1 - CELL AND MOLECULAR BIOLOGY Flashcards

1
Q

define electronegativity

A

ability of an atom to attract electrons

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2
Q

what are the 3 main type of chemical bonds

A

ionic

covalent

hydrogen

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3
Q

what are ionic bonds?

A

transfer of electrons between atoms of differing electronegativity

the one with a higher electronegativity, takes the electrons

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4
Q

what are covalent bonds?

A

sharing of electrons

atoms can be single/double/triple -bonded

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5
Q

what are non-polar covalent bonds?

A

equal sharing of electrons between two atoms of similar electronegativity

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6
Q

what are polar covalent bonds?

A

unequal sharing of electrons between two atoms of differing electronegativity

FORMS A DIPOLE!!

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7
Q

what are van der waal interactions?

A

weaker and more transient than hydrogen bonding. more of an interaction which gets stronger, the larger the molecule is

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8
Q

what are hydrogen bonds?

A

weak interaction between a hydrogen (attached to a highly electronegative atom) and a negatively charged atom of another molecule (F, O, N)

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9
Q

what are the 5 most important properties of water?

A

it’s a good solvent

it has a high heat capacity

ice floats. water expands as it freezes and becomes less dense

it has strong cohesion/surface tension. its strong cohesion between H2O molecules produces high surface tension

it has adhesion. adheres to unlike objects - water sticks to skin/glass

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10
Q

why is water a good solvent?

A

the dipoles (the slight positive and negative charges) of H2O break up charged ionic molecules, by disrupting the attractive forces between the atoms of that molecule

this makes it easier for water to dissolve substances

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11
Q

why does water have a high heat capacity?

A

due to the hydrogen bonds between water molecules which require (the absorption) heat to break

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12
Q

what is heat capacity?

A

the amount of heat needed to change the temperature of a substance by 1 unit (e.g. 1 degree)

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13
Q

why does ice float?

A

water expands as it freezes and becomes less dense

the H-bonds become rigid and forms a crystal that keeps molecules separated. their attractions arrange them into fixed positions

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14
Q

why is there strong cohesion between water molecules?

A

due to H2O’s ability to form hydrogen bonds - and the extremely electronegative oxygen and the comparatively positive hydrogen

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15
Q

why does water possess the adhesive property?

A

due to H2O’s polar nature, it can also attract “unlike” structures. it’s attracted to substances with charges

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16
Q

what are minerals?

A

inorganic ions the body needs to function

can be found intracellularly and extracellularly

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17
Q

what are vitamins?

A

organic molecules the body needs to function

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18
Q

what are the (2) major categories of vitamins? when consumed in excess, where are they stored?

A

fat-soluble
- deposited in body fat; overconsumption can lead to toxic levels in the body

water-soluble
- excreted in the urine

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19
Q

what is vitamin B? describe it

A

a water-soluble vitamin

8 types of vitamin B

vitamin B usually functions as coenzymes or their precursors in metabolic processes – also important in blood synthesis

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20
Q

what is vitamin C? describe it

A

a water-soluble vitamin

vitamin C is necessary for synthesizing collagen, an important structural protein, thus a deficiency in vitamin C can lead to scurvy (if the collagen structure is less stable, we get weakened connective tissues)

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21
Q

what are the (2) important water-soluble vitamins?

A

B and C

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22
Q

what are the (4) important fat-soluble vitamins?

A

A, D, E, and K

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23
Q

what is vitamin A? describe it

A

a fat-soluble vitamin

important for:

  • vision (visual pigmentation)
  • epithelial (skin) maintenance
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24
Q

