Biology 2

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what are nucleotides made of?

nitrogenous base attached to the 1' carbon of the sugar, pentose sugar, phosphate group attached at the 5' carbon


what are the pyrimidines?

a 6 membered ring of carbon and nitrogen
cytosine, thymine (DNA), uracil (RNA)


what are the purines?

a 6 membered ring fused to a 5 membered ring
adenine, guanine


what are two differences between DNA and RNA?

1) DNA only has an H on its 2' carbon= deoxyribose
RNA has an OH on its 2' carbon= ribose
2) RNA exists in one strand with covalent phosphodiester linkages connecting the nucleotides
DNA exists in a double helix with two strands running in opposite directions from each other aka antiparallel


describe DNA (4)

1) double helix
2) nitrogenous bases held together by hydrogen bonds
3) two strands run antiparallel to each other, one side is the 5' end the other is the 3' end (can only grow from this end) (one way street form 5' to 3')
4) one end of a strand has a phosphate group attached to the 5' carbon, the other has a hydroxyl group attached to the 3' carbon


phosphodiester linkages

5'-3' phosphodiester linkages are formed when there is dehydration synthesis when the hydroxyl group on the 3' carbon of a nucleotide makes a bond with the phosphate group attached to the 5' carbon of the other nucleotide, which then makes another phosphodiester linkage with a hydroxyl group of another nucleotide, etc


metabolism/ metabolic pathway

totality of an organism's chemical reaction, begins with a specific molecule which i then altered in a series of defined steps


catabolic pathways

release energy by breaking down complex molecules to simpler compounds (picture ball rolling downhill)
exergonic (negative ΔG)


anabolic pathways

consumes energy to build complex molecules from simpler ones (picture pushing a ball uphill)
endergonic (positive ΔG)


two laws of thermodynamics

1) energy cannot be created or destroyed, just transferred or transformed
2) every energy transfer increases entropy (disorder)


spontaneous process

occurs without an input of energy= increases entropy (ball rolling downhill, diffusion, etc)


free energy

"available energy" to do work
the more available energy there is... the more unstable it is (ball at top of the hill)
the less available energy there is... the more stable it is (ball at bottom of hill)


ΔG, Gibbs Free Energy, what is the equation to find ΔG?

Gibbs Free Energy... the difference in free energy between the products and the reactants... ΔG= ΔH- TΔS


negative ΔG is what kind of reaction?

if the ΔG is negative (the products have less free energy than the reactants.... less minus more= negative)- reaction is exergonic, releases energy, can occur spontaneously


positive ΔG is what kind of reaction?

if the ΔG is positive (the products have more free energy than the reactants... more minus less= positive)- the reaction is endergonic, consumes energy, needs an input of energy, cannot occur spontaneously


what do the letters stand for? ΔG= ΔH- TΔS

G= free energy
H= enthalpy (potential energy stored in bonds)
T= temperature
S= entropy


in an exergonic reaction (aka spontaneous reaction)... the gibbs free energy equation should look like...

negative G= lower potential energy (ball rolled down hill and now is at bottom)- high entropy (after diffusion now the molecules are more disordered)


to couple an endergonic reaction with an exergonic reaction... ?

the absolute value of the ΔG of the exergonic reaction has to be more than the ΔG of the endergonic reaction it wants to couple with


the absolute value of the ΔG of hydrolyzing ATP... and therefore can be coupled with...?

(breaking down) the ΔG is -7.3 so the absolute value is 7.3... with an endergonic reaction with the absolute value of its ΔG less than 7.3


definition of enzyme and how it works

a catalyst, an organic molecule that increases the rate of the reaction without itself being changed by the reaction .. how? it lowers the activation energy and increases the rate of reaction


what is activation energy? why do you need to put in that little bit of energy to yield more energy? why would raising the temp help this?

the reactants need to be oriented correctly, turned towards each other, etc... raising the temp makes the molecules move faster and have a greater chance that they will collide



the reactant that binds with an enzyme


how do reactants bond to enzymes?

active site- "lock and key" the active site on the enzyme is where the reactant bonds to the enzyme, only certain reactants fit into certain active sites


why do enzymes lower the activation energy? (4)

1) bring the substrates into close proximity
2) orients the substrates correctly
3) induced fit- puts stress on the bonds making them easier to break
4) makes a better environment for the reaction


cofactors and coenzymes

cofactors are non proteins that come to help the catalytic activity... coenzymes are organic cofactors


as you increase the concentration of substrate, the rate of the reaction increases until it reaches a certain point where it stays the same.. why?
after this "peak" what can you do to increase the rate of reaction?

