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
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!!!
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
Prokaryote – simpler cells – no membrane bound organelles, circular rather than linear DNA -
Eukaryote – compartmentalized – separate areas for different types of reactions and processes - more efficient – more complex.
How do feedback mechanisms regulate systems?
Metabolic reactions have to be regulated – there has to be ways to start and stop chemical reactions.
Most chemical reactions in the bodies are facilitated by enzymes (catalysts).
Enzymes can be regulated with competitive or noncompetitive inhibition or activation
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 –
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.
Diversity – with evolution and adaptations to environmental conditions, we have evolved to different species
Describe the three domains
Archaea – old prokaryotes that can survive in extreme conditions
Bacteria – modern prokaryotes
Both archaea and bacteria belong to the Kingdom called Monera
Eukarya are all the eukaryotes and include kingdoms of Fungi, Protista, Animalia, Plantae
Explain Charles Darwin’s theory of Natural Selection
Evolution is not planned or intentional
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:
Atoms
Elements
Compounds
Ionic bonds
Covalent bonds
Metals
Nonmetals
Subatomic particles and their location
Atomic mass
Atomic number
Isotopes
How is potential energy related to electron levels?
Electrons occupy energy levels that have a maximum occupancy
Further away from the nucleus  higher energy level.
What happens when an electron moves from one level to another?
Electrons absorb and release energy all the time
It takes energy for an electron to go to a higher energy level
When it returns to its own energy level, it releases that energy back out.
How does electron distribution relate to chemical properties and bonding?
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?
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.
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:
Cohesion
Adhesion
Surface tension
High specific heat
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
Carbohydrates
Proteins
Lipids
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
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:

Define exergonic and endergonic
Exergonic reactions give off energy that could be trapped to do work (i.e. run other reactions, build molecules, move things).
Endergonic reactions require an input of energy – often they are coupled to an exergonic reaction.
How do the structures of ATP and, conversely, ADP, allow them to store and release energy?
ATP is an adenosine molecule that has 3 phosphate groups attached to it
The breaking of one Pi off ATP releases some energy (exergonic) and leaves products of ADP and Pi.
ADP has two phosphates –
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?
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.
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
ATP is regenerated when energy is added to the reaction of ADP and Pi.
How do enzymes work based on a specfic shape?
Enzymes are proteins with a very specific 3-D shape
Enzymes have a specific active site that will only fit the target “substrate” unless an inhibitor.
Define substrate, active site
Substrate is the specific reactant(s) that an enzyme matches.
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.
Even spontaneous reactions need to breach an energy of activation -
Enzymes lower the activation barrier and make it easier for the reaction to start.
What factors affect enzyme activity?
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.
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

Give a brief summary of redox reactions (oxidation and reduction).
The transfer of electrons from one element to another
Oxidation occurs to the element that loses an electron
Reduction occurs to the element that gains an electron
One cannot occur without the other.
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?
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).
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.
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.
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.
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.
Explain how fermentation occurs in the absence of oxygen
In the absence of oxygen the processes in the mitochondria cannot occur –
Fermentation is basically glycolysis followed by alcohol or lactic acid production.
Distinguish between alcohol and lactic acid fermentation
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
Fermentation only yields 2ATP/glucose.
Aerobic respiration can produce 38 ATP/glucose
What is significant about glycolysis?
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?

Compare/contrast anabolism to catabolism
Anabolism is building molecules
Catabolism is breaking them down
How are stages of cellular metabolism regulated?
Enzymes!
Feedback from different steps can slow or stop previous reactions by working on the enzymes –

Chapter 10

Distinguish between autotrophs and heterotrophs
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.
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?
Plant is covered with a waxy coating to prevent dehydration but also prevents gas exchange.
There are openings in the leaf called stomata that let gases through.
What is the pigment that captures most of the sun's energy?
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.
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).
Mitochondria and chloroplasts have their own DNA and their own ribosomes so they can reproduce and make their own proteins.
Chloroplasts have inner membranous stacks surrounded by their own fluid.
They contain pigments
Trace the chemical reactions and energy change through the process
Photosynthesis – 6CO2 + 6 H2O  C6H12O6 + 6O2
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.
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.
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 –
Reason is to conserve water in plants that live in arid environments.
Problem is that stomata need to be open to exchange gases but there is a loss of water in the process.
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?
When O2 is in higher concentration than normal compared to CO2, it interferes with the Calvin cycle
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.
C3 plants trap CO2 into a 3-carbon intermediate.
What are CAM plants?
Using another method for “fixing carbon” by having stoma open at night and storing the fixed carbon in an acid intermediate.