Ch. 6-8 Flashcards
Cells, membranes, and enzymes
cell
is the simplest unit necessary for all the activities of life
Robert Hooke
used the first microscope and coined the term “cell”
Antonie van Leeuwenhoek
the father of microbiology
magnification
the process of making an object appear larger when viewed through a microscope or other optical devices
resolution
a measure of image clarity
contrast
the difference in light intensity between a sample and its background (ex: staining samples)
plasma membrane
the membrane at the boundary of every cell that acts as a selective barrier, regulating the cell’s chemical composition
cytoplasm
the contents of the cell bounded by the plasma membrane, in eukaryotes, the portion exclusive of the nucleus
chromosomes
organizing units of DNA
ribosomes
complexes made of ribosomal RNA and protein; sites of protein synthesis
bacteria cell walls
composed of peptidoglycan; typically a singular circular DNA based chromosome
nucleoid
a region in a prokaryotic cell that contains most or all of the cell’s genetic material
capsule
a protective, gelatinous layer that surrounds the cell wall of certain bacteria and some fungi, typically composed of polysaccharides, which acts as a barrier against harmful substances and helps the cell adhere to surfaces
flagella
microscopic hair-like structures involved in the locomotion of a cell
fimbriae
thin, hair-like protein appendages found on the surface of bacterial cells, which function to help the bacteria adhere to surfaces by acting as attachment points to specific receptors on host cells
Why are most cells microscopic?
-oxygen and nutrients need to diffuse across the plasma membrane into the cell and wastes need to diffuse out of the cell
-cells must maintain a high surface area to volume ratio
-more surface area provides cells with more contact points with the environment
prokaryotes
single cell organisms that do not have a nucleus or other organelles
eukaryotes
have a nucleus and other internal membrane bound organelles
nucleus
a membrane-bound organelle that contains the cell’s genetic material (DNA) organized into chromosomes
chromosomes
cellular structures carrying genetic material found in the nucleus of eukaryotic cells; consists of a very long DNA molecule and associated proteins
chromatin
the complex of DNA and proteins that make up eukaryotic chromosomes
nucleolus
a specialized region within a nucleus that contains the genes from multiple chromosomes that code for rRNA; primarily responsible for producing and assembling the cell’s ribosomes, which are imported from the cytoplasm
nuclear envelope
double membrane that surrounds the nucleus; a complex structure that separates the nucleus from the cytoplasm in eukaryotic cells
nuclear pore complex
mediates transport of all macromolecules between the nucleus and the cytoplasm
nuclear lamina
a netlike array of protein filaments that lines the inner surface of the nuclear envelope and helps maintain the shape of the nucleus
nuclear matrix
a framework of protein fibers extending throughout the nuclear interior
endomembrane system
the collection of membranes inside and surrounding a eukaryotic cell, related either through direct physical contact or by the transfer of membraneous vesicles
free ribosomes
are suspended in the cytosol
cytosol
the semifluid portion of the cytoplasm
bound ribosomes
are attached to the outside of the endoplasmic reticulum
endoplasmic reticulum (ER)
an extensive membraneous network in eukaryotic cells, continuous in the outer nuclear membrane
lumen or cisternal space
interior of the ER that is separate from the cytosol
smooth ER
does not have ribosomes attached to its surface; the site for lipid synthesis (including steroids), metabolism of carbohydrates, detoxification of drugs and poisons, storage of calcium ions
rough ER
does have ribosomes attached to its surface; protein synthesis (including hormones)
transport vesicles
small, membrane bound sacs that function to move molecules like proteins and lipids between different organelles within a cell
Golgi apparatus
shipping and receiving center of a cell
cisternae
flat stacks of membrane found in the ER and Golgi apparatus
cis face
the receiving side of the Golgi that faces the ER; transport vesicles coming from ER fuse to the cis face of Golgi
trans face
the shipping side of the Golgi that faces away from the ER; transport vesicles leaving the Golgi exit from the trans face
lysosomes
a membranous sac of hydrolytic enzymes used to digest macromolecules
phagocytosis
when large particulate substances or small organisms are taken up by a cell (cellular “eating”)
autophagy
a natural process that helps cells recycle and break down damaged or unnecessary parts (“self-eating”)
vacuoles
large vesicles produced from the ER and Golgi; a membrane-bound organelle within a cell that functions as a storage compartment, filled with fluid and containing various substances like water, nutrients, waste products, and pigments
mitochondria
sites of cellular respiration; use oxygen to extract energy from sugars and fats to generate ATP