what is vitamin K? describe it

A

a fat-soluble vitamin

important for blood clotting. it produces proteins involved in the process

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25
what is vitamin D? describe it
a fat-soluble vitamin regulates calcium and phosphorous levels by promoting its absorption from the intestine synthesized by the skin in the presence of sunlight
26
what is vitamin E? describe it
a fat-soluble vitamin an antioxidant which prevent cell damage by neutralizing free radicals which (highly unstable unpaired electrons which can destroy cells)
27
what are the key properties of hydroxyl (OH) groups?
polar and hydrophilic generally a strong base. but can be acidic depending on conditions
28
what are the key properties of carboxyl (COOH) groups?
polar, hydrophilic, weak acid
29
what are the key properties of amino (NH2) groups?
polar, hydrophilic, weak base
30
what are the key properties of phosphate (PO4 -3) groups?
polar, hydrophilic, acid
31
what are key properties of carbonyl (C=O) groups?
polar and hydrophilic
32
what are key properties of methyl (CH3) groups?
non-polar and hydrophobic
33
what are the 3 disaccharides you need to know for the exam? list what monosaccharides are combined
sucrose: glucose + fructose lactose: glucose + galactose maltose: glucose + glucose
34
in a disaccharide, what joins the two monosaccharides?
glycosidic linkage
35
briefly describe the reactions of dehydration synthesis and hydrolysis
monomers combine together to form polymers via dehydration synthesis. water is formed during this process. polymers are broken down to form monomers via hydrolysis. water is consumed
36
in a polymer, how are bonds broken and formed?
formed: dehydration synthesis; water is formed as by-product broken down: hydrolysis; water consumed this applies to all polymers, regardless of it's a glycosidic linkage, a phosphodiester bond, or a peptide bond.
37
what are the (2) types of glycosidic bonds?
alpha and beta determined by the -OH groups of the sugars
38
describe the alpha-glycosidic bond
between 2 alpha-monosaccharide molecules the -OH groups forming the bond are both pointing down
39
describe the beta-glycosidic bond
between an alpha and a beta-monosaccharide molecule the bond is between an -OH pointing down and an -OH pointing up
40
what are considered to be under carbohydrates?
saccharides, starch, glycogen, cellulose, chitin
41
how are starch and glycogen similar and different?
both are polymers of alpha-glucose molecules (thus, have alpha-glycosidic bond) they differ in their polymer branching and where they are found glycogen has more branching glycogen found in animal cells and starch found in plant cells
42
where is starch found? what's its function?
in plant cells stores energy
43
where is glycogen found? what's its function?
found in animals stores energy
44
how does one differentiate between alpha and beta monosaccharides?
if the OH on the anomeric carbon is pointing DOWN, it's alpha if the OH on the anomeric carbon is pointing UP, it's beta
45
describe cellulose
a polymer of beta-glucose a structural molecule for walls of plant cell and wood
46
describe chitin
a polymer of beta-glucose that's attached to a nitrogen containing group: (n-acetylglucosamine) a structural molecule found in fungal cells and insects' exoskeleton
47
how are cellulose and chitin similar?
they are both comprised of beta-glucose molecules (but chitin also includes N-molecules) thus, they both use beta-glycosidic bonds
48
can humans digest glycosidic linkages?
our digestive system can digest only alpha-glycosidic linkages they can't digest beta-glycosidic linkages - cows have bacteria in their gut that produces the enzymes that can break down beta-glycosidic linkages
49
what are the macromolecules (polymers) and their monomer components?
carbohydrates (aka polysaccharides): monosaccharides lipids: a bit complicated, but generally composed of hydrocarbons - lipids are not really considered polymers but are macromolecules proteins (aka polypeptides): amino acids nucleic acids (DNA/RNA): nucleotides
50
briefly describe lipids. what bonds are seen in lipids?
long hydrocarbon chains that are non-polar and hydrophobic they are not considered polymers bc they are not made of repeated units covalent bonds between the hydrocarbons
51
what are the general functions of lipids?
insulation: preserves heat energy storage: energy reserves we can burn when needed endocrine molecules (steroid hormones) structural (phospholipids and cholesterol are key components of the cell membrane)
52
what are triglycerides (triacylglycerols)
consists of 3 fatty-acid chains attached to a glycerol backbone (3 carbons). the fatty acids can be saturated or unsaturated body converts calories it doesn't need right away to triglycerides which are then stored in fat cells. later, hormones release them for energy (in between meals)
53
differentiate between saturated and unsaturated fatty acid chains
saturated has no double bonds which lead to straight chains. these straight chains can stack densely and form plaques - bad for health unsaturated has double bonds which lead to kinks in the chains. they stack less densely - good for health. can be cis/trans
54
what are phospholipids (diacylglycerols)?
2 fatty-acids and a phosphate group (w/ +R) attached to a glycerol backbone major component of cell membranes they are amphipathic: has both hydrophilic and hydrophobic properties - hydrophobic tail: fatty acids - hydrophilic head: glycerol and phosphate group
55
what are steroids? what are considered steroids?
contains 3 six-membered rings and 1 five-membered rings (4 rings in total) e.g. hormones and cholesterol
56
what's the most common precursor to steroid hormones?
cholesterol
57
what are waxes?
esters of fatty acids and monohydroxy alcohol used as protective coating of skin and exoskeletons
58
what are carotenoids?
fatty acid carbon chain with conjugated double bonds and five/six-membered rings at each end - includes pigments which produces colour in plants/animals subgroups: carotenes and xanthophylls
59
what are porphyrins? give 2 examples
4 joined pyrrole rings often complexes with a metal in the center - Fe in hemoglobin (from transporting O2) - Mg in chlorophyll (for absorbing light)
60
what are adipocytes?
specialized fat cells major energy storage site in the body
61
what are glycolipids?
similar to phospholipids, but instead of a phosphate group, they have a carbohydrate group
62
what are lipoproteins?
bc lipids are insoluble, lipoproteins are used to transport lipids in the blood lipoproteins are a lipid core surrounded by phospholipids (lipid bilayer) and apolipoproteins
63
how does the cell membrane maintain its fluidity in different temperatures?
by changing membrane fatty acid composition the cell membrane becomes more rigid in cold weather. to avoid rigidity, the cell membrane has cholesterol (prevents tight packing of phospholipids) and mono/polyunsaturated fatty acids incorporated into the membrane which increases fluidity the cell membrane becomes more fluid and flexible in warm weather. to prevent itself from collapsing, cholesterol is added to restrict movement. the fatty acids become more saturated, allowing it to densely stack itself, increasing rigidity.
64
describe the general structure of an amino acid
a amino group, carboxyl group, a hydrogen group, and a R-side chain linked to an alpha-carbon
65
what functions do proteins have?
structural (e.g. collagen) mechanical/movement (e.g. actin/myosin) enzymes hormones (e.g. insulin) antibodies fluid balance acid-base balance - pH (albumin) channels/pumps transport (e.g. hemoglobin which moves oxygen) storage (e.g. casein which stores amino acids in mammalian milk)
66
what do enzymes do? what do they not do?
catalyze reactions in both forward and reverse directions -- lower the activation energy required for a reaction, accelerating the rate of the overall reaction. they do not change the spontaneity of a reaction or the equilibrium they have varying function based on pH and temp
67
what determines the efficiency of an enzyme?
temperature (it can cause denaturation), the ideal temperature for enzymes can vary. but as you raise temperature, you generally see an increase in enzyme activity and reaction rate due to the increase in kinetic energy, having molecules bounce around more quickly. BUT, if temperature raised too high, the enzyme will denature and lose its function pH (it can cause denaturation), the ideal pH for enzymes vary - e.g. pepsin prefers low pH - urease and trypsin prefer moderate pH substrate and enzyme concentration presence/absence of inhibitors
68
what does amylase do?
