APBIO Final review info.
Unit 1
Enduring Understanding - These are the BIG overarching concepts you need to understand
Living systems are organized in a hierarchy of structural levels that interact. (1.1, 1.3, 1.4, 1.5)
The highly complex organization of living systems requires constant input of energy and the exchange of macromolecules. (1.2)
Heritable information provides for continuity of life. (1.6)
TOPIC 1.1 - Structure of Water and Hydrogen Bonding
(BIG IDEA 4 - SYSTEMS INTERACTIONS)
Properties of water result from
polarity
hydrogen bonding between water molecules result in…
Cohesion
adhesion
surface tension
Biological function of water is determined by the subcomponents and sequence of the molecule.
Living systems depend on properties of water
TOPIC 1.2 - Elements of Life
(BIG IDEA 2 - ENERGETICS)
Organisms must exchange matter with the environment to
Grow
Reproduce
maintain organization
Atoms and molecules from the environment are necessary to build new molecules Carbon used to build
Carbohydrates
Proteins
Lipids
Nucleic acids
Carbon is used in
storage compounds
cell formation in all organisms
Nitrogen used to build
proteins
nucleic acids
Phosphorus used to build
nucleic acids
certain lipids
TOPIC 1.3 - Introduction to Biological Macromolecules
(BIG IDEA 4 - SYSTEMS INTERACTIONS)
Properties of each monomer in biological macromolecules
The type of bonds that connect the monomers in biological macromolecules Process of forming and breaking covalent bonds in biological macromolecules
Hydrolysis
used to cleave (split apart) covalent bonds between monomers
dehydration synthesis
used to form covalent bonds between monomers
TOPIC 1.4 - Properties of Biological Macromolecules
(BIG IDEA 4 - SYSTEMS INTERACTIONS)
Structure and function of polymers are derived from the way their monomers are assembled
Nucleic acids
biological information is encoded in sequences of nucleotide monomers
Each nucleotide has structural components
a five-carbon sugar (deoxyribose or ribose)
a phosphate
a nitrogen base (adenine, thymine, guanine, cytosine, or uracil).
DNA and RNA differ in structure and function.
Proteins
Amino acids have directionality
an amino (NH2) terminus and a
carboxyl (COOH) terminus
The R group of an amino acid can be categorized by chemical properties
Hydrophobic
Hydrophilic
Ionic
the interactions of these R groups determine structure and function of that region of the protein
the specific order of amino acids in a polypeptide (primary structure) determines the overall shape of the protein
Complex carbohydrates
Made up of sugar monomers
structure determine the properties and functions of the molecules
Lipids
nonpolar macromolecule
Differences in saturation determine the structure and function of lipids.
Phospholipids
Have polar regions
interact with other polar molecules, such as water
have nonpolar regions
are often hydrophobic
TOPIC 1.5 - Structure and Function of Biological Macromolecules
(BIG IDEA 4 - SYSTEMS INTERACTIONS)
Changing the subunits of a polymer may lead to changes in structure or function of the macromolecule
Directionality of the subcomponents influences structure and function of the polymer
Nucleic acids
have a linear sequence of nucleotides that have ends
3’ end has a hydroxyl group
5’ end has a phosphate attached to the sugar
During DNA and RNA synthesis
nucleotides are added to the 3’ end of the growing strand, resulting in the
formation of a covalent bond between nucleotides.
DNA is structured as an antiparallel double helix
each strand running in opposite 5’ to 3’ orientation
Adenine nucleotides pair with thymine nucleotides via two hydrogen bonds
Cytosine nucleotides pair with guanine nucleotides by three hydrogen bonds
Proteins
Have linear chains of amino acids
connected by the formation of covalent bonds at the carboxyl (COOH) terminus of the growing peptide chain
The four types of protein structure determine the function of a protein.
primary structure (1o)
determined by the sequence order of their amino acids
secondary structure (2o)
local folding of the amino acid chain
alpha-helices and/or beta-sheets
tertiary structure (3o)
overall three-dimensional shape of the protein
often minimizes free energy
quaternary structure (4o)
arises from interactions between multiple polypeptide units
Carbohydrates
linear chains of sugar monomers connected by covalent bonds.
