1.3/2.1/2.2 Flashcards
Acid
A substance that produces hydrogen ions, H+, when dissolved in water
Base
A substance that produces hydroxide ion, OH-, when dissolved in water
pH Scale
A numerical scale ranging from 0 to 14 that is used to classify aqueous solutions as acidic, basic, or neutral
Neutralization Reaction
A chemical reaction between an acid and a base, producing water and a salt (ionic compound)
Buffer
A substance that minimizes changes in pH by donating or accepting hydrogen ions as needed
Oxidation
A process involving the loss of electrons
Reduction
A process involving the gain of electrons
Redox Reaction
A chemical reaction that involves the transfer of electrons from one substance to another; also called oxidation-reduction reaction
Condensation Reaction (Dehydration Synthesis)
A chemical reaction that results in the formation of a covalent bond between two molecules with the production of a water molecule
Hydrolysis Reaction
A chemical reaction that results in cleavage of a covalent bond with the addition of a water molecule
Activation Energy
The energy required to initiate a chemical reaction
Catalyst
A substance that speeds up the rate of a chemical reaction by lowering the activation energy for the reaction; is not consumed by the reaction
Enzyme
A biological macromolecule that catalyzes, or speeds up, chemical reaction in biological systems
Active Site
The site on an enzyme where the substrate binds; where the chemical reaction that is catalyzed by the enzyme takes place
Substrate
A reactant that interacts with the enzyme in an enzyme-catalyzed reaction
Enzyme-Substrate Complex
The combined structure of an enzyme with a substrate that is bound to the enzyme’s active site
List the ways in which enzymes prepare substrates for reaction (4)
1) The active sight may contain amino acid R groups that end up close to certain chemical bonds in the substrate, causing these bonds to stretch or bend (makes bonds weaker and easier to break)
2) Brings two substrates together in the correct position for a reaction to occur
3) Transfer electrons to or from the substrate (reduce or oxidize), destabilizing it
4) Add or remove hydrogen ions from the substrate (act as acid or base), destabilizing it and making it more likely to react
How are enzymes classified?
According to the type of reaction they catalyze.
-suffix “ase”
Coenzymes
Organic molecules that assist an enzyme
Cofactors
Metal ions that are required by some enzymes
What two factors affect enzyme activity?
Temperature and pH
pH Range: 6 to 8
Temperature: 37 degrees
Inhibitor
- A molecule that binds to the allosteric or active site of an enzyme and causes a decrease in the activity of that enzyme (no substrates can bind)
- stabilizes the inactive form of the enzyme
Competitive Inhibitors
Interact with the active site of the enzyme by out-competing substrate for active site
Allosteric Site
A site on an enzyme that is not the active site, where other molecules can interact with and regulate the activity of the enzyme
Non-competitive Inhibitors
- bind to allosteric site and reduce the ability of the enzyme to interact with substrate
- causes a conformational change in the enzyme so the active site shape no longer matches the substrate
- decrease in enzyme activity
- eg. DDT
Activator
- A molecule that binds to the allosteric site of an enzyme and keeps an enzyme alive or causes an increase in the activity of that enzyme
- stabilize active form of enzyme
Allosteric Regulation
The regulation of enzyme activity by activators and inhibitors binding to allosteric sites
Why is water the “universal solvent”?
- polar molecule
- small molecule
- capable of hydrogen bonding
What type of molecule is water?
Polar
Why is water a polar molecule? Which atom are the electrons more attracted to?
- electrons are more attracted to the oxygen so the electrons spend more time around it
- result is a partial positive hydrogen and partial negative oxygen that create a polar bond
- bent shape
Boiling and Freezing Point of Water
Boiling: 100 degrees Celsius
Freezing: 0 degrees Celsius
Heat of Vapourization
- the amount of heat needed to turn a given amount of liquid water into water vapour
- water has a high heat of vapourization
Specific Heat Capacity
- amount of heat needed to raise the temperature of 1 g of water by 1 degree Celsius
- water as a high specific heat capacity
What is meant by the phrase “water has strong cohesive properties”?