ex) 10 enzymes.... if you put 2 substrates in that pool it will make 2 products... if you put 9 substrates in it will make 9 products... but if you give it 17 substrates it still can only make 10 at a time
to increase the rate of reaction after that you must add more enzymes


competitive/ non competitive inhibitors

competitive- mimics substrate and blocks substrates from binding to the active site by taking its place
non competitive- binds to another part of the enzyme causing it to change shape and change the shape of its active site


allosteric enzyme

has an allosteric site in addition to its active site


allosteric activator

binds to the allosteric site on the allosteric enzyme to keep the enzyme in shape to accept its substrates= stabilized active form


allosteric inhibitor

binds to the allosteric site on the allosteric enzyme to keep the enzyme in a wrong shape and therefore blocks substrates from binding



when a substrate binds to an active site which causes the rest of the active sites to be open to their substrates


feedback inhibition

a metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway... aka an initial substrate binds to an enzyme... then continues down the metabolic pathway.. eventually makes a product... when there is enough of that product to bind to that beginning enzyme to act an an allosteric inhibitor and change the active site so the who pathway stops until there isn't enough product and the active site is available again



a molecule that has both hydrophilic and hydrophobic regions ex) phospholipids in cell membrane


properties of the plasma membrane

phospholipid hydrophilic head which faces outwards
hydrophobic tail faces inwards
dynamic, moving, very often the phospholipids move laterally but not as often do they "flip flop" across
contains- proteins and carbohydrates


proteins in the membrane (2)

1. integral proteins- within the membrane a)transmembrane span the entire membrane, the hydrophobic parts many times have one or more stretches of nonpolar amino acids usually coiled in alpha helices
some have hydrophilic channels through them to transport polar things
b) some are only partially in the hydrophobic interior

2. peripheral proteins- held by cytoskeleton or extracellular mix


what is the point of the cholesterol in the plasma membrane?

makes the membrane less fluid by restraining movement of phospholipids or more fluid by preventing them from packing too tightly "fluidity buffer"


carbohydrates in the membrane (2)

usually short branched chains of 15 sugar units
1. glycolipids- carbs covalently bonded to lipids
2. glycoproteins- carbss covalently bonded to proteins (more common)



carbs covalently bonded to proteins which function as "markers" to distinguish one cell from another
cell- cell recognition


molecules going through the membrane easiest to hardest

hydrophobic, non polar have the easiest time
hydrophilic, polar have a harder time (ex glucose and water)
charged atom or molecule and its hydration shell have the hardest time



transport proteins which have channel to facilitate the passage of water molecules


carrier proteins

facilitated diffusion, holds its hydrophilic passanger and changes shape in a way that allows the protein to bring it through the membrane


passive transport

diffusion of a substance across a membrane with NO ENERGY INVESTMENT, can be spontaneous



the diffusion of free water across a membrane


what is tonicity?

the ability of a surrounding solution to cause a cell to gain or lose water



the concentration is the same on both sides of the membrane, there will be no net movement


hypertonic solution

a solution that has more more non penetrating solutes than the cell (less water) this causes the cell to LOSE water, shrivel and die


hypotonic solution

a solution that has less non penetrating solutes than the cell (more water) will cause the cell to gain water and swell or lyse (burst)



when a cell bursts because it takes in too much water because it was surrounded by a hypotonic solution



a cell that doesn't live in an isotonic environment may have a less permeable membrane and organelles that function as pumps to control the water balance


turgor pressure

when a cell with a cell wall takes on water so the actual cell pushes against the cell wall and becomes "turgid" or firm= a healthy state for the cell



when a cell with a cell wall is in an isotonic environment, the cell doesn't take on water and have the turgor pressure it needs, becomes flaccid (limp)



when a cell with a cell wall loses water and shrinks away from the cell wall, it wilts and dies


facilitated diffusion

when polar molecules or ions are helped to diffuse through the cell membrane by transport proteins- STILL DOESN'T NEED ENERY INPUT because it provides an environment where they can still travel down its concentration gradient


channel proteins (2)

1. ion channels- transport ions
2. gated channels- open or close in response to stimulus (electrical stimulus or something binding to the channel etc)


active transport

needs energy, involves transport proteins (never channel proteins) that alters the direction of transport and move solute AGAINST their concentration gradient (from a side where they are less concentrated to a side where they are more concentrated)


voltage (in relation to the cell membrane)

electrical potential energy


what are the charges on either side of the cell membrane?

cytoplasmic side is negative in charge relative to the extracellular side


membrane potential

the voltage across a membrane, acts like a battery which affects diffusion of ions across the membrane, it favors the passive transport of cations into the cell and anions out of the cell (makes sense because of the relative charge of cytoplasm and extracellular environment)


what are the two forces involved in diffusion of ions across a membrane?