polymers may be linear or branched
TOPIC 1.6 - Nucleic Acids
(BIG IDEA 3 - INFORMATION STORAGE AND TRANSMISSION)
structural similarities and differences between DNA and RNA relate to their function
Structural similarities of DNA and RNA
have three components
A sugar
a phosphate group
a nitrogenous base
nucleotide units are connected by covalent bonds to form a linear molecule with 5’ and 3’ ends
nitrogenous bases are perpendicular to the sugar-phosphate backbone
Structural differences between DNA and RNA
The sugar
DNA contains deoxyribose
RNA contains ribose
The bases
RNA contains uracil
DNA contains thymine
The structure
DNA is usually double stranded
The two DNA strands in double-stranded DNA are antiparallel in directionality
RNA is usually single stranded
Unit 2
Enduring Understanding - These are the BIG overarching concepts you need to understand
Living systems are organised in a hierarchy of structural levels that interact. (2.1, 2.2)
The highly complex organisatio nof living systems requires constant input of energy and the exchange of macromolecules. (2.3)
Cells have membranes that allow them to establish and maintain internal environments that are different from their external enviorments. (2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 2.10)
Evolution is characterised by a change in the genetic makeup of a population over time and is supported by multiple lines of evidence. (2.11)
TOPIC 2.1 - Cell Structure: Subcellular Components
The cell theory says…
all living things are made up of 1 or more cells
cells are the basic unit of life
all cells are related due to an ancestral cell
There’s 2 cell types:
Prokaryotic, which lacks internal membranes
holds 2 domains of life, Archaea + Bacteria
Eukaryotic, which has internal membranes in the form of membrane bound organelles
holds Eukarya domain of life
i.e. protists, fungi, plants, animals
All cells on earth, regardless of cell type, have…
plasma membranes
selective lipid boundary to keep the inside in and outside out
typically a phospholipid bilayer
cytosols
semifluid gel that fills the cell
chromosomes
DNA strands containing genes
ribosomes
made up of ribosomal RNA(rRNA) + protiens
responsible for taking mRNA sequences and creating protiens based off it
Prokaryotic cells
no nucleus, DNA floats around in an unbound nucleoid region
no membrane bound organelles, cytoplasm bound by plasma membrane
Eurkaryotic cells
DNA stored in membrane bound nucleus
membrane bound organelles
organelles are small, internal, subcellular structures with specific functions
cytoplasm lives between the plasma membrane + nucleus
eukaryotes are generally larger than prokaryotes
SA:V(surface area : volume) ratio is critical for effective functioning
smaller cells = larger SA:V ratio (beneficial as less stuff inside to take care of, more surface area to absorb resources with)
Eurkaryotic organelles
the ER (endoplasmic reticulum) manufactures, processes, and transports the chemical compounds that the cells use
made up by a network of sacs
exists in 2 forms
rough form, with ribosomes stuck to the outside to help compartmentalise the cell
smooth form, acts as the site of cellular detoxification + lipid synthesis
golgi complex modifies protiens and packages them for distribution
mitochondrions hold double membranes, with the outer one being smooth and the inner one being incredibly folded and convoluted
lysomes are membranous sacs with hydrolytic enzymes for intercellular digestion
vacuoles are membrane bound sacs, used for storage of mostly waste + nutrients
chloroplasts are found in plant cells and perform photosynthesis
TOPIC 2.2 - Cell Structure + Function
mitochondrion possess double membranes which increase efficiency of cellular respiration(transfer of chemical energy of organic compounds into ATP, think of it as an electrical adaptor head)
mitochondrial membranes isolate metabolic reactions into its little compartments to improve efficiency, folded membrane = more space for membrane-bound molecules that produce ATP
the mitochondrion's highly convoluted inner membrane’s folds are known as cristae, the fluid in it is called the matrix, and the space between membranes is known as the intermembrane space
chloroplasts are home to grana/granum, stacks of membranous sacs called thylakoids, surrounded by stroma, a fluid that fills the chloroplast
lysosomes contain enzymes meant for digesting materials within vacuoles, they also recycle materials + old organelles, initiate apoptosis (programmed cell death, necessary for old/damaged cells)