- the tendency of “like” molecules to stick together
- water molecules stick to other water molecules
Strong Adhesion
-the tendency of “unlike” molecules to cling together
“Tensile Strength”
-the resistance of molecules to being pulled apart; results in surface tension
Density of Water
-solid water floats as opposed to sinking like other substances
Ionization of Water
-water has a slight tendency to ‘fall apart’ or to ‘dissociate’
What are enzymes made of?
Proteins
‘Induced Fit’ Model
When the substrate enters the active site, the shape of the site changes to induce a better fit between the substrate and the enzyme
Cofactors
Additional factors required for the enzyme to function; inorganic
Coenzymes
Additional factors required for the enzyme to function; organic-usually synthesized from vitamin precursors
Mechanisms of Enzyme Activity
- structure dictates function
- if the structure is changed, it will influence the reaction rate of the enzyme
Factors Affecting Enzyme Activity
- Temperature
- pH
- Substrate Concentration
Temperature and Enzyme Activity
- each enzyme has an optimal temperature
- outside the specific temperature the enzymes can lose their shape and the bonds can weaken
PH and Enzyme Activity
- all enzymes have optimal pH ranges
- change in pH affects the tertiary structure of proteins
Substrate Concentration and Enzyme Activity
-with increasing substrate amounts, the enzyme spends less time “looking” for a substrate and more time catalyzing reactions
What are the two ways in which allosteric regulation works?
1) Controlling the production of the enzyme.
2) Monitoring the action of an enzyme that has already been produced.
Feedback Inhibition
-a method used to control metabolic pathways that involve a series of reactions, each catalyzed by a specific enzyme
How does feedback inhibition work?
- A product formed later in the sequence of reaction steps allosterically inhibits an enzyme that catalyzes a reaction occurring earlier in the process
- stops the series of reactions until they are needed again
Cell Theory
1) All cells come from pre-existing cells.
2) Cell are the simplest of life forms that carry out the most simple life processes.
3) All cells come from pre-existing cells.
What structures do animal cells have that plant cells do not?
- lysosomes
- centrioles
What structures for plant cells have that animal cells do not?
- central vacuole
- chloroplast
- granum
- cell wall
Nucleus
- control centre of the cell
- contains DNA which stores and replicates the genetic information of the cell
Nucleoplasm
A thick fluid that fills the nucleus
Nuclear Matrix
A network of protein fibres that provide internal structure and support.
Nucleolus
A non-membrane bound structure in the nucleus, which contains RNA and proteins
Nuclear Envelope
A double membrane surrounding the nucleus.
made of two phospholipid bilayers separating the nucleus from the rest of the cell
Nuclear Pore Complexes
A group of proteins forming openings in the nuclear envelope.
Endoplasmic Reticulum
A complex system of channels and sacs composed of membranes enclosing a lumen; made up of two parts, the rough ER and the smooth ER
Ribosomes
A structure composed of RNA and proteins, and responsible for synthesis of polypeptides in the cytoskeleton and on the surface of the rough ER
Which proteins are synthesized by rough ER ribosomes?
Ones that are part of membranes or intended for export from the cell.
Which proteins are synthesized by ribosomes that are freely suspended?
Ones that function in the cytosol.
Smooth ER
Regions of the ER that have no bound ribosomes
What is the function of the smooth ER?
-synthesis of lipids and lipid-containing molecules such as phospholipids that make up the cell membrane
Function of smooth ER in the Liver
-detoxifying of drugs and alcohol
Function of Smooth ER in Testes and Ovaries
-produces testosterone and estrogen
Endomembrane System
The system within the cell that acts to synthesize, modify, and transport proteins and other cell products; includes the endoplasmic reticulum, Golgi apparatus, vesicles and the cell membrane, among other structure.
The organelles that make up the endomembrane system are connected to one another by what?
Some are connected directly and other are connected by transport vesicles.
Vesicle
A membrane-enclosed sac used for transport and storage.
Golgi Apparatus
A stack of curved membrane sacs that packages, processes, sorts, and distributes proteins, lipids, and other substances within the cell; acts like a “post office” for the cell
Lysosome
A membrane-bound vesicle containing enzymes that catalyze hydrolysis reactions, breaking down macromolecules.