catalyzes reaction that breaks the alpha-glycosidic bonds in starch
69
all enzymes are considered proteins, except..?
RNA enzymes / ribozymes / riboenzymes
70
what type of proteins are there?
storage, transport, enzymes
71
what are cofactors?
non-protein molecules that assist enzymes, usually by donating or accepting some component of the reaction, such as electrons or functional groups some bind reversibly or some permanently
72
what's a holoenzyme?
cofactor + protein
73
what's a apoprotein/apoenzyme?
when an enzyme is not combined with a cofactor but requires it for activity
74
what's a coenzyme?
an organic coenzyme, like vitamins enzymes can also be inorganic (like metals, Fe2+ or Mg2+)! can be categorized into prosthetic group (bind covalently) and cosubstrates (bind reversibly)
75
in regards to enzymes, what's a prosthetic group?
if a cofactor is covalently or tightly bound to an enzyme
76
what are simple proteins?
proteins formed entirely of amino acids
77
what are the (2) types of simple proteins?
albumins & globulins: functional proteins that act as carriers or enzymes scleroproteins: fibrous proteins with a structural function (e.g. collagen)
78
what are conjugated proteins?
a simple protein linked to a non-protein
79
what are (5) types of conjugated proteins?
lipoprotein: bound to a lipid mucoprotein: bound to a carbohydrate chromoprotein: bound to a pigmented molecule metalloprotein: protein complexed around a metal ion nucleoprotein: contains histone or protamine, linked to a nucleic acid
80
what are the different levels of protein structures? describe them
primary: sequence of amino acid, connected by peptide bonds secondary: the 3D shape from hydrogen bonding between the carboxyl and amino groups of amino acids, side-by-side (involves the peptide backbone) tertiary: 3D structure mainly from non-covalent interactions between the R-groups of amino acids quaternary: 3D shape of a protein that is a grouping of 2 or more, separate peptide chains
81
how is the primary structure of a protein determined?
sequence of nucleotides in the mRNA determine the sequence of amino acids
82
what are the types of secondary structures of proteins?
alpha-helix beta-sheet
83
when talking about the non-covalent interactions that hold the tertiary structure of a protein together, what does it include? (5)
hydrogen bonds ionic bonds hydrophobic effect/interaction: R-groups push away from water disulfide (covalent interaction, an exception): between cysteines van der waals forces
84
what are the (3) main protein categories?
globular structural/fibrous membrane
85
describe globular proteins
water soluble mainly tertiary structures diverse range of functions enzymes are globular !!
86
describe structural/fibrous proteins
not water soluble mainly secondary structures long polymers function: to maintain/add strength to cellular/matrix structures e.g. collagen or keratin
87
describe membrane proteins
not water soluble includes proteins that function as membrane pumps, channels, or receptors
88
what is protein denaturation?
when a protein reverts back to its primary structure
89
give (4) examples of denaturing agents
temperature, pH, UV light/chemical, and salt concentrations
90
a protein's function is determined by what?
its overall shape! aka 3D structure when denatured, it won't be able to function properly
91
can protein denaturation be reversed?
generally irreversible, but in some cases, can be reversed by removing the denaturing agent
92
what does protein denaturation imply about the protein's information?
all information needed for a protein to assume its folded, functional (native) form is encoded in its primary structure
93
differentiate between protein denaturation and digestion
denaturation reverses a protein to its primary structure digestion eliminates all protein structures, including primary
94
what are the functions of nucleic acids?
to encode, express, and store genetic information
95
how are the strands of DNA connected?
via base pair hydrogen bonds that occur between nucleotides on opposite strands
96
how are nucleotides bonded?
phosphodiester bond between the phosphate group of one nucleotide and the five-carbon sugar of another
97
describe the structure of nucleotides
nitrogenous base, a five-carbon sugar, and a phosphate group
98
differentiate between nucleosides and nucleotides
a nucleoside does not have a phosphate group nucleotide: nitrogenous base, sugar, phosphate group nucleoside: nitrogenous base, sugar - e.g. "adenosine" instead of "adenine"
99
what are the nitrogenous bases for DNA and RNA?
DNA: guanine, cytosine, adenine, thymine RNA: guanine, cytosine, adenine, uracil
100
in DNA and RNA, which nitrogenous base pairs with what? and how many bonds? what does that implicate
GCAT -> GC AT guanine and cytosine - 3 hydrogen bonds adenine and thymine - 2 hydrogen bonds since G and C have more hydrogen bonds, they require a higher (melting) temperature to break the same goes for RNA, just replace thymine with uracil
101
which of the nitrogenous bases are purines? pyramidines?
purines: guanine, adenine pyrimidines: cytosine, thymine, uracil
102
differentiate between the structures of DNA and RNA
DNA: GCAT RNA: GCAU DNA: has deoxyribose sugar (missing an O on C2). it's double helix, with 2 strands that are anti-parallel (both run 5' to 3' but in opposite directions) RNA: has ribose sugar. USUALLY single stranded
103
in regards to DNA, why is the direction called " 5' to 3' " ?
phosphate is attached to C5 of the deoxyribose sugar and the OH group is attached to C3 looking at DNA we see that the phosphate (at C5) begins the sequence and the OH (at C3) ends it
104
what is chargaff's rule?
the number of purines = the number of pyrimidines because they are base paired A + G = T + C A = T G = C
105
describe the discovery of the cell. who? how?
robert hooke was the first to discover cells when he looked at a piece of tree bark under a microscope and observed the cell walls of dead plant cells a decade later, van leeuwenhoek enhance the magnification of microscope lenses and was the first to observe living cells
106
what does the Cell Theory state (3+4=7)?
all living organisms are composed of 1 or more cells the cell is the basic unit of function, structure, and organization in all organisms all cells come pre-existing, living cells NEW TENANTS FROM THE MODERN INTEPRETATION OF THE CELL THEORY: activity of an organism depends on the total activity of independent cells (each cell contributes to the overall activity of an organism) energy flow occurs within cells (cells have a functional metabolism) cells carry hereditary information all cells have similar basic composition among similar species
107
what characteristics are shared by all cells?
bound by plasma membrane: a selective barrier that separate its contents from the outer environment contains genetic material (DNA) contains ribosomes: synthesizes functional proteins from genetic material (RNA)
108
describe the RNA World Hypothesis theory. what does it state/believe? why? backed by what?
suggests that RNA was the precursor of current life (based on DNA, RNA, and proteins) states that RNA stores genetic information like how DNA does, catalyzes chemical reactions like how enzymes do - a reason behind the belief that RNA played a major role in the evolution of cellular life also backed by the fact that RNA is more unstable than DNA, due to its extra hydroxyl group which makes it more likely to participate in chemical reactions
109
what does the Central Dogma of Genetics (a theory) state?
states that information must travel from DNA -> RNA -> protein cannot travel backwards from protein! information however, can travel back and forth between DNA and RNA in special cases
110
describe the stereomicroscope. what are the pros and cons?
uses visible light to view the surface of a sample pros: can view living samples cons: has low light resolution compared to a compound microscope
111
describe the compound microscope. what are the pros and cons?
uses visible light to view a thin section of the sample pros: can view some living samples (single cell layer) cons: may require staining for good visibility which kills cells - samples that are thin enough don't require staining
112
describe phase contrast microscope. what are the pros and cons?
uses light phases and contrast for a detailed observation of living organisms. including internal structures if thin pro: good resolution and contrast cons: not ideal for thick samples. produces a "halo" effect around the perimeter of the samples
113
describe the confocal laser scanning microscope and fluorescence. what are the pros and cons?
