Biology Exam Study Guide
I. Membrane Structure and Function
A. All cells are defined by a cell membrane that establishes “inside” versus “outside”. - The cell membrane is a “fluid mosaic” of two types of molecules:
- Protein molecules
- Fluid bilayer of phospholipids
B. Membrane lipids compose the structural parts of the membrane.
• Amphipathic phospholipids arrange in a bilayer with hydrophobic tails oriented inward.
• Phospholipids that make up the membrane each contain one head and two tails. • Amphipathic: the tails of the phospholipids are hydrophobic and the head is hydrophilic, so the head attracts water and the tails repel water, sending the tails in towards each other and creating the bilayer with heads on the outside and tails on the inside.
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C. The degree of movement and space in-between molecules in a membrane is a function of membrane fluidity, which is determined by the saturation and length of fatty acid tails • Saturated fatty acids: the tails are straight, so the membrane is more viscous • Unsaturated fatty acids: the tails are more curved, so the membrane is more fluid. • Cholesterol can be added to the membrane to modulate fluidity: If you want to learn more check out What is dna replication?
• It keeps more fluid membranes from becoming too fluid
• Also keeps less fluid membrane from becoming too viscous If you want to learn more check out What are victimless crimes?
D. Membrane proteins are largely responsible for determining the functions of a cell membrane.
• Functions of protein:
• Enzymatic activity
• Signal transduction We also discuss several other topics like What is the state of the evidence for emotional disclosure in the pennebaker study?
• Cell-cell recognition
• Peripheral membrane proteins associate with the membrane on one side but don’t enter the membrane
• Integral membrane proteins insert into the lipid bilayer and penetrate the hydrophobic interior of the bilayer, either partially (monotopic) or passing all the way through (transmembrane)
• Transmembrane proteins provide mechanisms for the transport of solutes across the cell membrane in a regulated fashion, which makes membranes selectively permeable.
• Selective permeability allows cells to protect themselves from unwanted elements and to allow for wanted items in the cell
• 2 kinds of transport proteins allow for some ions and polar molecules to enter the membrane:
1. Channel proteins have a hydrophillic channel through which certain molecules or atomic ions can use as a tunnel to get through the membrane. • Aquaporins are a kind of channel protein that allow 2 billion water If you want to learn more check out What do motor maps really represent?
molecules to pass into the cell every second.
2. Carrier proteins hold onto their passengers and change shape in a way that the movement of particles of any substance so that they spread out into the available space. shuttles them across the membrane.We also discuss several other topics like What is the study of death?
E. Passive transport requires no energy investment
• Occurs when solutes are moving “down” a concentration gradient. • Concentration gradient: the region along which the density of a chemical substance increases or decreases. Every substance diffuses down its concentration gradient.
• The cell uses facilitated diffusion: the movement of particles of any substance so that they spread out into the available space.
• Through channel proteins or carrier proteins to allow them to cross the membrane without expanding energy
F. Active transport requires the cells to spend energy to move solutes “up” a concentration using protein pumps.
• Uses energy to move solutes against their gradients
• 3 kinds of protein pumps:
• Uniport: moves one solute through the membrane
• Antiport: moves two solutes across the membrane in opposite directions • Symport: moves two solutes across the membrane in the same direction G. Bulk transport — moves large or abundant molecules or groups of molecules across a membrane, using endocytosis and exocytosis.
• Endocytosis: the movement of material into the cell
• 3 Main mechanisms:
• Phagocytosis: the cell engulfs a particles by extending pseudopodia around it and packaging it within the vacuole
• Pinocytosis: the cell continuously “gulps” droplets of extracellular fluid into tiny vesicles so that the cell can obtain molecules that are
dissolved in the droplets. It is nonspecific for the substances it
transports. The vesicles are often lined with a protein coating called clathrin.
• Receptor mediated endocytosis: a specialized type of pinocytosis that allows the cell to acquire bulk quantities of things, but is more specific than the other mechanisms. The receptor proteins in the plasma
membrane cluster in coated pits and each pit forms a vesicle that
contains the molecules. These proteins are very selective about what enters and exits the cell.