TOPIC 2.3 - Cell Size
SA grows by n² + V grows by n³
high SA:V makes exchanging materials more efficient, leading cells to prefer having wonky membranes to increase surface area significantly
i.e. root hair cells on roots to increase water absorption
when cells/organisms increase in size, metabolic efficiency decreases
cells undergo various adaptations to make exchange more efficient
TOPIC 2.4 - Plasma Membrane
cell membrane creates a unique and separate environment inside the cell
typically composed of a phospholipid bilayer and a whole lot of proteins
polar/hydrophilic phosphate head + nonpolar hydrophobic lipid tail
peripheral proteins on surfaces of the membrane
integral proteins penetrate the membrane, transmembrane pass completely through the membrane
membrane proteins can either be…
hydrophilic with polar + charged R-groups
OR
hydrophobic with non-polar R-groups
Other membrane components include steroids, glycoproteins, + glycolipids
membrane components are fluid + move through the structure
steroids contribute to membrane fluidity, more steroids more fluidity, think saturated or unsaturated lipids
TOPIC 2.5 - Membrane Permeability
TOPIC 2.6 - Membrane Transport
TOPIC 2.7 - Facilitated Diffusion
TOPIC 2.8 - Tonicity + Osmoregularity
TOPIC 2.9 - Mechanisms of Transport
TOPIC 2.10 - Cell Compartmentalisation
TOPIC 2.11 - Origins of Cell Compartmentalisation
Unit 3
Enduring Understanding - These are the BIG overarching concepts you need to understand
The highly complex organization of living systems requires constant input of energy and the exchange of macromolecules. (Topics 3.1 - 3.6)
Naturally occurring diversity among and between components within biological systems affects interactions with the environment. (Topics 3.7)
3.1 - Enzyme Structure
Enzyme Structure
The active site interacts with a specific substrate
Enzyme-mediated chemical reaction
The shape and charge of the substrate must be compatible with the active site
3.2 - Enzyme Catalysis
Structure and function of enzymes
Contribute to the regulation of biological processes
Catalyst
What is it and why are enzymes considered to be one?
Enzymes lower activation energy
3.3 - Environmental Impacts on Enzyme Function
Change structure will change function
Denaturation
Occurs when protein structure is disrupted
Cannot catalyze reactions
Environmental temperatures and pH outside the normal range
Some enzymes can be renatured, allowing to regain activity
Environmental pH
Alter efficiency of enzyme activity
Disrupts hydrogen bonds
EQUATION: pH = -log[H+]
Do NOT need to calculate anything with this equation, but you do need to understand it
The higher [H+], the lower the pH is (more acidic)
Concentration of substrates and products
Affects the efficiency of reactions
Higher environmental temperatures
Increase the speed of movement of molecules
Increase the frequency of collisions between enzyme and substrate
Increase rate of reaction
Inhibitors
Competitive
Binds reversibly and irreversibly to the active site
Noncompetitive
Binds to the allosteric site
Changing the activity of the enzyme
3.4 - Cellular Energy
Living systems require constant input of energy
Life does not violate the 2nd law of thermodynamics
Energy input
must exceed energy loss to…
maintain order
power cellular processes
Cellular processes that release energy may be coupled with cellular processes that require energy.
Loss of order or energy flow results in death
Energy-related pathways in biological systems
are sequential to allow for a more controlled and efficient transfer of energy
A product of a reaction in a metabolic pathway is generally the reactant for the next step in the pathway
3.5 - Photosynthesis
Organisms capture and store energy for use in biological systems
Photosynthesis evolved in prokaryotic organisms
prokaryotic (cyanobacterial) photosynthesis produced an oxygenated atmosphere
foundation of eukaryotic photosynthesis
Light-dependent reactions of photosynthesis in eukaryotes
involve a series of coordinated reaction pathways
capture energy present in light to
yield ATP and NADPH
power the production of organic molecules
Cells capture energy from light and transfer it to biological molecules for storage and use
chlorophylls
absorb energy from light
boosting electrons to a higher energy level in photosystems I and II
embedded in the internal membranes of chloroplasts
Are connected by the transfer of higher energy electrons through an electron transport chain (ETC).