1. chemical force- the ion's concentration gradient
2. electrical force- the effect of the membrane potential on the ion's movement


electrochemical gradient

the combination of the chemical and electrical force involved in ion diffusion, sometimes they work with each other, sometimes they work against each other


electrogenic pumps and how do they work?

a transport protein that generates voltage across a membrane ex) sodium- potassium pump, proton pump, they transfer positive charge from the cytoplasm to the extracellular solution which cause an increase in voltage across the membrane which can be stored for future work


what is a proton pump?

the main electrogenic pump of plants, fungi, and bacteria


sodium- potassium pump

example of active transport, 3 molecule of Na+ are pumped out of the cell and 2 molecules of K+ are brought back in to the cell


co- transport

a substance is actively pumped out of the cell and then diffuses back into the cell (with another substance) providing energy that can be coupled with that other substance that needs that energy to be actively transported into the cell... the two substances enter the cell together



vesicles made from the Golgi apparatus moves along the microtubules of the cytoskeleton to the plasma membrane... the vesicles membrane and the plasma membrane then fuse and the contents of the vesicle are emptied outside the cell


endocytosis (3)

reverse exocytosis
1. phagocytosis
2. pinocytosis
3. receptor- mediated endocytosis



a type of endocytosis
the cell engulfs a particle by wrapping it in pseudopodia and packaging it in a food vacuole
breaks down in lysosome



a type of endocytosis
cell "gulps" drops of extracellular fluid into tiny vesicles for the molecules dissolved in the fluid (non specific in the substances it transports)


receptor- mediated endocytosis

enables cell to acquire bulk quantities of specific substances even if its concentration in the extracellular is small
proteins embedded in the plasma membrane with specific receptor sites bind to ligands (specific substances to that bind to these sites) which then cluster into coated pits which are lined on their cytoplasmic side by a fuzzy layer of coat proteins
then it forms a vesicle with lots of the ligands in it (can have other molecules in the vesicle as well)



specific substances in the extracellular solution that bind to receptor sites on the proteins of the plasma membrane


coated pits

what ligands are in when they bind to the receptor sites on proteins in the plasma membrane


coat proteins

coated pits are lined with this on the inside


differences between prokaryotic and eukaryotic cells (4)

1) most of the DNA is located in the nucleus bound by a double membrane
2) organelles in the cytoplasm suspended in cytosol
1) DNA is concentrated in a region called the nucleoid which is not membrane enclosed


all cells have (5)

plasma membrane, cytosol, chromosomes, ribosomes, cytoplasm



long thin projections from a cells surface which increase surface area without an appreciable increase in volume


describe the nucleus

information center of the cell, contains most genes, double membrane perforated by pore structures


pore complex

lines each pore in the nuclear envelope to regulate the the entry and exit of proteins and RNA's


nuclear envelope

encloses the nucleus separating it from the cytosol


nuclear lamina and nuclear matrix

nuclear side of the nuclear envelope is lined with this netlike array of protein filaments which maintains the shape of the nucleus
nuclear matrix also contributes to this


chromosomes, what are they made of?

carry genetic information, made of chromatin, each contains a long DNA molecule associated with many proteins, when a cell is not dividing it appears as a diffuse mass, when a cell prepares to divide it coils further becoming thick enough to be distinguished from one another
(typical human cell has 46 chromosomes)



where rRNA (ribosomal RNA) is synthesized from instructions in the DNA, proteins are imported form the cytoplasm and are assembled with rRNA into large and small subunits which than exit the nucleus and a small and large subunit come together into a ribosome (can be more than one nucleolus)


ribosomes, two types

protein factories, made of RNA and protein
1) free ribosomes suspended in the cytosol, most proteins made here function in the cytosol
2) bound ribosomes are attached to the outside of the ER or nuclear envelope, most proteins made here are destined for insertion into membranes, packaging within other organelles, or for secretion


endomembrane system includes (6)

nuclear envelope, the ER, the Golgi apparatus, lysosomes, vesicles/ vacuoles, plasma membrane


endoplasmic reticulum

biosynthetic factory "little net" which consists of membranous tubules and sacs called cisternae, the ER membrane separates them from the cytosol


inner sacs in the ER are called?