mitochondrial matrix
the compartment of mitochondrion enclosed by the inner membrane and containing the enzymes and substrates for the citric acid cycle, as well as ribosomes and DNA
citric acid cycle
produces substrates for the electron transport chain
mitochondrial membranes
inner and outer membrane
cristae
folds in the inner membrane of mitochondria that increase the surface area for chemical reactions to take place
inner membrane
is much more selective, acting as a barrier to most ions and molecules, crucial for maintaining the proton gradient necessary for ATP production
outer membrane
is highly permeable to small molecules due to the presence of porin proteins
Endosymbiont Theory
mitochondria and chloroplasts originated as prokaryotic cells engulfed by an ancestral eukaryotic cell. the engulfed cell and its host cell then evolved into a single organism
chloroplasts
organelles found in plants and algae that are the sites of photosynthesis
chlorophyll
the green pigment located within chloroplasts necessary for capturing light
thylakoids
membrane-bound compartments in chloroplasts and cyanobacteria that are responsible for the light-dependent reactions of photosynthesis
granum
a coin-shaped stack of thylakoids, which are the membrane-like structures found inside the chloroplasts of plant cells
cytoskeleton
a network of protein fibers that extend throughout the cytoplasm and serve a variety of mechanical, transport, and signaling functions
stroma
area between the inner membrane and the thylakoids
motor proteins
a protein that interacts with cytoskeletal elements and other cell components, producing movement of the whole cell or parts of the cell
microtubules
support the cell and provide compression resistance
centrosomes
a cellular organelle that functions as the primary microtubule organizing center in animal cells
centrioles
barrel-shaped organelles that play a key role in cell division and organization
cilia
a small, hair-like projection that extends from the surface of a cell, often found in large numbers on a single cell, and functions to move fluid or particles across the cell surface by beating back and forth
convergent evolution
the process where distantly related organisms independently evolve similar cellular features or functions, often as a response to similar environmental pressures, resulting in analogous structures that perform similar tasks despite having different evolutionary origins (ex: flagella in prokaryotic vs eukaryotic cells)
chemoheterotrophic
refers to an organism that obtains its energy from the oxidation of organic compounds (ex: E. coli)
photosynthetic bacteria
a group of prokaryotes that use light to make energy
microfilaments
also known as actin filaments; are protein filaments in the cytoplasm of eukaryotic cells that are part of the cytoskeleton
order of the 3 types of filaments in the cytoskeleton from largest to smallest
microtubules, intermediate filaments, microfilaments
myosin
a motor protein that binds to actin and uses the energy of ATP to walk along an actin microfilament
cell’s cortex
a three dimensional network of actin filaments underneath the plasma membrane, provides shape for the cell
microvilli
small plasma membrane coated projections from the cell that increase surface area
cytoplasmic streaming
circular flow of cytoplasm in plants that is driven by the dynamic nature of actin filaments along with actin/myosin interactions
intermediate filaments
-in between microtubules and microfilaments in terms of size (8 to 12 nm)
-nuclear lamina is made of intermediate filaments
-more stable networks than microtubules and microfilaments
glycoproteins
proteins with one or more covalently attached carbohydrates (most abundant is collagen)
proteoglycans
have small protein cores with many carbohydrates attached (mucin is an example)
cell wall
-a protective layer external to the plasma membrane in the cells of plants, prokaryotes, fungi, and some protists
-made of polysaccharides
plasmodesmata
-membrane-lined channels filled with cytoplasm that connect adjacent plant cells
-allows communication and coordination between cells that are separated by cell walls
-can move water, ions, and small molecules between cells
tight junctions
bind the adjacent cells together through the interaction of trans-membrane proteins (prevent fluid from moving between cells)
desmosomes
anchor cells together (intermediate filaments bind to desmosomes, linking the cytoskeleton of adjacent cells together)
gap junctions
cytoplasmic channels between adjacent cells that allow water, ions, and small molecules to move between cells
the endomembrane system consists of:
-plasma membrane
-nuclear envelope
-endoplasmic reticulum (ER)
-vesicles
-Golgi apparatus
-lysosomes
-vacuoles
fluid mosaic model
describes structure of plasma membrane:
-the fluid part is the lipid bilayer, made of phospholipids
-mosaic refers to the various proteins that float in the lipid bilayer
amphipathic
containing both hydrophobic and hydrophilic regions
how does cholesterol affect fluidity?