-break down bacteria and other foreign particles
How does the endomembrane system modify and transport proteins? (6 Steps)
1) On the surface of the rough ER, polypeptides are produced by bound ribosomes and extruded into the lumen, rather than being released into the cytosol.
2) Polypeptides travel through the lumen to the smooth ER, where they are stored and processed. When proteins are ready for transport, pieces of smooth ER pinch off to form vesicles containing the protein.
3) Vesicles from the smooth ER travel across the cell to the cis face of the Golgi Apparatus (stack of curved membrane sacs).
4) Vesicles merge with the membrane of the Golgi apparatus and release their contents into the interior.
5) In the Golgi body, some proteins are stored and others are modified further.
6) When the modified proteins are ready for transport, pieces of the Golgi body pinch off from the trans faces to form vesicles. The vesicles transport the proteins to the cell membrane, or to other destinations within the cell.
Other Functions of the Endomembrane System
- smooth ER synthesizes and metabolizes lipids including steroids and phospholipids
- Golgi body sorts, packages and distributes lipids as well as proteins
- Golgi body manufactures macromolecules (carbohydrates)
Pectins
Non-cellulose structural polysaccharides found in cell walls.
Peroxisomes
Membrane-bound sac containing oxidative enzymes that break down excess fatty acids and hydrogen peroxide, and participate in the synthesis of bile acids and cholesterol.
How do peroxisomes form?
By budding off from the ER
Which type of reactions do peroxisomes catalyze?
Redox Reactions (the enzymes are oxidases)
What organ contains many peroxisomes?
Liver (because toxic substances accumulate in the liver and peroxisomes breaks down some toxic molecules)
-breaks down alcohol molecules
What do many reactions that take place in the peroxisomes produce?
Hydrogen Peroxide (Therefore all peroxisomes contain catalase to break it down)
How do vesicles form?
By pinching off from the cell membrane and organelle membranes.
How do vesicles release their contents?
They fuse with cell membranes and organelle membranes.
What is different between animal and plant cells with respect to vesicles?
- Animal cells contain many small vesicles.
- Plant cells contain a single large central vesicle called a vacuole.
Vacuole
A large membrane-bound sac in plant cells and some other cells that stores water, ions, macromolecules, sugars and amino acids
also contains enzymes that break down macromolecules and cell wastes
Chloroplast
An organelle in the cells of photosynthetic organisms in which light energy from the Sun is captured and stored in the form of high-energy organic molecules such as glucose.
Stroma
A thick liquid in the inner membrane of a chloroplast that surrounds the thylakoids.
Thylakoids
Flattened disks that contain chlorophyll in their membranes.
Granum
A stack of thylakoids.
Mitochondrion
An organelle in eukaryotic cells in which high-energy organic molecules are oxidized to obtain energy.
Convert stored energy into usable energy
What are the two membranes in a mitochondrion?
- Smooth Outer Membrane
- Folded Inner Membrane
Cristae
Folds in the inner membrane of mitochondria
Matrix
Fluid-filled space in the inner membrane of mitochondria
What is a cell wall usually made up of?
Combination of polysaccharides, glycoproteins or both.
Cell Wall
A rigid layer surrounding a plant, algae, fungal, bacterial and some archaea cells, composed of proteins and/or carbohydrates; gives the cell its shape and structural support.
Cytoskeleton
A network of protein fibres that extends throughout the cytosol, providing structure, shape,support, and motility.
Cytoskeleton Fibres
- Vesicles and other organelles move along them (act like tracks that lead from one part of the cell to another)
- in some cases they form appendages that enable the cell to propel itself through the fluid surrounding it
Three Types of Protein Fibres in the Cytoskeleton
- Microtubules
- Intermediate Filaments
- Microfilaments
Size and Structure of Microtubules
- thickest fibres (25 nm in diameter)
- proteins that form hollow tubes
Size and Structure of Intermediate Filaments
- intermediate thickness (10 nm in diameter)
- proteins coiled together into cables
Size and Structure of Microfilaments
- thinnest fibres (8 nm in diameter)
- two strands of actin wound together
Functions of Microtubules
- maintain cell shape
- facilitate movement of organelles
- assist in cell division (spindle formation)
Functions of Intermediate Filaments
- maintain cell shape
- anchor some organelles
- form the internal scaffolding of the nucleus
Functions of the Microfilaments
- maintain cell shape
- involved in muscle contractions
- assist in cell division (cleavage furrow)
Flagella
-one or two longer appendages that act as a tail to propel cells
Cilia
-lots of shorter appendages that are composed of an internal shaft made of microtubules covered with an outer membrane that is a continuation of the cell membrane
Fluid Mosaic Model
The accepted model of the cell membrane, which is a basic framework of a semi-fluid phospholipid bilayer with a mosaic of proteins; carbohydrates may be attached to lipids or proteins
If the bilayer of a cell membrane is too fluid, then..