used to observe thin slices while keeping a sample intact pros: can observe specific parts of a cell via fluorescent tagging cons: can cause artifacts - not naturally present and caused by the process note: can be used with light instead of fluorescence
114
what is a common microscopy method used to observe chromosomes during mitosis?
confocal laser scanning microscope and fluorescence
115
describe scanning electron microscope (SEM)? what are the pros and cons?
shoots electrons across the surface of a specimen, allowing high definition image pros: view surface of 3D objects with high resolution cons: can't use on living samples as the preparation kills samples. preparation is extensive as samples need to be dried and coated. and is costly
116
describe cryo scanning electron microscope (Cryo SEM). what are the pros and cons?
similar to SEM pros: sample is not dehydrated, so you can observe samples in their more "natural" form cons: can't be used on living samples. samples must be frozen, which might cause artifacts
117
describe transmission electron microscope (TEM). what are the pros and cons?
electron beams passed thru a thin section of the sample, producing very high resolution 2D images. can see internal structures - not just tissue and cells pros: can observe very thin cross-sections in high detail, and can observe internal structures with very high-resolution cons: cannot be used on living samples. requires extensive preparation (samples must be dehydrated, fixed into resin, and sliced into thin sections) and is costly
118
which microscope has the highest magnification?
transmission electron microscope (TEM)
119
describe electron tomography. what are the pros and cons?
not a type of microscope, but a technique used to build a 3D model of the sample via TEM (transmission electron microscope) data pros: can look at objects in 3D and see objects relative to one another cons: same as TEM cons: cannot be used on living samples. requires extensive preparation and is costly
120
what is centrifugation?
common technique used to prepare sample for observation or further experimentation it spins and separated liquified cell homogenates into layers based on density
121
in centrifugation, what is the order in which cells separate?
most dense to least dense most dense will pellet to the bottom and so on
122
in differential centrifugation that deals with organelles, which parts are expected to separate first, to the bottom?
nuclei layer -> mitochondria/ chloroplasts/lysosomes -> microsomes/small vesicles -> ribosomes/viruses/larger macromolecule
123
differentiate between differential centrifugation and density centrifugation
differential: density, shape, and speed - spin, separate dense pellet, repeat density: density
124
what should be noted about solubility in differential centrifugation?
differential centrifugation forms continuous layers of sediment, where insoluble proteins are found in pellet and soluble proteins remain in the supernatant, liquid above the pellet
125
differentiate between anabolic and catabolic processes/reactions
anabolic: small molecules assembled into bigger ones -- requires energy catabolic: large molecules broken into smaller ones -- releases energy (CATACLYSM LOL!!!!)
126
what is ATP?
a common source of activation energy ATP stores its potential energy in the form of chemical energy. ATP is an unstable molecule because the 3 phosphates in ATP are negatively charged and repel one another. when one phosphate group is removed via hydrolysis, a more stable ADP molecule results. the change from a less stable molecule to a more stable molecule always releases energy it provides energy for all cells by transferring phosphate from ATP to another molecule
127
how is new ATP formed?
via phosphorylation ADP and phosphate come together using energy from an energy-rich molecule, like glucose
128
define Km and Vmax in regards to enzymes
Km: "michaelis constant", represents the substrate concentration at which the rate of reaction is half of the max velocity (rate) of the enzyme, or Vmax Vmax: max velocity (rate) of the enzyme
129
what are allosteric enzymes?
they have both an active site for substrate binding AND an allosteric site for binding of an allosteric effector (can be an activator/inhibitor) they can have multiple sites for regulatory enzymes to bind
130
what is competitive inhibition? describe Km and Vmax in this situation
substance is an inhibitor (by mimicking the substrate) that binds at the active site, preventing substrates from attaching. this binding is reversible and brief the effect of competitive inhibition can be combated by increasing concentration of substrate competitive inhibitors increase Km (bc it directly interferes with how substrates bind) but Vmax remains the same
131
what is non-competitive inhibition? describe Km and Vmax in this situation
substance inhibits enzyme by binding somewhere other than the active site, allowing the substrate to still bind, but the enzyme's ability to catalyze a reaction has decreased and reaction doesn't reach completion (bc the enzyme conformation has changed but the ability of a substrate to bind has not been) Kmax remains the same but Vmax decreased
132
what is allosteric inhibition?
substance binds to enzyme (at the allosteric site, affecting the ability of the active site to function) and induces its inactive form does not follow Km and Vmax trends
133
what is uncompetitive / anti-competitive inhibition?
when an enzyme inhibitor binds to the enzyme-substrate (ES) complex -- preventing the formation of the product
134
describe the relationship between Km and binding affinity
recall, Km: the substrate concentration at which the rate of reaction is half of the max velocity of the enzyme, or Vmax Km inversely represents binding affinity a higher Km = worse substrate binding lower Km = better substrate binding Km and binding affinity are both intrinsic properties so increasing/decreasing substate/enzyme concentration doesn't affect this property
135
what is cooperativity, in regards to enzymes?
positive cooperativity: phenomenon where an enzyme becomes more receptive to other substrates after binding to a substrate at its active site negative cooperativity: enzyme becomes less receptive to other substrates after binding to a substrate at its active form cooperativity isn't limited to enzymes can also be done by non-enzymes e.g. oxygen in hemoglobin
136
what are the (3) classifications of membrane proteins?
peripheral: loosely attached to surface of one side of the membrane integral: embedded in the cell membrane transmembrane: type of integral; travels all the way through the membrane
137
what are the (8) types of membrane proteins?
channel proteins recognition proteins ion channels porins carrier proteins transport proteins adhesion proteins receptor proteins
138
what are channel proteins?
proteins that provide a passageway through the membrane for hydrophilic (water soluble), polar, and charged substances can also be done for substances that can normally diffuse, to allow the protein to regulate how much goes in, more quickly, etc (e.g. aquaporins for water)
139
what are recognition proteins?
type of glycoprotein (has an attached oligosaccharide/carbohydrate) used to distinguish between self and foreign -- healthy vs diseased -- by immune cells cell-to-cell recognition
140
what are ion channels?
used to pass ions across the membrane they can be open or gated (3 types) so there are 4 types overall referred to as gated channels in nerve and muscle cells
141
what are glycoproteins?
play a role in cell-cell recognition; immune cells can check membrane glycoproteins to identify if a cell is foreign or not cell signaling: glycoproteins can act as receptors by binding to signalling molecules used in cell adhesion by binding to molecules outside the cell help stabilize them
142
what are the (3) different types of ion, gated channels?
voltage-gated: responds to difference in membrane potential to open/close ligand-gated: chemical (signalling molecule) binds to open channel mechanically-gated: responds to pressure or vibration AND open channel
143
what are porins?
allows the passage of certain ions and small polar molecules increases the rate of water passing in kidney and plant root cells tends to be less specific: if you can fit through the large passage, you can go through
144
what are transport proteins?
proteins that transport materials across the membrane they do this by active transport and facilitated diffusion (note that only active transport uses ATP)
145
what are the types of transport proteins? (2)
carrier and channel
146
what are carrier proteins?