cholesterol buffers fluidity by making plasma membrane more viscous at high temperatures and less viscous at low temperatures
integral proteins
are proteins that penetrate the hydrophobic interior of the lipid bilayer; usually span the whole width of the lipid bilayer
peripheral proteins
are loosely bound to the surface of the plasma membrane and do not penetrate the lipid bilayer
6 membrane protein functions
- transport
- enzymatic activity
- signal transduction
- cell-cell recognition
- intercellular joining
- attachment to the cytoskeleton and extracellular matrix (ECM)
signal transduction
the linkage of a mechanical, chemical, or electromagnetic stimulus to a specific cellular response
cell-cell recognition
proteins on the cell surface are important for joining cells of the same type together, and to separate cells of a different type
lipid bilayer sidedness
each side of the lipid bilayer has a unique lipid, protein, and carbohydrate composition
flipping lipids
need enzymes to catalyze the movement of lipids from one side of the lipid bilayer to the other
scramblase
catalyzes flipping of phospholipid molecules
flippase
catalyzes flipping of specific phospholipids to cytoplasmic monolayer
membrane function
plasma membranes regulate the exchange of material into and out of cells
selective permeability
some substances can cross the plasma membrane more easily than others
transport proteins
transmembrane proteins that help a certain substance or class of closely related substances to cross the membrane
channel proteins
provide a hydrophilic channel through the plasma membrane that allow certain molecules to pass through
carrier proteins
bind to specific molecules and then change shape allowing the specified molecules to shuttle across the plasma membrane
aquaporins
are channel proteins that allow 3 billion water molecules to pass through the molecules to pass through the plasma membrane per second
substances that cross the plasma membrane easily
-non-polar molecules (CO2, O2)
-lipids (fats, steroids)
substances that do not cross the plasma membrane easily
polar molecules
-water
-glucose and other sugars
-ions (K+, Na+, Ca2+)
passive transport
when molecules are able to diffuse across the membrane without an energy input (ex: movement of water through aquaporin)
concentration gradient
a region along which the density of a chemical substance increases or decreases
diffusion
the movement of molecules of any substance so that they spread out evenly into the available space
facilitated diffusion
the passage of molecules or ions down their electrochemical gradient across a biological membrane with the assistance of specific transmembrane transport proteins, requiring no energy expenditure
osmosis
the diffusion of free water across a selectively permeable membrane
tonicity
the ability of a surrounding solution to cause a cell to gain or lose water
hypertonic solutions
are solutions with a higher concentration of a non-penetrating substance (ex: glucose) on the outside of a cell
hypotonic solutions
are solutions with a lower concentration of a non-penetrating substance of the outside of a cell (ex: pure water)
isotonic solutions
are solutions with an equal concentration of a non-penetrating substance on each side of the cell
osmoregulation
the regulation of solute concentrations and water balance by a cell or organism
turgid
hypotonic; normal state for plants
flaccid
isotonic
plasmolysis
the process in which cells lose water in a hypertonic solution
channel proteins
proteins that allow substances to pass through cell membranes (ex: aquaporins)
ion channels
proteins that transport ions across biological membranes; some ion channels are gated and only open in response to a stimulus, often electrical
(important for transmitting signals in the nervous system)
carrier proteins
move substances down a concentration gradient with no energy expenditure
active transport
The movement of a substance across a cell
membrane against its concentration or
electrochemical gradient, mediated by specific
transport proteins and requiring an
expenditure of energy (ex: sodium and potassium pumps)
phosphorylation
the process of adding a phosphate group to a molecule, most commonly a protein, which acts as a key regulatory mechanism in cells by changing the protein’s function and activity, often in response to external signals
membrane potential
the difference in electrical charge (voltage) across a cell’s plasma membrane due to the differential distribution of ions
voltage
electrical potential energy
electrochemical gradient
the diffusion gradient of an ion, which is affected by both the concentration difference of an ion across a membrane (a chemical force) and the ion’s tendency to move relative to the membrane potential (an electrical force)
electrogenic pumps
a transport protein that generates voltage across a membrane (ex: animal cells use Na+ and K+ pumps; bacteria, plants, and fungi use proton pumps)
cotransport
some transport proteins couple the movement of one substance down its electrochemical gradient with the movement of another substance against its concentration gradient (ex: sucrose- H+ transporter in plants)
