Biology 2

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1

what are nucleotides made of?

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

2

what are the pyrimidines?

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

3

what are the purines?

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

4

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

5

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

6

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

7

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

8

catabolic pathways

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

9

anabolic pathways

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

10

two laws of thermodynamics

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

11

spontaneous process

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

12

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)

13

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

14

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

15

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

16

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

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

17

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)

18

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

19

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

20

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

21

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

22

substrate

the reactant that binds with an enzyme

23

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

24

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

25

cofactors and coenzymes

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

26

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

27

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

28

allosteric enzyme

has an allosteric site in addition to its active site

29

allosteric activator

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

30

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

31

cooperativity

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

32

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

33

amphipathic

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

34

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

35

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

36

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"

37

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)

38

glycoproteins

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

39

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

40

aquaporins

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

41

carrier proteins

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

42

passive transport

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

43

osmosis

the diffusion of free water across a membrane

44

what is tonicity?

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

45

isotonic

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

46

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

47

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)

48

lyse

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

49

osmoregulation

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

50

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

51

flaccid

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)

52

plasmolysis

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

53

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

54

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)

55

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)

56

voltage (in relation to the cell membrane)

electrical potential energy

57

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

cytoplasmic side is negative in charge relative to the extracellular side

58

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)

59

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

60

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

61

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

62

what is a proton pump?

the main electrogenic pump of plants, fungi, and bacteria

63

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

64

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

65

exocytosis

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

66

endocytosis (3)

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

67

phagocytosis

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

68

pinocytosis

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)
"drinking"

69

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)

70

ligands

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

71

coated pits

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

72

coat proteins

coated pits are lined with this on the inside

73

differences between prokaryotic and eukaryotic cells (4)

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

74

all cells have (5)

plasma membrane, cytosol, chromosomes, ribosomes, cytoplasm

75

microvilli

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

76

describe the nucleus

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

77

pore complex

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

78

nuclear envelope

encloses the nucleus separating it from the cytosol

79

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

80

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)

81

nucleolus

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)

82

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

83

endomembrane system includes (6)

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

84

endoplasmic reticulum

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

85

inner sacs in the ER are called?

cisternae or ER lumen (continuous with the nuclear envelope)

86

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

87

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)

88

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

89

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)

90

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)

91

trans face

the shipping department of the Golgi apparatus

92

lysosomes

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

93

autophagy

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)

94

vacuoles 3 types

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

95

when are food vacuoles formed?

formed during phagocytosis

96

contractile vacuole

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

97

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

98

mitochondria

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

99

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

100

thylakoids

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

101

stroma

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

102

peroxisome

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

103

glyoxysomes

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

104

parts of the cytoskeleton (3) and its role

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

105

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

106

centrosome

contains a pair of centrioles, "microtubule organizing center"

107

structure of centriole

nine sets of triplet microtubules arranged in a ring

108

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

109

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

110

basal body

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

111

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

112

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
pseudopodia
cytoplasmic streaming

113

myosin

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

114

pseudopodia

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

115

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

116

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

117

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

118

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

119

middle lamella

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

120

plasmodesmata

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

121

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

122

proteoglycans

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

123

integrins

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

124

fibronectin

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

125

cell junction is animal cells (3)

tight junctions
desmosomes
gap junctions

126

tight junction

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

127

desmosomes

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)

128

gap junction

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

129

what are organelles that include DNA?

chloroplasts, nuclei, mitochondria

130

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

2

131

what is the net gain of glycolysis?

2 NADH and 2 ATP, 2 pyruvate + 2 H2O

132

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

1 CO2, 1 NADH, 1 Acetyl CoA

133

what is produced with one turn of the Krebs cycle?

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

134

what is kinase?

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

135

what is isomerase?

the enzyme that transfers glucose to its isomer fructose in glycolysis

136

dehydrogenase

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)

137

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)

138

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)

139

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

2

140

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