Download Honors Bio – Key concepts for final

Honors Bio – Key concepts for final
Chapter 1:
 pp. 4-5 What are the levels of organization and describe their interaction?
 What is the flow of chemical matter and energy in an ecosystem? Which is
recycled and which needs constant input? Why? p. 6
o Because of laws of thermodynamics – we understand that energy is
constantly transformed but in the process the entropy of the universe
increases (i.e. some energy become unavailable for our use – usually
dissipates as heat energy). So we have to have constant renewal from an
outside source – the sun!!!
o Chemicals are recycled – we have a finite supply of atoms on the Earth
that are constantly recycled – rebuilt – reused…Metabolism is the
chemical processes that recycle those materials – energy is transferred,
used, etc… in the system.
 What is meant by the statement that cells are basic unit of structure and function
o Prokaryote – simpler cells – no membrane bound organelles, circular
rather than linear DNA o Eukaryote – compartmentalized – separate areas for different types of
reactions and processes - more efficient – more complex.
 How do feedback mechanisms regulate systems?
o Metabolic reactions have to be regulated – there has to be ways to start
and stop chemical reactions.
o Most chemical reactions in the bodies are facilitated by enzymes
(catalysts).
o Enzymes can be regulated with competitive or noncompetitive inhibition
or activation
o Feedback works when the product of a reaction acts as an inhibitor to slow
the continuing reaction down – in other words – an enzyme breaks down a
molecule (X) to parts A and B
 Once the reaction has occurred to build up a certain concentration
of A and B, part A might start to bind with the original enzyme to
stop the process.
 Product of a process feeds back to stop the process from
continuing = negative feedback
 Positive feedback is an amplification – childbirth
 Explain how evolution is the basis for unity and diversity –
o Unity in that we have some common roots – we have some parts of our
DNA in common with bacteria – same mechanism are in place in all
organisms.
o Diversity – with evolution and adaptations to environmental conditions,
we have evolved to different species
 Describe the three domains
o Archaea – old prokaryotes that can survive in extreme conditions
o Bacteria – modern prokaryotes
 Both archaea and bacteria belong to the Kingdom called Monera
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o Eukarya are all the eukaryotes and include kingdoms of Fungi, Protista,
Animalia, Plantae
Explain Charles Darwin’s theory of Natural Selection
o Evolution is not planned or intentional
o Theory says:
 More organism born than can survive – struggle for survival
 Variation among organisms in their traits (DNA)
 Some traits may allow organisms to survive and reproduce better
than others so that those traits are more apt to be passed to other
generations.
 Environmental conditions change so that at different times,
different traits may be more advantageous.
Chapter 2:
 Review basics of chemistry including terms like:
o Atoms
o Elements
o Compounds
o Ionic bonds
o Covalent bonds
o Metals
o Nonmetals
o Subatomic particles and their location
o Atomic mass
o Atomic number
o Isotopes
 How is potential energy related to electron levels?
o Electrons occupy energy levels that have a maximum occupancy
o Further away from the nucleus  higher energy level.
 What happens when an electron moves from one level to another?
o Electrons absorb and release energy all the time
o It takes energy for an electron to go to a higher energy level
o When it returns to its own energy level, it releases that energy back out.
 How does electron distribution relate to chemical properties and bonding?
o The number of valence electrons need to complete the shell will determine
the number and type of bonds an atom forms
 Distinguish between covalent and ionic bonds
 Distinguish between polar and nonpolar covalent bonds
 Describe hydrogen bonds and Van der Waals forces. What is their significance?
 How does a molecules shape relate to its function?
o Enzymes are made of chains of amino acids that interact and give it a very
specific 3 –D shape – needs a specific shape to create an active site.
o Water is bent which makes it asymmetrical and it is this asymmetry that
makes it overall polar.
 What are chemical reactions and what factors affect the rate of chemical
reactions?
Chapter 3:
 How does the shape of a water molecule affect its properties?
 What contribution do polar bonds have?
 Describe what hydrogen bonding does for water.
 Distinguish among:
o Cohesion
o Adhesion
o Surface tension
o High specific heat
o Universal solvent
 How do each of the above contribute to water’s properties and what is the
significance in contributing to water’s role in living systems?
 Describe all the ways that water can moderate temperature – give examples for
each.
 Why is water such a good solvent?
 Distinguish between hydrophobic and hydrophilic. What makes something one or
the other?
 Review pH scale – what it means
 What makes something basic?
 What makes something acidic?
 How do buffers work?
Chapter 4
 What properties of carbon make it so suitable for the type of organic molecules it
can form as the foundation for living systems?