allows for selective transport across the membrane via integral membrane protein changes shape (undergoes conformational changes) after binding to specific molecule that enables it to be passed across - also changes shape to release it
147
what's the major difference between active transport and passive transport
active transport uses ATP
148
what are adhesion proteins?
attach cells to neighbouring cells and provide anchors for stability via internal filaments and tubules
149
what are receptor proteins?
these membrane proteins are binding sites for signalling molecules which then transmit changes to the inside of the cell
150
what are the (3) major components/properties that contribute to the cell membrane? describe them
phospholipid membrane permeability: allows small, uncharged, non-polar, hydrophobic molecules to freely pass through the membrane. polar molecules may pass through if they're small and uncharged (everything else requires a transporter) cholesterol: adds rigidity to the membrane in normal conditions and maintains fluidity at lower temperatures glycocalyx: carbohydrate coat; covers the outer side of the cell wall (in some bacteria) or plasma membrane (in some animal cells).
151
what are the functions of the glycocalyx?
glycocalyx: carbohydrate coating on the outer side of the cell wall or plasma membrane possible functions: - adhesive capabilities - barrier to infection and chemical/physical damage OR - markers for cell-cell recognition can be found on the inside of blood vessels where it helps to provide a protective barrier and maintains the vascular walls beyond the plasma membrane
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what does the glycocalyx consist of?
glycocalyx: carbohydrate coating on the outer side of the cell wall or plasma membrane consists of glycolipids attached to the cell membrane AND glycoproteins that may serve as recognition proteins
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what performs the same role cholesterol does in animal cells' membranes but in plant cells and prokaryotes?
cholesterol: adds rigidity to the membrane in normal conditions and maintains fluidity at lower temperatures plant equivalent = sterols prokaryotes equivalent = hopanoids
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what are the (4) main functions of the cell membrane?
acts as a barrier between the inside and outside of the cell allows for communication with other cells has selective permeability to regulate transport of substances in and out of a cell provides structural support and protection
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what's the fluid mosaic model?
a biological term used to describe the cell membrane fluid: cell membrane components are constantly shifting around - even the phospholipids which frequently rotate and move laterally within the same layer (can even flip vertically into another layer) mosaic: composed of multiple different parts (phospholipids and proteins)
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how are peripheral proteins held in place to a side of the cell membrane? how can this attachment be disrupted?
peripheral membrane proteins are generally hydrophilic and held together by hydrogen bonding and electrostatic interactions this can be disrupted by changing salt concentration or pH
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how can integral proteins be detached from the membrane?
integral proteins are hydrophobic and can be detached using detergent
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differentiate between chromatin and chromosomes
chromosomes are tightly condensed chromatin when the cell is ready to divide
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how many chromosomes do humans have?
46 23 from their mother, 23 from their father
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what's chromatin?
general packaging structure of DNA around proteins (histones) in eukaryotes tightness in packaging depends on the cell stage
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what's a histone?
proteins that provides structural support for DNA
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what's a nucleosome?
a unit of DNA wrapped around 8 histones
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what's the nucleolus?
found in the nucleus; the site of ribosome synthesis
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briefly describe the process of ribosome synthesis
rRNA synthesizes in the nucleus ribosomal subunits are synthesized using rRNA and ribosomal proteins (imported from the cytoplasm). once ribosomal subunits have formed, they're exported to the cytoplasm for final assembly of a complete ribosome
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what is the substitute of cytoplasm in the nucleus? (what's there instead?)
instead of cytoplasm, the nucleus has nucleoplasm
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describe the outer layer of the nucleus and what it uses for transport
the nucleus is bound by a double layer nuclear envelope with nuclear pores for transport (for mRNA, ribosome subunits, dNTPs, proteins like RNA polymerase and histones). the double membrane means it has two phospholipid bilayers
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what is the nuclear lamina?
found in the nucleus of eukaryotic cells a dense fibrillar network (intermediate filaments and membrane associated proteins) that provide mechanical support AND help regulate DNA replication, cell division, and chromatic organization
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differentiate between the nucleus and nucleoid
nucleus found in eukaryotic cells nucleoids found in prokaryotes
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what's the nucleoid?
for prokaryotes contains all or most of the cell's genetic material
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what's the cytoplasm?
most of the cell's metabolic activity and transport happens here the area includes the cytosol and organelles
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what is cytoplasmic streaming?
the streaming movement within the cytoplasm
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differentiate between cytoplasm and cytosol
cytosol is just the gel-like substance but cytoplasm is the gel-like substance and everything, including organelles, suspended within
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what are ribosomes?
site of protein synthesis made of protein and rRNA one of the only organelles that are not membrane bound found in both prokaryotes and eukaryotes
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what are the 2 subunits of ribosomes in eukaryotes? in prokaryotes? (in S units)
eukaryotes: 60S + 40S = 80S prokaryotes: 50S + 30S = 70S the 2 subunits are created in the nucleus and moved to the cytoplasm where they are assembled into a single larger ribosome s larger S value (Svedberg unit) indicates a heavier molecule
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where can you find ribosomes? what can be said about this?
floating in the cytosol or bound to the rough endoplasmic reticulum ribosomes floating in the cytosol make proteins that function within the cell ribosomes bound to the ER make proteins that will be exported
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what is the endoplasmic reticulum?
an extensive network of interconnect membranes with flattened areas called "cisternae" the ER membrane separates the cytosol from its inner contents, the ER lumen
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what are the (2) types of endoplasmic reticulum?
rough ER smooth ER note that the rough ER is closer to the nucleus
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describe the rough endoplasmic reticulum. what does it make? what should you note about rough ER in eukaryotes?
the ER is covered in ribosomes creates glycoproteins by attaching polysaccharides to polypeptides as they are assembled by ribosomes --- in eukaryotes, the rough ER is continuous with the outer nucleus membrane
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what is the process that occurs with proteins in the ER lumen? describe it
post translational modification when ribosomes on the rough ER synthesize proteins, they're injected into the lumen where it can be modified and prepared for transportation can add groups like carbohydrates/phosphates to proteins!!
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describe the smooth endoplasmic reticulum. what does it make? what unique function does it have in liver cell?
not covered in ribosomes, hence "smooth" synthesizes lipids and steroid hormones for export in liver cells, it break down toxins, drugs, and toxic by-products from cellular reactions