bulk transport
the process by which cells move large quantities of materials, like large molecules or particles, across their cell membrane using membrane-bound vesicles, requiring energy (ATP)
-exocytosis and endocytosis
exocytosis
the cellular secretion of biological molecules by the fusion of vesicles containing them with the plasma membrane
-mediated by transport vesicles moving from the Golgi along microtubules
endocytosis
the cellular uptake of biological molecules and particulate matter via formation of vesicles from the plasma membrane
pinocytosis
when a cell ingests extracellular fluid and its dissolved solutes (cellular “drinking”)
receptor-mediated endocytosis
the movement of specific molecules into a cell by the inward budding of vesicles containing proteins with receptor sites specific to the molecules being taken in
metabolism
the totality of an organism’s chemical reactions; manages the material and energy resources of the cell
metabolic pathway
a series of chemical reactions that either builds a complex molecule or breaks down a complex molecule
catabolic pathways
breakdown complex molecules into simpler molecules and release energy (ex: cellular respiration)
anabolic pathways
consume energy to build complicated molecules (ex: photosynthesis, protein synthesis)
energy
the capacity to cause change
kinetic energy
the energy associated with the relative motion of objects
heat (thermal energy)
the total amount of kinetic energy due to the random motion of atoms or molecules in a body of matter
potential energy
the energy that matter possesses as a result of its location or spatial arrangement (structure)
chemical energy
refers to the potential energy available for release in a chemical equation
thermodynamics
the study of energy transformations that occur in a collection of matter
system
refers to the matter being studied (ex: cell)
surroundings
everything outside the system, aka the rest of the universe
isolated system
matter that is unable to exchange either matter or energy with its surroundings
open system
matter that can transfer matter and energy with its surroundings (cell=open system)
first law of thermodynamics
energy can be transferred and transformed, but it cannot be created or destroyed; principle of conservation of energy
second law of thermodynamics
every energy transfer or transformation increases the entropy of the universe
entropy
the measure of disorder or randomness
spontaneous process
a process that occurs without an input of energy
-free energy decreases and the stability of a system increases
free energy
- is the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout a system
-is also a measure of a system’s instability, its tendency to change to a more stable state
free energy change equation
delta G = delta H - (T)*(delta S)
delta G
change in free energy
delta H
change in a system’s total energy
enthalpy
refers to the total heat content of a system
T
absolute temperature in Kelvin (K=C+273)
delta S
change in a system’s entropy
when do spontaneous reactions occur?
only if delta G is negative
-the total energy of the system (delta H) must decrease
-or the temperature must increase
-or the total entropy of the system (delta S) must increase
equilibrium
is the state of maximum stability:
-G is at its lowest possible value for a system
-delta G = 0
-any change in the system will require energy since delta G > 0
catabolic reactions
-release energy
-break macromolecules
-ex: hydrolysis
-negative delta G (spontaneous)
-exergonic reactions
-cellular respiration
anabolic reactions
-require energy
-build macromolecules
-ex: dehydration
-positive delta G (non-spontaneous)
-endergonic reactions
-photosynthesis
exergonic reaactions
a spontaneous chemical reaction, in which there is a net release of free energy
endergonic reactions
a non-spontaneous chemical reaction, in which free energy is absorbed from the surroundings
respiration
an exergonic reaction that occurs spontaneously (without an input of energy)
C6H12O6 + 6 O2 —> 6 CO2 + 6 H2O
delta G = -686 kcal/mol
^cells that break down 1 mol of glucose into water and carbon dioxide liberate 686 kcal of energy to perform work
photosynthesis
an endergonic reaction that requires an input of energy
6CO2 + 6H2O —> C6H12O2 + 6O2
delta G = 686 kcal/mol
^plants must absorb 686 kcal of energy from their surroundings (sunlight) to generate 1 mol of glucose from water and carbon dioxide
metabolism
refers to the sum of all chemical reactions that occur within a living organism’s cells
energy coupling
the use of an exergonic process to drive an endergonic one
3 types of cellular work
chemical work, transport work, and mechanical work
chemical work
the pushing of endergonic reactions that would not occur spontaneously, such as the synthesis of polymers from monomers
transport work
the pumping of substances across membranes against their concentration gradients
mechanical work
beating of cilia, contraction of muscle cells, and the movement of chromosomes during cell division
