is neither harmed nor hurt

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• Examples of biotic interactions
• Predation lion feeds on zebra
• Parasitism tapeworms in the intestines of
  another organism
• Mutualism small fish cleans big fish
• Commensalism orchids attach themselves to the
  trunks of trees to get more sunlight in the forest

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• Limiting factors factors that can affect the
  size of a population
• Abiotic limiting factors weather, climate,
  amount of water available
• Biotic limiting factors amount of food
  available, diseases and parasites, number of
  predators, human activities (such as habitat
  disruption, introducing diseases, introducing
  non-native species, pollution, fires)

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The Water Cycle
The suns rays cause fresh water to evaporate
from the oceans Water rises into the atmosphere,
cools, and falls as rain over oceans and
land. Water is held in lakes, ponds, streams, and
groundwater. Evaporation from terrestrial
ecosystems includes transpiration from
plants. Eventually all water returns to the
oceans.
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The water cycle
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The Carbon Cycle
In the carbon cycle, a gaseous cycle, organisms
exchange carbon dioxide with the atmosphere.
Shells in ocean sediments, organic compounds in
living and dead organisms, and fossil fuels are
all reservoirs for carbon. Fossil fuels were
formed during the Carboniferous period, 286 to
360 million years ago.
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The carbon cycle
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The Nitrogen Cycle
Nitrogen makes up 78 of the atmosphere but
plants are unable to make use of this nitrogen
gas and need a supply of ammonium or nitrate.
The nitrogen cycle, a gaseous cycle, is
dependent upon a number of bacteria. During
nitrogen fixation, nitrogen-fixing bacteria
living in nodules on the roots of legumes convert
atmospheric nitrogen to nitrogen-containing
organic compounds available to a host plant.
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The nitrogen cycle
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The Phosphorus Cycle
The phosphorus cycle is a sedimentary cycle.
Only limited quantities are made available to
plants by the weathering of sedimentary rocks
phosphorus is a limiting inorganic nutrient. The
biotic community recycles phosphorus back to the
producers, temporarily incorporating it into ATP,
nucleotides, teeth, bone and shells, and then
returning it to the ecosystem via decomposition.
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The phosphorus cycle
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1. The figure above represents a a. trophic
net. b. food chain. c. food net. d. food web.  
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2. The main products formed during aerobic
cellular respiration are energy, a. oxygen and
water. b. oxygen and carbon dioxide. c. water and
carbon dioxide. d. sugar and oxygen. e. sugar and
carbon dioxide.
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Use the diagram below to answer question 91.
3. The diagram models how a poison bonds to the
active site of an enzyme. Which function is the
enzyme most likely unable to perform because of
the attachment of the poison molecule? a. The
release of stored chemical energy, b. The
donation of electrons to the substrate. c. The
supply of activation energy for a reaction. d.
The catalysis of the reaction with the substrate.
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4. An analysis of the DNA from these organisms
would indicate that a. their DNA is
identical. b. they all have tails. c. their DNA
sequences show many similarities. d. they all
have the same number of chromosomes
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5. Which statement best compares the energy
transformations of photosynthesis and cellular
respiration? a. Only photosynthesis uses oxygen
to create energy. b. Only photosynthesis
causes an increase in kinetic energy. c.
Photosynthesis and cellular respiration both
store energy in chemical bonds. d.
Photosynthesis and cellular respiration both
require chemical energy to make food.
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6. Which of the following is NOT an enzyme? a.
lipase b. maltase c. urease d. lactose
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7. The main reason why organisms would use
fermentation is a. lack of oxygen. b. lack of
enzymes. c. it produces the greatest amount
of ATP. d. lack of carbon dioxide.
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8. The raw materials or reactants of the
photosynthetic process include a. glucose and
oxygen. b. carbon dioxide and glucose. c. carbon
dioxide and water. d. carbon dioxide and
oxygen. e. glucose and water.
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9. Which of the following is a way in which
variations can arise in a population? a.
natural selection b. mutation c. crossing
over during meiosis d. both B and C
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  10. The algae are __________________ while the
leopard seals are ___________________. a.
producers, carnivore b. carnivore, omnivore c.
producer, omnivore d. carnivore, producer
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Use the graph below for question 11.
11. The optimum pH for pepsin is a. 2 b.
8 c. 3 d. 7
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12. The oxygen generated during photosynthesis is
derived from a. carbon dioxide. b.
water. c. cytochrome. d. glucose.
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13. The order of the major pathways and reactions
of aerobic cellular respiration is a. glycolysis
transition reaction citric acid cycle
electron transport system. b. electron transport
system glycolysis transition reaction
citric acid cycle. c. glycolysis electron
transport system transition reaction - citric
acid cycle. d. citric acid cycle glycolysis
electron transport system transition reaction.
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14. Which of the following best describes
natural selection? a. Individuals who adapt
during their lifetime are more likely to survive
and reproduce. b. Individuals born with certain
favorable traits are more likely to survive and
reproduce. c. There are little or no variations
in populations, which makes adaptations rare over
time. d. Individuals with little or no
variation are more likely to survive and
reproduce.
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• 15. In a marine food web, there is a far greater
  mass of algae than of all the killer whales. Why
  is this so?
• whales are bigger than algae
• b. an alga has more mass than a killer whale
• c. whales dont eat algae
• d. it takes a massive amount of algae to support
  a food web with a killer whale at the top.