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what is the sarcoplasmic reticulum?
smooth ER found in smooth and striated muscle it stores and releases ions like Ca2+
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where do proteins go after being synthesized?
golgi apparatus
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what is the golgi?
aids in the transport of various substances in vesicles helps sort, modify, and transport proteins a series of flattened membrane sacs called cisternae also creates lysosomes and transports lipids
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what are lysosomes?
vesicles produced from the golgi they contain digestive enzymes with low pH, function in apoptosis (by releasing their contents), and break down nutrients, bacteria, pathogens, and cell debris. they can also partake in autophagy which is where they fuse with damaged organelles to break them down and recycle
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how do lysosomes break down nutrients?
when a cell ingests food materials, the cell forms a food vacuole which the lysosome fuses with to break down its contents into useful nutrients
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differentiate between the faces of the golgi
cis face: for incoming vesicles trans face: for secretory vesicles the cis face is more "bent" than the trans face the cis face is closer to the endoplasmic reticulum
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what are the steps the golgi takes in transporting and processing substances?
proteins are made by the rough ER or steroid hormones are made by the smooth ER they're packaged into vesicles and then sent to the golgi apparatus on the cis face where they can be further packaged and modified transported in vesicles from the trans face to various parts of the cell or outside the cell
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what happens to enzymes that escapes from the lysosome?
they remain inactive in the neutral pH of the cytosol
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what are peroxiosomes? where are they found? what do they do (and in plant cells and in germinating seeds)?
found in the liver and kidney break down substances, fatty acids, and amino acids. can also inactivate toxic substances they produce hydrogen peroxide, H2O2, which they use to oxidize substrates, and can also break down H2O2 if necessary (H2O2 → H2O + O2) using the enzyme catalase in plant cells, peroxisomes modify by-products of photorespiration. in germinating seeds, peroxisomes are called glyoxysomes that break down stored fatty acids to help generate energy for growth
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what are microtubules? what are they made up of? what do they do? where can they be found?
hollow tubes formed from polymers of the protein, tubulin provides support and movement for cellular activities act as spindle apparatus, guiding chromosomes during cell division bundles of microtubules make up other cellular structures like: flagella and cilia of all animal cells and lower plants like mosses and ferns. and in centrioles
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describe intracellular transport
microtubules help support motility within the cell. they provide tracks along which organelles and vesicles are transported using motor proteins (kinesin and dynein) kinesin is a motor protein that binds to the cargo it's transporting on one end and the other end moves along the microtubule. moves from the center to the periphery (outer area of the cell, where the cell membrane is) dynein. also binds to cargo on one end and moves with the other end. moves from periphery to center
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what are cilia?
hair-like projections from a cell made of microtubules allows the cell to move. for cells that are in a fixed position (e.g. in the respiratory tract, the cilia move the debris that's trapped in the mucus out of the airway), cilia move substances in the environment across the cell surface
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what are centrioles?
are MTOCs (microtubule organizing centers), a structure that microtubules emerge from 2 centrioles, perpendicular to another, make up a centrosome allows for development of spindle fibers of the spindle apparatus during cell division they do not have a membrane
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which organelles are not bound by a membrane?
ribosomes centrioles centrosomes cytoskeleton (FROM GOOGLE, UNSURE ACCURACY AND IF THERE'S MORE)
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what are microvilli?
projections from the cell membrane composed of actin filaments that support the microvilli and maintain its shape function to increase the surface area of the cell which leads to enhance absorption and secretion commonly seen in cells of the digestive system
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what is the arrangement of microtubules in flagella and cilia of all animal cells and lower plants like mosses and ferns?
in a 9+2 array - 9 pairs of microtubules with 2 singlets in the center
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what are intermediate filaments?
provide physical support and stability for maintaining cell shape (e.g. keratin)
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what are microfilaments?
made of actin involved in cell movement found in skeletal muscle, amoeba pseudopod, and cleavage furrows
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what are microtubule organizing centers (MTOCs)? give 3 examples!
a structure that microtubules emerge from includes centrosomes (centrioles) and basal bodies BASAL BODIES: are found at the base of each flagellum and cilium; organization of eukaryotic flagella and cilia and the CENTROSOMES: organization of the mitotic and meiotic spindle apparatus, which separate the chromosomes during cell division. plant cells lack centrioles and divide via cell plates rather than cleavage furrows — note that plants do have MTOCs called spindle pole bodies
200
how are microtubule organization centers (MTOCs) arranged?
unlike microtubules, MTOCs are found in a 9x3 array they are made of 9 triplets of microtubules held together
201
what are transport vacuoles?
moves materials between organelles or organelles and the plasma membrane
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what are food vacuoles?
temporary containers of nutrients that merge with lysosomes to break down food
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what are central vacuoles?
found only in plant cells generally large - can occupy most of the cell wall's interior exerts turgor when fully filled (pressure - pushes plasma membrane against cell wall - maintains rigidity) stores nutrients and water carries out functions performed by lysosomes in animal cells (degrades material taken up from outside the cell and to digest obsolete components of the cell itself)
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what's a tonoplast?
specialized membrane of central vacuoles
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what are storage vacuoles?
where plants store starch, pigments, and toxic substances such as nicotine ONLY FOUND IN PLANT CELLS
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what are contractile vacuoles?
usually found in single-celled Protista organisms like amoeba and paramecium living in hypotonic environments collects and pumps excess water out of the cell via active transport to prevent bursting
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what are cell walls?
provides support in plants, fungi, protists, and bacteria sometimes a secondary cell wall develops beneath the primary cell wall
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what are cell walls made up (for plants, fungi, bacteria, and archaea - 4)?
plants: cellulose fungi: chitin bacteria: - gram-negative: thin peptidoglycan layer surrounded by lipopolysaccharides attached to an outer membrane above the peptidoglycan layer - gram positive: thick peptidoglycan layer above one membrane layer (no outer membrane here!) archaea: polysaccharides
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what happens when gram-negative bacteria is destroyed?
the lipopolysaccharides are released from the outer membrane as endotoxins, a toxic compound which can trigger an immune response gram-positive doesn't have lipopolysaccharides, so no toxins released
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what is the extracellular matrix?