• Exocytosis: the movement of material out of the cell,
• In exocytosis, a transport vesicle from the Golgi apparatus moves along the microtubules of the cytoskeleton to the plasma membrane, where plasma and vesicle membranes come in contact and the proteins rearrange the lipid molecules of the membranes so that the two membranes fuse together. When the vesicle becomes part of the plasma membrane the contents of the vesicle spill outside of the cell.
II. Energy, Enzymes, and Reaction Coupling
A. Metabolism is the sum of all anabolic and catabolic reactions in an organism. • Metabolism is the sum of all biochemical reactions in every cell (the broad definition) • It is assembled into pathways that intersect different networks, called metabolic pathways.
• The metabolic pathways break the process of metabolism down into multiple steps, dividing small jobs up for different enzymes.
• Allows for complex, interconnected systems.
• Anabolic reactions (aka biosynthetic) refer to the body making things. • Catabolic reactions (aka degradative) refer to the body breaking things down. B. Energy is the capacity to do work.
• There are two main kinds of energy:
• Kinetic energy is transferred between objects in motion
• Potential energy is stored in an object and must be released
• For example, a ball at the top of a hill has potential energy.
• Free energy: the released potential energy that is available to do work. • In molecules, free energy is stored in covalent bonds. When the bonds break the energy is released. This reaction occurs, for example, when two logs are rubbed against each other hard enough to break the bonds that release heat that start a fire. C. The First Law of Thermodynamics: conservation of energy — energy can be transferred but cannot be created nor destroyed
• The Second Law of Thermodynamics: entropy in the universe always increases • Entropy = the drive for energy to spread out evenly throughout the universe • Measure of disorder
• Unusable energy
• Energy is made available to do work
• Energy can be used to increase order in the system.
D. Free energy = chemical energy that is available to do work
• It’s expressed as the difference between enthalpy and entropy
• Enthalpy = total energy
E. Any reaction involves change in free energy (delta G) between reactants and products. • The positivity or negativity of delta G determines whether it is spontaneous (exergonic) or non spontaneous (endergonic)
• If the change in G is negative, meaning that the free energy of the reactant is lower than the energy of the product, the reaction is exergonic.
• If the change in G is positive, meaning that the free energy of the reactant is higher than the energy of the product, the reaction is endergonic.
F. Enzymes are proteins that reduce activation energy of a reaction to speed up the reaction. • They are the “catalysts of biological systems”
• Activation energy is the free energy of activation; the energy that is required for a chemical reaction to start
• Enzymes speed up reactions without changing thermodynamics
G. Enzyme specificity and function are the result of the shape of the protein. • Most enzymes are proteins, and proteins’ shape determine their function. • The shape also determines the specificity of the active site
• Shape change causes activity change
• A substrate is a reactant that the enzymes act on
• The substrate binds to an active region of the enzyme called the active site. The active site is a small pocket or groove on the surface of an enzyme that binds to the substrate.
• Enzyme + substrate —> Enzyme-substrate complex —> Enzyme + products • When the active site and the substrate bind they form an enzyme-substrate complex with a close interaction through induced fit. Induced fit is the way that the binding between the substrate and the enzyme gets tighter as the enzyme shape shifts, which brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction.
H. Environmental factors interfere with the tertiary or quaternary structure of an enzyme will impact its activity.
• If protein structure is changed, the activity is also affected.
• Factors that could interfere:
• Temperature: when temperature increases, molecules move faster causing substrates to collide with active sites more often. Past a certain temperature the activity will decrease because the thermal agitation will cause the weak bonds to break. Optimal temperature for most humans is 35-40 C
• pH: a neutral or almost neutral pH provides the best environment for
enzymes (between 6-8, with a few exceptions)
I. Cofactors: nonprotein helpers that can be bound tightly to the enzyme as permanent residents or loosely and reversible with the substrate.
• Sometimes inorganic, such as zinc, iron, and copper
• Sometimes organic (coenzymes), such as vitamins
J. Optimal conditions refer to environment that process the most favorable active shape for the enzyme to work. Enzymes adapt, evolve, and diversify over generations, and enzymes have different optima.
K. Enzyme activity can be reduced by competitive inhibitors that compete with substrates for the active site.
• Inhibitors are chemicals that selectively inhibit the action of specific enzymes • Competitive inhibitors mimic normal substrates and compete for admission into the active sites.