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16. Each enzyme has particular substrate because
enzymes a. increase the energy of activation. b.
decrease the productivity of the cell. c. always
require coenzymes. d. have active sites
complementary in shape to their substrates.
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17. The largest number of ATP molecules are
produced in which part of the respiration
reaction? a. glycolysis b. transition
reaction c. Krebs cycle (citric acid
cycle) d. Electron transport system (chain)
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18. Which of the following is the correct
sequence of steps for photosynthesis? a.
Calvin cycle ? Photosystem I ? Photosystem
II b. Calvin cycle ? Photosystem II ?
Photosystem I c. Photosystem I ? Photosystem
II ? Calvin cycle d. Photosystem II ?
Photosystem I ? Calvin cycle
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Use the diagram below to answer questions 7-8.

• 19. The similarity of these structures suggests
  that the organisms
• a. have a common ancestor.
• b. evolved slowly.
• c. all grow at different rates.
• live for a long time.

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20. The Calvin cycle is dependent upon a supply
of a. water and carbon dioxide. b. carbon dioxide
and NADPH. c. carbon dioxide, NADPH and ATP. d.
oxygen and carbon dioxide. e. glucose and carbon
dioxide.
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Use the graph below to answer question 2.
21. The graph shows how the activity of an enzyme
changes at different temperatures. Which
statement best describes what happens to the
enzyme when the temperature of the reaction
reaches 63C? a. The enzyme is used up and the
reaction stops. b. The enzyme begins to
decrease the rate of the reaction. c. The
enzyme continues to increase the rate of the
reaction. d. The enzyme changes shape and can
no longer speed up the reaction.
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• 22. The maximum population that the environment
  can support for an indefinite period of time is
  called the __________________
• biotic potential
• b. environmental resistance
• c. carrying capacity
• d. replacement reproduction.

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23. During enzymatic action, the enzyme a.
becomes the product. b. is used up. c. The enzyme
and the substrate form a permanent complex. d.
The enzyme the substrate form a temporary complex
but the enzyme is not used up.
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24. The substance that initially traps solar
energy in photosynthesis is a.
chlorophyll. b. RuBP. c. water. d. glucose.
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25. Enzymes a. provide the energy for metabolic
reactions. b. speed up metabolic reactions. c.
act as a buffer in metabolic reactions. d. raise
the energy of activation for a reaction.
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26. Bulldogs have been bred by humans for
increasingly large heads. This has made the
birthing process more difficult for the mother,
and may decrease survival among newborn pups.
This intentional breeding is an example of a.
natural selection. b. founder effect. c.
genetic drift. d. artificial selection.
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27. Which method regulates enzyme action? a.
changing pH b. changing temperature c. a molecule
of similar shape to the enzyme competes for the
active site. d. All of the above are correct.