Chapter 5
 List and describe the main groups of organic compounds
o Carbohydrates
o Proteins
o Lipids
o Nucleic acids
 What makes each group unique? What are their primary roles? If they are
polymers, what are the monomers that make them up?
 Know important groups with in each group – i.e. polysaccharides include similar
but different compounds in starch, cellulose, and glycogen. Proteins have unique
levels of organization that determine their functions.
 Compare dehydration synthesis and hydrolysis – how do they relate to processes
within the cell and the creation and breakdown of organic compounds?
Chapter 6
 Distinguish between prokaryotic and eukaryotic cells
 Know the structure and diversity of prokaryotic cells
 Know eukaryotic organelles and their functions
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Compare and contrast eukaryotic to prokaryotic cells
Be able to describe differences and similarities between plant and animal cells
Trace the path of a protein through the endomembrane system from production to
shipping out of the cell.
What is unique about chloroplasts and mitochondria in terms of the their
structures and functions?
Know three main types of proteins in the cytoskeleton and how they support the
cell.
Know and define intracellular junctions
Chapter 7
 Describe the cell membrane and its make-up
 What is meant by the fluid mosaic model?
 What roles do cell membranes play?
 What roles can cell proteins play?
 What is selective permeability?
 What can pass easily through the membrane and what needs help?
 Describe diffusion – facilitated and simple – give examples
 Describe active transport – give examples and explain role in cell function.
 Describe osmosis – relate to our labs
 What are endocytosis and exocytosis?
Chapter 8:
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Define exergonic and endergonic
o Exergonic reactions give off energy that could be trapped to do work (i.e.
run other reactions, build molecules, move things).
o Endergonic reactions require an input of energy – often they are coupled
to an exergonic reaction.
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How do the structures of ATP and, conversely, ADP, allow them to store and
release energy?
o ATP is an adenosine molecule that has 3 phosphate groups attached to it
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The breaking of one Pi off ATP releases some energy (exergonic) and
leaves products of ADP and Pi.
o ADP has two phosphates –
o The restoration of ATP from ADP and Pi is endergonic and requires input
of energy. The breakdown of organic molecules like sugar releases energy
that is used to make ATP.
Describe how ATP can be "coupled" to a reaction to help drive it?
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For example, glucose is broken down with oxygen to finally be released as
carbon dioxide and water. It gives off energy that is used to “make” ATP.
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ATP can then be broken down to ADP and Pi and release the energy to
drive some other process in the cell.
How is ATP regenerated
o ATP is regenerated when energy is added to the reaction of ADP and Pi.
How do enzymes work based on a specfic shape?
o Enzymes are proteins with a very specific 3-D shape
o Enzymes have a specific active site that will only fit the target “substrate”
unless an inhibitor.
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Define substrate, active site
o Substrate is the specific reactant(s) that an enzyme matches.
o Active site matches the shape of the substrate (or is lined with
complementary charges on amino acids)
Briefly describe the concept of activation barrier and how an enzyme works on it.
o Even spontaneous reactions need to breach an energy of activation o Enzymes lower the activation barrier and make it easier for the reaction to
start.
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What factors affect enzyme activity?
o Enzymes are proteins and have a specific shape – anything that alters the
shape will affect it –
 Temperature - denature
 pH
 Presence of an inhibitor that might block the active site.
o Enzymes also operate under roles of physics which means that force of
collision will affect rate
 Temperature can speed up movement or slow it down (warm and
cold)
 Concentration of substrate
 Concentration of enzyme
Chapter 9
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Give a brief summary of redox reactions (oxidation and reduction).
o The transfer of electrons from one element to another
o Oxidation occurs to the element that loses an electron
o Reduction occurs to the element that gains an electron
o One cannot occur without the other.
o Electrons are a high energy particle and can be used to transfer energy.
How is energy harvested when electrons are trapped by NAD+ and then put
through the electron transport chain?
o Electrons are released along with hydrogen atoms as organic molecules
(like glucose) are broken down
These electrons can be “fed” into an electron transport chain (a series of
molecules that are alternately reduced and oxidized as they pass
electrons).
o Like electricity, the movement of electrons is transferring energy and that
energy is used to attach P to ADP making ATP.
Describe the stages of cellular respiration and account for the number of ATP
generated at each stage.
o Glycolysis occurs in the cytoplasm
 Glucose (6 –C) is broken into two 3-C molecules
 It takes a little energy to get started but it produces a net of 2 ATP
 The products of glycolysis in the presence of O2 can be further
broken down in the mitochondria.
o Citric Acid cycle – in mitochondria – BLACK BOX version – the 2 3-C
molecules are broken down fully to release 6 CO2 and the H that is
released is picked up by a carrier called NAD+  NADH. You get 2
ATP.
o Oxidative phosphorylation is where the NADH drops off both its electrons
and the H+. The electrons go through an ETC (electron transport chain) –
the energy generated is used to make a “charged” battery with a
concentration of H+ on one side of the membrane. Basically the PE of the
electrons goes to build PE of a H+ gradient. When the gradient is released,
the energy is used to build ATP. The final step is that O2 must be present
to take the H+ at the end. This process can generate up to 34 ATP.