• Noncompetitive inhibitors do not directly compete with the substrate to bind to the active site — they bind to another part of the enzyme causing the enzyme moleculed to change and to function less effectively.
L. Enzymes can be regulated by allosteric effectors.
• Allosteric effectors are noncompetitive inhibitors that bind somewhere not on the active site and change the shape of the protein.
• Can either inhibit, activate, or stabilize the enzyme function
M. Metabolic pathways can be regulated at different steps depending on the demands of the cell.
• Feedback inhibition: when a metabolic pathway is halted by the inhibitory binding its end product to enzyme that acts early in the pathway
• Negative feedback (aka feedback inhibition) loops use the product of a pathway to inhibit an enzyme at the beginning of the pathway.
• Substrates are usually competitive, so as the product increases in concentration, it will bring the reaction back up.
• When the inhibitor changes the shape of the enzymes, the substrate is not competitive. This is an exception to the rule of adding more to a substance to increase the reaction.
N. Positive ∆G reactions are driven by reaction coupling with negative ∆G reactions to give a net overall negative ∆G for the combined reactions.
• Energy coupling: an enzyme causes an endergonic reaction to be driven by an exergonic one.
O. The most common energy couple is ATP/
• ATP has stress bonds between oxygen-rich phosphate groups that are weak (easy to break).
• Yields -.73 kcal/mole (∆G)
• The exergonic process of ATP hydrolysis drives endergonic reactions by transfer of a phosphate group to specific reactants, forming a phosphorylated intermediate that is more reactive.
P. ATP is recycled.
• ATP is used and regenerated from ADP as they exchange a phosphate. • The cell gains the free energy required to phosphorylate ADP from the exergonic breakdown reactions, and then ATP becomes regenerated with the repeated addition of an inorganic phosphate.
Q. ATP is made by enzyme driven substrate-level phosphorylation or by redox driven oxidative phosphorylation.
• Oxidation: the loss of electrons from one substance
• Reduction: the addition of electrons to another substance
• Oxidation-reduction (redox) reactions: the transfer of one or more electrons from one reactant to another
• Substrate-level phosphorylation: the enzyme-catalyzed formation of ATP by direct transfer of a phosphate group to ADP form an intermediate substrate in catabolism. • Redox driven oxidative phosphorylation: the production of ATP using energy derived from the redox reactions of an electron transport chain
• The three steps of aerobic respiration include (1) glycolysis, (2) pyruvate oxidation and the citric acid cycle, and (3) redox driven oxidative phosphorylation.
R. NADH (or NADPH) is an important energy couple.
• It shuttles electrons between redox reactions
• During aerobic respiration (aka cellular respiration), electrons are usually passed to NAD+, reducing it to NADH, and then from there to an electron transport chain.
S. The energy from redox reactions is extracted in small amounts by electron transport chains. • Electron transport chains: a number of molecules (mostly protein) that are built into the inner membrane of the mitochondria of eukaryotic cells
• The ETC conducts them to O2 in energy-releasing steps.
• It also captures H+, and forms water.
• That energy is used to make ATP.
the transportation of large molecules or a group of molecules from the cell at the same time
the process of bringing things into the cell
reversed endocytosis; the secretion of molecules from the cell
“cell eating”, the form of endocytosis that allows the cell to consume large things at once
"cell drinking”, the form of endocytosis that brings in water by fusing the vesicle membrane with the plasma membrane
A more specific version of pinocytosis that uses both peripheral and receptor proteins.
the sum of all biochemical reactions in every cell
Biosynthetic; the body making things
Degradative; the body breaking things down
reactions that occur one after another, in a specific order; they allow for complex metabolic systems, and break down the process into small steps
the capacity to do work
energy that goes from motion to something else
non-kinetic energy that is stored in bonds and released by the movement from higher concentration to a lower one
1st Law of
Conservation of Energy: energy can be transferred, but it cannot be created nor destroyed
2nd Law of
Entropy in the universe is always increasing
the drive for energy to spread out evenly throughout the universe; a measure of randomness/disorder
The model that shows the constructs of a plasma membrane; a mosaic of protein molecules bobbing in a fluid bilayer of phospholipids; called mosaic because membranes within each cell have a unique collection of membrane functions
the characteristic of the phospholipids that make up a plasma membrane: they have hydrophilic heads and two hydrophobic tails that lead to the bilayer formation of the membrane.m
The two-layered membrane arranged with hydrophilic tails on the inside and hydrophobic heads on the outside.