found in animals between adjacent cells (beyond the plasma membrane and glycocalyx) - provides mechanical support and helps bind adjacent cells occupied by fibrous structural proteins, adhesion proteins, and polysaccharides secreted by cells provides structural support (with it's support proteins); cell adhesion (EM serves as an area of anchorage for cells to attach to); and transmits mechanical and chemical signals between the inside and outside of the cell
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describe the network of proteins found in the extracellular matrix that helps bind adjacent cells
collagen and proteoglycans and glycoproteins connected to integrins in the cell membrane via fibronectin collagen is the most common, followed by integrin and fibronectin --- proteoglycan and glycoproteins are proteins that have carbohydrate groups attached. the carbohydrates in glycoproteins are short and branched (used in cell signaling and adhesion), while the carbohydrates in proteoglycan are long and unbranched (used for structural support). collagen, an incredibly strong protein fiber embedded throughout the EM. fibronectin attaches proteoglycans, glycoproteins, and collagen to integrin integrin are proteins located in the cell membrane by using fibronectin and integrin, cells can anchor themselves to the collagen, proteoglycan, and glycoproteins of the EM, facilitating cell adhesion
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how do cells adhere/connect to the extra cellular matrix (2)?
focal adhesions (connection of the ECM to actin filaments in the cell) AND hemidesmosomes (involve the connection of ECM to intermediate filaments like keratin)
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what are fibroblasts?
cells that produce collagen and other connective tissue elements found in the extracellular matrix
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what is collagen?
the most abundant protein in mammals found in bones, muscles, skin, and tendons fibrous protein present in tissue as triple helix (its structure provides strength) a repeating pattern of amino acids, every 3rd amino acid is glycine
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what are plastids? what does it include (6)?
organelles found in plant cells includes: chloroplasts (the site of photosynthesis) leucoplasts: specialized storage of... - starch [as amyloplasts] - lipids [as elaioplasts] - proteins [as proteinoplasts] chromoplasts (store carotenoids)
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what are chloroplasts?
double membrane layered organelle site of photosynthesis (light -> sugar) has its own circular DNA most likely descended from a bacteria capable of photosynthesis, cyanobacteria
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why do chloroplasts appear to be green?
they absorb red and blue wavelengths of light but reflect green
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describe the structure of mitochondria
double-layered organelle (2 separate phospholipid bilayers)... multiple "layers": outer mitochondrial membrane, intermembrane space, inner mitochondrial membrane (folded numerous times to increase surface area and ATP production), mitochondrial matrix
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how does the mitochondria make ATP?
makes ATP thru aerobic cellular respiration
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what does the endosymbiotic theory state?
states that mitochondria and chloroplasts were once prokaryotic organisms that lived on their own they were absorbed by a larger cell and formed a symbiotic relationship (larger cell provides protection and they provide energy) with it. eventually they became organelles in eukaryotes
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what evidence backs the endosymbiotic theory?
mitochondria and chloroplasts have their own genome (circular DNA --- eukaryotes have linear DNA and prokaryotes have circular DNA) -- also have their own ribosomes mitochondria and chloroplasts divide by binary fission (they divide independently of the eukaryotic cell they reside in) contain other structures similar to prokaryotes
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what is the cytoskeleton? what are the components? where's it?
helps cells maintain their shape, mechanical support/motility (helps move components within the cell as well), helps anchor/stabilize membrane proteins, and internal organization includes microtubules (e.g. flagella and cilia), microfilaments, and intermediate filaments found in eukaryotic cells aids in cell division, cell crawling, and the movement of cytoplasm and organelles
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what are microfilaments?
2 intertwined polymer strands of actin involved in cell motility and other functions used in skeletal muscle contraction helps to form the amoeba pseudopod, a projection from a cell that's used in movement and ingestion forms the cleavage furrow that's involved in separating cells at the end of mitosis
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what are intermediate filaments?
tubes of intertwined coil proteins the proteins that make up an intermediate filament depends on the type of cell they appear in e.g. keratin in skin cells
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describe the behaviour a plant cell undergoes when placed in a hypotonic, isotonic, and hypertonic solution (plant cell and water balance)
hypotonic solution (where there's less stuff dissolved in water than in the cell): plant cells swell as their central vacuole fill up, making them turgid/firm. fungal cells stay firm in hypotonic conditions due to their cell wall isotonic solution (where the concentration of dissolved stuff is the same inside and outside the cell): plant cells are flaccid - not swollen and not pushing against the cell wall hypertonic solution (where there's more stuff dissolved in water than in the cell): the cell shrinks and pulls away from the cell wall, a process called plasmolysis.
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describe the behaviour an animal cell undergoes when placed in a hypotonic, isotonic, and hypertonic solution (animal cell and water balance)
hypotonic solution (where there's less stuff dissolved in water than in the cell): animal cells undergo lysis and burst isotonic solution (where the concentration of dissolved stuff is the same inside and outside the cell): water moves in and out at equal rates hypertonic solution (where there's more stuff dissolved in water than in the cell): water rushes out of the cell, making it shrink - plasmolysis
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what is the endomembrane system? what does it include?
the network of organelles and structures, either directly or indirectly connected, that help in the transport of proteins and other macromolecules into/out of the cell includes: plasma membrane, endoplasmic reticulum, golgi apparatus, nuclear envelope, lysosomes, vacuoles, vesicles, and endosomes does not include: mitochondria and chloroplasts
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differentiate between the movement of flagella and cilia
flagella: undulates like a snake cilia: beats in rapid back and forth motions
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what are the (2) methods of circulation throughout the cell?
intracellular extracellular
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describe intracellular circulation
follows brownian movement, the random particle movement due to kinetic energy; spreads small particles throughout the cytoplasm - prevents particles from settling down the cyclosis (flow/stream of cytoplasm) the circular motion of cytoplasm within the cell
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what is cyclosis?
movement by the streaming of cytoplasm within a cell. cytoplasm flow is driven by the movement of the cytoskeleton (generated by the contraction and relaxation of actin and myosin filaments) circulates the cytoplasm around the cell which allows cellular components to be moved around
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what organelle plays a key role in intracellular circulation? describe the role
endoplasmic reticulum provides channel through the cytoplasm provides direct continuous passageway from plasma membrane to nuclear membrane
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describe extracellular circulation
through diffusion if cells are close enough to their external environment, diffusion can fulfill food and respiration needs also used for transport of materials between cells and interstitial fluid around cells in more complex animals