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Explain how fermentation occurs in the absence of oxygen
o In the absence of oxygen the processes in the mitochondria cannot occur –
o Fermentation is basically glycolysis followed by alcohol or lactic acid
production.
Distinguish between alcohol and lactic acid fermentation
o The product differs –
 Yeast are an example that have alcohol fermentation and produce
ethanol.
 Humans and other mammals use lactic acid fermentation – in our
muscles during heavy use we run short of O2 so we have some
fermentation which produces lactic acid. Lactic acid must be
reconverted to glycogen in the liver.
Compare fermentation to aerobic respiration
o Fermentation only yields 2ATP/glucose.
o Aerobic respiration can produce 38 ATP/glucose
What is significant about glycolysis?
o It is an ancient system that nearly all organisms perform to get ATP.
How do organic molecules other than sugar feed into the metabolic pathways?
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Compare/contrast anabolism to catabolism
o Anabolism is building molecules
o Catabolism is breaking them down
How are stages of cellular metabolism regulated?
o Enzymes!
o Feedback from different steps can slow or stop previous reactions by
working on the enzymes –
Chapter 10
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Distinguish between autotrophs and heterotrophs
o Autotrophs (self-feeding) – photo-autotrophs use light energy to make
organic compounds and then use those organic compounds to do work.
Chemo-autotrophs – use inorganic chemicals to trap energy and make
organic compounds.
o Heterotrophs – must ingest energy in the form of organic compounds
(chemical energy).
How does the plant exchange carbon dioxide for oxygen to and from the
atmosphere?
o Plant is covered with a waxy coating to prevent dehydration but also
prevents gas exchange.
o There are openings in the leaf called stomata that let gases through.
What is the pigment that captures most of the sun's energy?
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Chlorophyll is the primary pigment in chloroplast– it is green which
means it reflects green light and absorbs in the red/blue region. There are
other pigments Briefly describe the structure of a chloroplast.
o Both mitochondria and chloroplast have double membrane – it means it
has an internal membrane sac surrounded by an external one. The internal
one is either highly folded (mitochondria) or compartmentalized
(chloroplasts).
o Mitochondria and chloroplasts have their own DNA and their own
ribosomes so they can reproduce and make their own proteins.
o Chloroplasts have inner membranous stacks surrounded by their own
fluid.
o They contain pigments
Trace the chemical reactions and energy change through the process
o Photosynthesis – 6CO2 + 6 H2O  C6H12O6 + 6O2
o The process is driven by light energy which is used to rearrange the C, H,
O atoms in the reactants to make the products of sugar and oxygen.
Energy is now stored in the chemical bonds of the sugar.
What are the two key parts of photosynthesis? Describe each of them.
o Light reactions – use the sun’s energy to excite electrons in pigments, the
movement of those electrons generates energy that can be coupled to the
production of ATP. Water is split to generate the electrons for this
reaction.
o Carbon fixation - The ATP from the light reactions is used to power the
production of glucose in the Calvin cycle using CO2 and the H and
electrons from the splitting of water.
Describe alternate methods of carbon fixation –
o Reason is to conserve water in plants that live in arid environments.
o Problem is that stomata need to be open to exchange gases but there is a
loss of water in the process.
o Plants have evolved methods to utilize CO2 in such a way as to minimize
that water loss and to reduce waste of photorespiration.
 Stomata may be open at night (CAM) – succulents
 Use an intermediate (C4) that has greater affinity for CO2 than does
the standard C3 method. It means plants can still operate with
stomata partly closed and lower CO2 concentration. This 4 C
intermediate carries the CO2 deeper into the plant where it can be
released to go through the Calvin cycle.
What is photorespiration?
o When O2 is in higher concentration than normal compared to CO2, it
interferes with the Calvin cycle
o Instead of CO2 entering Calvin cycle, O2 gets in the way, O2 is used up but
not ATP is produced – wasteful step. Does produce a little CO2 but not
highly efficient.
Compare C4 to C3 plants
C4 plants trap CO2 into a 4 carbon intermediate – adaptation to reduce
photorespiration and water loss.
o C3 plants trap CO2 into a 3-carbon intermediate.
What are CAM plants?
o Using another method for “fixing carbon” by having stoma open at night
and storing the fixed carbon in an acid intermediate.
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