cisternae or ER lumen (continuous with the nuclear envelope)


smooth ER what are its functions? (4)

lacks ribosomes, functions in metabolic processes such as synthesis of lipids, metabolism of carbs, detoxification of drugs and poisons, storage of calcium ions


rough ER what are its functions? (3)

surface is studded with ribosomes, make proteins which are then threaded through the ER lumen through a pore and folds into its native shape there, carbs are attached to some proteins here called glycoproteins, membrane factory for the cell (makes phospholipids and proteins and adds to its own membrane and can be then transfered elsewhere)


transitional ER

when a protein is made for secretion it is wrapped in membranes of vesicles that bud like bubbles from the transitional ER to keep the protein separate from the cytosol


Golgi apparatus

the shipping and receiving center, has cisterns each with different enzymes to further change products of the ER which arrive through the cis face and exit through the trans face
(also manufactures macromolecules like polysaccharides)


cis face

the receiving department of the Golgi apparatus usually located near the ER (a transport vesicle that buds from the ER can add its membrane and contents of its lumen to the cis face by fusing with the Golgi membrane)


trans face

the shipping department of the Golgi apparatus



digestive compartments of cell... membranous sac of hydrolytic enzymes that animal cells use to hydrolyze macromolecules
work best in an acidic environment.. if the lysosome leaks or breaks the enzymes dont function in the cytosol



a process in which lysosomes use their hydrolytic enzymes to recycle the cells own organic material (the damaged organelle becomes surrounded by a double membrane and is taken to the lysosome)


vacuoles 3 types

derived from the ER and Golgi apparatus
food vacuole, contractile vacuole, central vacuole


when are food vacuoles formed?

formed during phagocytosis


contractile vacuole

(protists) pumps excess water out of the cell, maintaining a suitable concentration of ions and molecules inside the cell


central vacuole.. what does it contain? what purpose does it serve?

in mature plant cells there is a vacuole made from smaller vacuoles contains cell sap... this vacuole takes in water so when the cell grows it can be with minimal investment in new cytoplasm



energy center, site of cellular respiration (metabolic process that uses oxygen to generate ATP be extracting energy from sugars, fats, and other fuels


chloroplasts (5 key words)

member of the family of plant organelles called plastids, found in plants and algae are the sites of photosynthesis, (convert solar energy to chemical energy by absorbing sunlight and using it to drive the synthesis of organic compounds such as sugars from carbon dioxide and water)
contains the green pigment chlorophyll
thylakoids, stroma



found in chloroplasts membranous system in the form of flattened interconnected sacs



fluid outside the thylakoids which contains the chloroplast DNA, ribosomes, and many enzymes



oxidation, specialized metabolic compartment bounded by a single membrane, contains enzymes that remove hydrogen atoms from various substrates and transfer them to oxygen producing hydrogen peroxide as a byproduct (toxic but it carries an enzyme that converts it to water) the oxygen is then used to break fatty acids down into smaller molecules to be transported to mitochondria and are fuel for cellular respiration... also can detox alcohol in the liver



found in the fat storing tissues of plant seeds, used to make a source of energy until the seedling can produce its own sugar by photosynthesis


parts of the cytoskeleton (3) and its role

microtubules, microfilaments, intermediate filaments
role is to support the cell and give it shape


microtubules what are they? what are their structure? what are its roles?

hollow rods made of protein called tubulin dimers (each dimer composed of one α- tubulin and one β- tubulin) shape and support the cell, function as compression resisting girders of the cel



contains a pair of centrioles, "microtubule organizing center"


structure of centriole

nine sets of triplet microtubules arranged in a ring


what are cilia made of? what is their structure? what motion do they have? what is their role?

made of microtubules, 9 doublets around 2 single microtubules (9+2 pattern) helps propel the cell, works like an oar with alternation power and recovery strokes, can also function as a signal receiving antenna for the cell but these are usually nonmotile and are only one per cell (these dont have the central microtubules) , anchored by a basal body


what are flagella made of? what is their structure? what motion do they have? what is their role?

made of microtubules, 9 doublets around 2 single microtubules (9+2 pattern), help propel the cell beat like the tail of a fish, anchored by basal body


basal body

where the cilia and flagella are anchored, made of 9 microtubule triplets in a ring


dyneins, how do they work?

the motor proteins which are responsible for the movement of the cilia and flagella
each microtubule is connected to its neighbor by a non tubulin protein and then the dyneins "walk" alone the neighboring microtubule and this causes the bending motion without the microtubules "walking" past each other


what are microfilaments made of? what is their role?