the opposite of fluidity; when the lipid tails are packed more tightly together and allow for less to enter the membrane
proteins that penetrate the hydrophobic interior of the lipid bilayer
proteins that are not embedded in the lipid bilayer and are just loosely bound to the surface of the membrane; held down by the cytoskeleton or attached to fibers of the extracellular matrix
the membrane carbohydrates that are covalently bonded to lipids
a property of the membrane that allows only some substances to exit and enter the cell
proteins that help move some ions and polar molecules into the membrane
a kind of transport protein that have hydrophilic channels through which certain molecules or atomic ions can use as a tunnel to get through the membrane
a kind of channel protein that allow water through the membrane
hold onto their passengers and change shape in a way that shuttles them across the membrane
diffusion of a substance across a membrane with no energy investment needed
the movement of particles of any substance so that they spread out into available space
the region along which the density of a chemical substance increase or decreases; every substance diffuses down one; substances move from high to low gradients in diffusion
the diffusion of water molecules through the pores of a membrane
the ability of surrounding solution to cause a cell to gain or lose water, depending on the solute concentration and membrane permeability (if concentration is high water leaves, if it’s lower, water enters)
when there is no net movement of water in or out of the cell because water diffuses in and out of the membrane at the same rate
a solution that does not maintain enough water because the water leaves the cell faster than it enters; could result in shrivel and death
solution that has too much water because the water enters the cell faster than it leaves; could cause swelling and bursting
the control of solute concentrations and water balance; usually achieved by rigid cell walls
very firm, created by turgor pressure in a hypertonic cell
very limp, created when the cell is isotonic
when the cell shrivels up it develops this, which can be deathly
when polar molecules and ions diffuse passively with the help of transport proteins on the membrane
the channel proteins that function as gated channels and open or close in response to stimulus
the pumping of a solute across a membrane that requires work, undergone by carrier proteins
a pump that exchanges sodium for potassium across the membrane in order to maintain higher concentrations of potassium ions and lower concentration of sodium ions in the cell
electrical potential energy; all cells have it
voltage across a membrane, which is negative on the cytoplasmic side and positive on the extracellular side because of unequal distribution of anions and cations
the combination of two forces that drive diffusion of ions across a membrane
the transport protein that generates voltage across a membrane
when transport protein couples the “downhill” diffusion of the soul to the “uphill” transport of a second substance against its own concentration gradient
the peripheral protein with a coated pit that helps with receptor-mediated endocytosis
a major pathway of catabolism where sugar glucose and other organic molecules become available to do the work of the cell
the study of how energy flows through living organisms
kinetic energy associated with random movement of atoms or molecules
thermal energy that transfers from one object to another
potential energy that is available to be released in a chemical reaction
the process that leads to an increase in entropy and can proceed without requiring an input of energy; notated by a negative delta G
the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system
reactions propelled forward by a net release of free energy (G is negative); usually random
absorbs free energy from its surroundings (G is positive)
total energy (marked by H in the delta G equation)
free energy of activation, the energy required to start a reaction
the biological catalysts; speed up reactions by lowering activation energy
Cell’s 3 kinds of work
chemical, transport, and mechanical work
pushing of endergonic reactions that would occur as the synthesis of polymers from monomers (like dehydration or hydrolysis - the breaking down of molecules)
the pumping of spontaneous movement (like diffusion or pumping an ion)
any physical movement in the cell (like arrangement of the cytoskeleton or muscle contraction)
the use of exergonic processes to fuel an endergonic one
adenosine triphosphate, a nucleotide that is used to drive endergonic reactions in cells
block the active site to inhibit a reaction
turns on, off, or stabilizes enzymes with the use of noncompetitive
the active site going back and forth from bad shape to good shape on its own (adding an inhibitor keeps it in bad shape and adding an activator keeps it in a good shape)
a reactant that an enzyme acts on
the loss of electrons
the gaining of electrons
a number of molecules (mostly proteins) that are built into the inner membrane of the mitochondria of eukaryotic cells