Electrons are transferred between molecules in a sequence of reactions as they pass through the ETC
an electrochemical gradient of protons (hydrogen ions) is established across the internal membrane.
proton gradient is linked to the synthesis of ATP from ADP and inorganic phosphate via ATP synthase
The energy captured in the light reactions and transferred to ATP and NADPH powers the production of carbohydrates from carbon dioxide in the Calvin cycle, which occurs in the stroma of the chloroplast.
3.6 - Cellular Respiration
Fermentation and cellular respiration
Use energy from biological macromolecules to produce ATP.
Are characteristic of all forms of life.
In eukaryotes it is
a series of coordinated enzyme-catalyzed reactions
capture energy from biological macromolecules
The electron transport chain
transfers energy from electrons in a series of coupled reactions
establish an electrochemical gradient across membranes
occur in chloroplasts,mitochondria, and prokaryotic plasma membranes.
In CR electrons delivered by NADH and FADH2 are passed to a series of electron acceptors as they move toward the terminal electron acceptor, oxygen.
In photosynthesis, the terminal electron acceptor is NADP+
Aerobic prokaryotes use oxygen as a terminal electron acceptor
Anaerobic prokaryotes use other molecules
The transfer of electrons is accompanied by
formation of a proton gradient across the inner mitochondrial membrane or the internal membrane of chloroplasts with the membrane(s) separating a region of high proton concentration from a region of low proton concentration.
In prokaryotes, the passage of electrons is accompanied by the movement of protons across the plasma membrane.
The flow of protons back through membrane-bound ATP synthase by chemiosmosis drives the formation of ATP from ADP and inorganic phosphate.
oxidative phosphorylation in cellular respiration
decoupling oxidative phosphorylation from electron transport generates heat
This heat can be used by endothermic organisms to regulate body temperature
photophosphorylation in photosynthesis
Glycolysis
releases energy in glucose to form
ATP from ADP and inorganic phosphate
NADH from NAD+
Pyruvate
transported from the cytosol to the mitochondrion, where further oxidation occurs.
Krebs cycle
carbon dioxide is released from organic intermediates
ATP is synthesized from ADP and inorganic phosphate
electrons are transferred to the coenzymes NADH and FADH2
electron transport chain
electrons extracted in glycolysis and Krebs cycle reactions are transferred by NADH and FADH2
in the inner mitochondrial membrane.
electrons are transferred between molecules in a sequence of reactions
forms an electrochemical gradient of protons (hydrogen ions) across the inner mitochondrial membrane is established
Fermentation
allows glycolysis to proceed in the absence of oxygen
produces organic molecules, including alcohol and lactic acid, as waste products
The conversion of ATP to ADP releases energy, which is used to power many metabolic processes.
3.7 - Fitness
Variation
molecular level
ability to respond to a variety of environmental stimuli.
number and types of molecules within cells
provides organisms a greater ability to survive and/or reproduce in different environments
Examples: types of phospholipids and adaptation to environmental temperatures, types of hemoglobin and oxygen absorption at different developmental stages, different chlorophylls allow plants to exploit different forms of wavelengths for photosynthesis
Unit 4
Enduring Understanding - These are the BIG overarching concepts you need to understand
Cells communicate by generating, transmitting, receiving, and responding to chemical signals. (4.1 - 4.4)
Timing and coordination of biological mechanisms involved in growth, reproduction, and homeostasis depend on organisms responding to environmental cues. (4.5)
Heritable information provides for continuity of life. (4.6 - 4.7)
4.1 - Cell Communication
Direct contact with other cells
Long distance communication
Use chemical signals
Short distance communication
Use local regulators
Target cells in the vicinity of signal-emitting cells
Signals
Released by one type of cell
Can travel short or long distances
Targets a different cell type
Examples of Cell to Cell contact:
Immune cells interact by cell-to-cell contact, antigen-presenting cells (APCs), helper T-cells, and killer T-cells.