The bilayer permits too many molecules to diffuse in and out of the cell
If the bilayer in a cell membrane is not fluid enough then…
The bilayer prevents too many molecules from crossing
Factors Affecting the Fluidity of Lipid Bilayer
- Temperature
- Presence of Double Bonds in Fatty Acid “Tails”
- Fatty Acid “Tail” Length
- Presence of Cholesterol
Temperature and its Affect on the Fluidity of a Lipid Bilayer
- increase in temp causes increase in fluidity until it is an able to act as a barrier
- decrease in temp causes it to eventually solidify into a gel-like state
Presence of Double Bonds in Fatty Acid “Tails”
- double bonds form kinks in a fatty acid tail
- presence of one or more double bonds causes fatty acids to be less tightly packed and more fluid
Fatty Acid “Tail” Length
-longer tails have more intermolecular attractions and hold together more tightly compared to shorter fatty acid tails (reduces fluidity)
Presence of Cholesterol in Cell Membranes
- presence of cholesterol increases the intermolecular forces in the membrane and holds it more together (reduces fluidity)
- at lower temperatures, cholesterol molecules break up the pacing that occurs and increases the fluidity
Proteins Associated With Membranes
- Integral: embedded in the membrane
- Peripheral: loosely and temporarily attached to the outer regions of the membrane of to integral proteins
Functions of Membrane Proteins
- Transport
- Reaction Catalysis
- Cell Recognition
- Signal Reception and Transduction
Transport (Membrane Proteins)
-transport substances across cell membrane
Reaction Catalysis (Membrane Proteins)
-enzymes in cell membranes carry out chemical reactions
Cell Recognition (Membrane Proteins)
- carbohydrate chains that protrude from glycoproteins on the outer layer of the cell membrane enable cells to “recognize” each other
- allows for recognition of intruders (disease-causing agents)
Signal Reception and Transduction (Membrane Proteins)
- receptor proteins in cell membranes bind to signal molecules such as hormones and change shape as a result
- initiates a cellular response to the signal, enabling cells to receive and respond to signals from the brain and other organs
What is true about phospholipids in the cell membrane?
- tightly packed together (molecules that are too large cannot pass through this portion
- hydrophilic molecules (not fat soluble) cannot pass through middle fatty acid portion of membrane
Proteins in the Phospholipid Bilayer
- embedded in bilayer
- provides entryway for certain small molecules that cannot enter through the bilayer portion of the membrane
Glycoproteins in the Phospholipid Bilayer
- identity markers
- carry special sugar molecules providing a unique identity
How does the cell membrane maintain the integrity of the cell?
It regulates the passage of molecules and ions into and out of the cell.
Passive Transport
The movement of ions or molecules across a cell membrane from a region of higher concentration to a region of lower concentration, without the input of energy
Concentration Gradient
A difference in concentration between one side of a membrane and the other
Diffusion
The net movement of ions or molecules from an area of higher concentration to an area of lower concentration.
Will continue until the concentration is the same in all regions.