ATP (adenosine triphosphate)
-cells use H2O to hydrolyze the covalent bond of the last phosphate group to liberate inorganic phosphate (Pi), ADP, and energy
- ATP + H2O = ADP + Pi
- delta G = -7.3 kcal/mol
-the energy released by breaking the covalent bond in ATP is larger than breaking the covalent bond of other molecules
-multiple negatively charged phosphate groups repulse each other, making the triphosphate region of ATP more unstable
phosphorylated intermediate
is more unstable than the original reactant and will react with a second molecule to form a more stable
product
ATP cycle
-cells recycle ADP back to ATP
-regenerating ATP is an endergonic reaction
- ADP+Pi=ATP
- delta G = 7.3 kcal/mol
-cells use cellular respiration, an exergonic reaction (catabolic), to generate ATP from ADP (anabolic)
enzymes
a macromolecule that acts as a catalyst
catalyst
a chemical agent that speeds up a reaction without being consumed by the reaction
-most biological catalysts are proteins, some are RNA molecules such as rRNA
activation energy
-the initial investment of energy for starting a reaction
-the energy required to contort the reactant molecules so the covalent bonds can break
-each reaction has a different activation energy
-increasing the temperature provides more energy in the surroundings so that reactions are more likely to occur
breaking covalent bonds
-an electron pair must be split so that each electron is now orbiting a different atom
-the covalent bond between 2 atoms must be contorted, which requires energy
contorted molecule
-absorbs energy from its surroundings that contorts the covalent bond
-contorted shape of the molecule is less stable
forming new covalent bonds
-covalent bonds of the new product are more stable than the contorted covalent bonds of the reactants
-energy is released to the surroundings as the new bonds form
enzymes lower activation energy…
-they don’t change the amount of free energy (delta G) released by a reaction
-do not make endergonic reactions exergonic
-DO lower the activation energy so that at moderate temperatures reactants can absorb enough energy from the surroundings to reach the transition state
substrate
the reactant that an enzyme works on
enzyme-substrate complex
-the enzyme and substrate bind together
-occurs at the active site of an enzyme
active site
-the location on an enzyme that binds to a substrate
-are usually in a groove or pocket in the enzyme
induced fit
when the substrate binds to the active site, the enzyme changes shape to better bind the substrate
enzymatic rate
in general, enzymes can process thousands of substrates per second
enzymes can lower activation energy using 4 different methods:
- the enzyme brings the reactants (substrates) close together
- the enzyme may stretch the substrate towards its transition state
- the enzyme may provide an appropriate chemical environment
- the enzyme may form a covalent bond with the substrate as it transitions to the product
factors that affect enzyme activity:
temperature, pH, cofactors, coenzymes, enzyme inhibitors, competitive inhibitors, noncompetitive inhibitors, cellular location
how does temperature affect enzyme activity?
-higher temperatures make substrates hit the active site more frequently
-if the temperature is too high, then the enzyme starts to denature
-the optimal temperature is shaped by the environment that an organism lives in or maintains (human enzymes like 37 degrees Celsius)
how does pH affect enzyme activity?
-the concentration of H+ can affect enzymatic reactions
-most enzymes work at pH 6-8
-some enzymes work in extreme conditions
coenzymes
are organic molecules that act as cofactors
cofactors
-are any non-protein molecule or ion that is required for the proper functioning of an enzyme
-can be permanently bound to the active site or may bind loosely and reversibly along with the substrate, during catalysis
vitamins
-are organic molecules that are required in our diet
-our bodies can not synthesize these organic molecules
-many are coenzymes
enzyme inhibitors
are chemicals that prevent enzymatic activity
competitive inhibitors
bind to the active site and prevent the substrates from binding (ex: carbon monoxide)
noncompetitive inhibitors
bind a different part of the enzyme, causing the enzyme to change shape such that the active site is less effective in catalyzing the reaction
allosteric regulation
when a protein’s function at one site is affected by the binding of a regulatory molecule on a separate site
inhibition
the inhibitor stabilizes the inactive form of an enzyme
activation
the activator stabilizes the active form of an enzyme
feedback inhibition
is a method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme in that pathway
how does cellular location affect enzyme activity?
-Cells locate enzymes in the same
compartment so that products from one
enzymatic reaction will be supplied as
substrates to the next enzyme
-Having enzymes located in specific organelles
provides the enzymes a defined chemical
environment (for instance, the correct pH)
that optimizes the enzymatic reaction