solid rods built from two twisted chains of actin subunits (protein)
bear tension for the cell and help it retain its shape
gives the cortex (the outer cytoplasmic layer of the cell) the semisolid consistency of gell rather than more fluid
involved in motility of muscle cells in particular
cytoplasmic streaming



motor protein which causes the actin filaments to slide past each other causing muscles to contract and move



cell extensions made of microfilaments that are made by assembling actin subunits that convert cytoplasm to gel and extend from the cell, the surface proteins on the pseudopodia make strong attachments to the "road" and crawl along it


cytoplasmic streaming

a circular flow of cytoplasm which may happen because of the actin- myosin interactions causing the cytoplasm to transform from sol to gel and back again


intermediate filaments

also specialize in bearing tension but are more permanent, aren't taken apart and put back together as often, therefore are especially sturdy play an important role in reinforcing the shape of the nucleus which is usually surrounded by intermediate filaments which extend into the cytoplasm, also helps fixing the position of organelles


cell wall, what is it made of? what enzyme synthesizes the reaction?

only in plant cells, made of microfibrils of the polysaccharide cellulose
synthesized by an enzyme called cellulose synthase


primary cell wall, secondary cell wall

the first cell wall a young plant makes which can grow with it until it makes its secondary cell wall which is in between the plasma membrane and the primary wall


middle lamella

a thin layer between primary walls of adjacent cells of sticky polysaccharides called pectins which glue adjacent cells together



cell walls are perforated with plasmodesmata which are membrane lined channels filled with cytoplasm which join the internal chemical environments of adjacent cells which unify mosts of the plant into one living continuum, also allows water and small solutes to pass freely from cell to cell


extracellular matrix (ECM), what is it made of?

animals have this instead of a cell wall
it is made of glycoproteins and other carb containing molecules secreted by cells
collagen is the most abundant glycoprotein which forms strong fivers outside the cells



embedded in the collagen fibers consist of a small core protein with many carb chains covalently attached



receptor proteins on the surface of cells that fibronectin can bind to so that the inside of the cell can communicate with the outside



a glycoproteins that some cells are connected to the ECM with
it binds to the cell surface receptor proteins called integrins that span the membrane and bind on their cytoplasmic side to associated proteins attached to microfilaments of the cytoskeleton, messages can then be conveyed through the integrins from the cytoskeleton to the ECM and vice versa


cell junction is animal cells (3)

tight junctions
gap junctions


tight junction

the plasma membranes of neighboring cells are very tightly pressed together forming seals which prevent leakage



function like rivets which fasten the cells together into strong sheets
intermediate filaments made of keratin proteins anchor desmosomes in the cytoplasm
(muscle tears are sometimes tears in desmosomes)


gap junction

provide cytoplasmic channels from one cell to an adjacent cell (similar to plasmodesmata in plant cells)
made of membrane proteins


what are organelles that include DNA?

chloroplasts, nuclei, mitochondria


how many ATPs are used in the energy investment phase of glycolysis?



what is the net gain of glycolysis?

2 NADH and 2 ATP, 2 pyruvate + 2 H2O


what is produced in the oxidation phase of pyruvate to Acetyl CoA?

1 CO2, 1 NADH, 1 Acetyl CoA


what is produced with one turn of the Krebs cycle?

3 molecules of NADH, 1 FADH2, 1 ATP, 2 CO2


what is kinase?

the enzyme that transfers the phosphate group from the ATP molecules to the fructose molecules during the energy investment phase


what is isomerase?

the enzyme that transfers glucose to its isomer fructose in glycolysis



the enzyme that takes the 2 e- and 2 H+ from the substrate and brings it to the NAD+ molecule reducing it to NADH (+ one H+ that goes away)


describe the steps of the Krebs cycle in terms of carbon

Acetyl CoA has 3 carbons, loses one C and joins an oxaloacetate which has 4 carbons= citrate has 6 carbons... then another C is lost (first CO2 lost) so it has 5 carbons in ketoglutarate... then it loses another carbon (second CO2 lost) and has 4 carbons again to form oxaloacetate (cycle)


starting with one molecule of isocitrate and ending with one molecule of fumerate, how many ATPs can be generated by oxidated phosphorolation?

8 (2 NADH= 2x3=6 plus 1 FADH2= 2..... 6+2=8)


how many CO2 are produced with one turn of the Krebs cycle?



how many CO2 are produced from one molecule of glucose?

4 from the Krebs cycle plus 2 from each pyruvate molecule oxidizing to Acetyl CoA= 6