Eg. Oxygen and Carbon Dioxide and small non-polar molecules
Factors Affecting the Rate of Diffusion
- Molecule Size
- Molecule Polarity
- Molecule or Ion Charge
- Temperature
- Pressure
Molecule Size and Diffusion
-the larger a molecules, the more difficult it is for it to diffuse across a membrane
Molecule Polarity and Diffusion
-polar molecules have lower rates of diffusion than those of non-polar molecules of the same size
Molecule or Ion Charge and Diffusion
-charged molecules and ions cannot diffuse across a cell membrane
Temperature and Diffusion
-at higher temperatures, molecules have more energy and move faster
Pressure and Diffusion
-at higher pressure molecules are forced across the membrane and the rate of diffusion increases
Osmosis
The movement of water from and area of higher concentration to an area of lower concentration, across a semi-permeable membrane
Equilibrium
A condition in which all acting influences are balanced, resulting in a stable environment
Isotonic Solution
A solution where the concentration of solute molecules outside of a cell is equal to the concentration of solute molecules inside the cell. (Same osmotic concentration)
No net movement of water
Hypotonic Solution
A solution where the concentration of solutes outside a cell is lower than that found inside the cell.
Net movement of water into the cell and it bursts
Hypertonic Solution
A solution where the concentration of solutes outside a cell is higher than that found inside the cell.
Net movement of water out of the cell causing it to shrivel up
Facilitated Diffusion
The transport of ions or molecules across a membrane by means of a membrane protein along the concentration gradient for that ion or molecule.
Channel Proteins
A membrane protein that forms a channel across a cell membrane, which allows specific ions or molecules to cross the membrane along their concentration gradients.
Permit the passage of ions or polar molecules because they have a hydrophilic interior
Carrier Protein
A membrane protein that binds to and transports one or more particles of a substance from one side of a membrane to the other, along the concentration gradient for that substance.
Transport larger molecules such as glucose and amino acids
Why do carrier proteins change shape while transporting molecules?
Because they bind to the molecules they are carrying
Why do carrier proteins have lower rates of diffusion compared to channel proteins?
Because they bind to only a few molecules at a time.
How are channel proteins and carrier proteins similar?
The exteriors are composed of non-polar amino acids that interact with the non-polar interior of the membrane.
Active Transport
The transport of a solute across a membrane against its gradient.
What is the main source of energy in the cell?
ATP: adenosine triphosphate
-derived from an adenosine nucleotide where a phosphate is removed by hydrolysis that releases energy
Primary Active Transport
A cellular process that uses ATP directly to move molecules or ions from one side of a membrane to the other.
Sodium - Potassium Pump
- transports sodium ions out of the cell while transporting potassium ions into the cell
- both processes occur against the concentration gradient so the carrier protein requires ATP to function
Ion Channel Proteins
Facilitate the diffusion of ions across the cell membrane.
-can be opened or closed to control the movement of the ions and maintain the charge across the cell membrane
Electrochemical Gradient
The combination of a concentration gradient and an electrical potential across a membrane.
Secondary Active Transport
The use of an electrochemical gradient as a source of energy to transport molecules or ions across a cell membrane.
Eg. Hydrogen-Sucrose Pump
Process of a Hydrogen-Sucrose Pump
1) Hydrogen ions are first pumped out of the cell by a hydrogen ion pump which uses ATP as an energy source.
2) This causes an electrochemical gradient with an area of higher concentration and greater positive charge outside the cell.
3) Sucrose molecules outside the cell bind to a hydrogen-sucrose pump in the cell membrane.
4) Carrier protein allows hydrogen ions to move into the cell and as they do the hydrogen ions provide the energy that transports sucrose against its concentration gradient.
Membrane Assisted Transport
Transport method used to move materials that are too large to cross the cell membrane through a channel or carrier protein.
Vesicles form around incoming or out-going material and move it across the cell membrane.
Two Forms of Membrane Assisted Transport
- Endocytosis
- Exocytosis
Endocytosis
Process by which the cell membrane engulfs extra cellular material to bring it inside the cell
Cell membrane folds around particles and then pinches off to form a vesicle inside the cell
Three Methods of Endocytosis
1) Phagocytosis
2) Pinocytosis
3) Receptor-Mediated Endocytosis
Phagocytosis
Endocytosis involving solid particles.
Pinocytosis
Endocytosis involving liquid particles.
Receptor-Mediated Endocytosis
Receptor proteins in the cell membrane bind to specific molecules outside the cell and then fold inward to create a vesicle.
Exocytosis
Transport method in which a vacuole fuses with the cell membrane and releases its contents outside the cell.