Plasmodesmata between plant cells allow material to be transported from cell to cell.
Examples of Cell Communication Using Local Regulators:
Neurotransmitters
Plant immune response
Quorum sensing in bacteria
Morphogens in embryonic development
Insulin
Human growth hormone
Thyroid Hormone
Testosterone
Estrogen
4.2 - Introduction to Signal Transduction
Components of pathway
Link signal reception with cellular responses
Include protein modification and phosphorylation cascades
Signaling cascades
relay signals from receptors to cell targets
Signaling begins with receptor protein
Recognition of a chemical messenger called a ligand
can be a peptide, a small chemical, or a protein
Receptor protein of target cell such as a G protein-coupled receptor in eukaryotes
Ligand-binding domain
Recognizes a ligand in a one-to-one relationship
Binding of ligand-to-ligand-gated channels can cause the channel to open or close
After the ligand binds
the intracellular domain of a receptor protein changes shape
and initiates transduction of the signal
amplify the incoming signals
Second messengers (such as cyclic AMP) are molecules that relay and amplify the intracellular signal
Results in the appropriate responses by the cell
Including cell growth, secretion of molecules, or gene expression
4.3 - Signal Transduction
Signal transduction pathways influence how the cell responds to its environment.
Different types of cellular responses are elicited by signal transduction pathway
changes in gene expression and cell function
may alter phenotype
or result in programmed cell death (apoptosis).
Examples of Using Signal Transduction to Respond to the Environment:
Use of chemical messengers by microbes to communicate with other nearby cells and to regulate specific pathways in response to population density (quorum sensing)
Epinephrine stimulation of glycogen breakdown in mammals
Cytokines regulate gene expression to allow for cell replication and division.
Mating pheromones in yeast trigger mating gene expression.
Expression of the SRY gene triggers the male sexual development pathway in animals.
Ethylene levels cause changes in the production of different enzymes allowing fruits to ripen.
HOX genes and their role in development.
4.4 - Changes in Signal Transduction Pathways
Changes in signal transduction pathways can alter cellular response
Mutations in any domain of the receptor protein
Mutations or changes in any component of the signaling pathway
affect the downstream components
altering the subsequent transduction of the signal
Chemicals that interfere with any component of the signaling pathway
may activate or inhibit the pathway
4.5 - Feedback
positive and/or negative feedback mechanisms
used to maintain internal environments
respond to internal and external environmental changes
Negative feedback helps to maintain homeostasis
regulate physiological processes
If a system is out of balance, negative feedback mechanisms return the system back to its target set point.
These processes operate at the molecular and cellular levels.
Positive feedback affects homeostasis
Amplify responses and processes in biological organisms
The variable initiating the response is moved farther away from the initial set point.
Amplification occurs when the stimulus is further activated, which, in turn, initiates an additional response that produces system change.
Examples of Negative Feedback: Blood sugar regulation by insulin/glucagon
Examples of positive feedback:
Lactation in mammals
Onset of labor in childbirth
Ripening of fruit
4.6 - Cell Cycle
Events of the eukaryotic cell cycle
For growth and reproduction of cells
Sequential stages
Interphase (G1, S, G2)
Mitosis
Results in the transmission of chromosomes from one generation to the next
ensures the transfer of a complete genome from a parent cell to two genetically identical daughter cells
plays a role in growth, tissue repair, and asexual reproduction
alternates with interphase in the cell cycle
occurs in a sequential series of steps (prophase, metaphase, anaphase, telophase)
Cytokinesis
G0
A cell can enter this stage where it no longer divides
it can reenter the cell cycle in response to appropriate cues.
Nondividing cells may exit the cell cycle or be held at a particular stage in the cell cycle
4.7 - Regulation of Cell Cycle
Checkpoints
regulate progression through the cycle
Interactions between cyclins and cyclin-dependent kinases control the cell cycle
Disruptions to the cell cycle may result in
cancer and/or
programmed cell death (apoptosis)