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what are cell junctions?
protein complexes that connect cells
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what are the (4) major cell junctions?
anchoring/adhesion gap tight plasmodesmata
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what are anchoring junctions? list the types (3) and describe them
desmosomes: (keratin intermediate filaments attached to adhesion plaques which bind adjacent cells via adhesion proteins), providing mechanical stability by holding cellular structures together (stronger than adherens) - present in animal cells with tissue experiencing mechanical stress - including skin epithelial cells and cells in the cervix/uterus adherens: also attached to actin filaments on the inside of the cell to further stabilize hemidesmosomes: attach the cell to the extracellular matrix (prevents it from being detached from the surface easily); also attached to intermediate filaments on the inside of the cell. can be found in the epidermis, the skin's outer layer
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what are tight junctions? where could they be found?
fully encircles each cell, producing a seal that prevents the passage of materials between cells. made of transmembrane proteins common to cells lining the digestive tract where materials are required to pass through the cells into the blood -- tight junctions prevent materials to escape between the cells. the materials must enter the cells (via diffusion or active transport) to pass through the tissues in animal cells
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what are gap junctions? where could they be found?
similar to transport proteins; narrow tunnels between animal cells that prevent cytoplasm of each cell from mixing but allows passage of ions and small molecules for effective cell-cell communication basically channel proteins of two adjacent cells that are closely aligned tissues like the heart include these to quickly pass electrical impulses, because ions like sodium can spread directly from one cardiac muscle cell to the next connexins: gap junction proteins - basically channel proteins of two adjacent cells that are closely aligned
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what is the apical side of the cell?
side of the cell facing the external environment or internal cavity (points outwards or outer surface/top side of the cell) there are no other cells/tissues touching that surface
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what is the lateral surface of the cell?
sides of the cell in the tissue touching the cells adjacent to it
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what is the basal side of the cell?
bottom of the cell surface of the cell anchored to the underlying connective tissue
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what are plasmodesmata?
narrow tunnels between plant cells desmotubule: narrow tube of endoplasmic reticulum: exchanges material through cytoplasm surrounding the desmotubule gated plant cell wall channels that allow the movement of molecules between cells
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what are some features we should note about prokaryotes?
no nucleus no chromatin level organization of DNA. DNA exists as single, circular, naked, and double-stranded ribosomes are produced like 50S + 30S = 70S has cell walls made of peptidoglycan but in archaea made of polysaccharides flagella constructed from flagellum, not microtubules
244
define a hypertonic solution
higher solute concentration
245
define a hypotonic solution
lower solute concentration
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define a isotonic concentration
equal solute concentration
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what is bulk flow?
collective movement of substances such as blood in response to a force or pressure
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what is considered passive transport? (6)
simple diffusion osmosis dialysis (diffusion of different solutes across a selectively permeable membrane) plasmolysis (movement of water out of a cell that results in its collapse) facilitated diffusion countercurrent exchange (diffusion by bulk flow in opposite directions such as blood and water in fish gills)
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differentiate between simple diffusion and facilitated diffusion
simple diffusion: no proteins used facilitated diffusion: substances move down the concentration gradient with the assistance of transmembrane transport proteins
250
what is a concentration gradient? what role does this play in passive and active transport?
when substance is more concentrated on one side of the permeable membrane a biological imbalance that's energetically unfavourable normally (to seek balance), substances would go down the concentration gradient (from high conc -> to low conc). this is passive transport active transport is when the substances move against the concentration gradient
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what is active transport?
movement of molecules against their concentration gradient -- requires energy! usually involves solutes like small ions, amino acids, and monosaccharides
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what are the (5) types of active transport?
primary active transport secondary active transport group translocation endocytosis: substances bought into a cell by enfolding them with cell membrane exocytosis: similar to endocytosis, but transportation out of the cell
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what are the (2) types of secondary active transport?
antiport: exchange symport: cotransport
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define primary active transport
energy (ATP) used to directly move against concentration gradient
255
describe receptor-mediated cytosis
a form of pinocytosis in which in which molecules called ligands bind to receptors first, molecules outside the cell bind to receptors on the cell membrane. once they bind, a protein called clathrin attaches itself to the areas of the membrane that have bound receptors on the inside. these clathrin proteins form a lattice that pulls the membrane inward and creates a vesicle. the clathrin detaches.
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define secondary active transport
energy indirectly used to move against concentration gradient (usually with an ion moving down its concentration gradient) using an established electrochemical gradient to move a substance against its concentration gradient example: if there's a high conc of sodium outside the cell and high conc of glucose inside the cell. can link the transport of two together so when sodium moves in (favourable), glucose moves in (unfavourable) the requirement is that one of the two substances must be moving down it's concentration gradient
257
define group translocation
seen in prokaryotes when the substance being transported across the membrane is chemically altered in the process --> prevents it from diffusing back out
258
what are the (3) types of endocytosis?
phagocytosis pinocytosis "cell-drinking" receptor-mediated cytosis
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describe phagocytosis
engulfing particles by extending structures like pseudopods. packaged into a vesicle and can be fused/broken down later. this process is common in the immune system where pathogens can be bought into the cell and then fused with organelles like lysosomes to be destroyed. deals with more larger substance than pinocytosis would
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describe pinocytosis
plasma membrane forms a pocket and pinches off to form a sort of vesicle in the cytoplasm around the extracellular fluid and dissolved material (liquid). a non-selective process, cell doesn't care what it's pulling in
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what is one way we can trigger exocytosis to occur?
increasing concentration of calcium on the inside of the cell
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what are (2) processes that tend to use exocytosis?
neurons releasing neurotransmitters endocrine cells releasing certain hormones into the bloodstream
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differentiate between diffusion and osmosis
in diffusion, SOLUTES move from higher conc to lower conc in osmosis, SOLVENT (usually water) moves from higher conc to lower conc
264
describe the relationship between basal metabolic rate (BMR) and body size and body weight
BMR overall, increases as size increases but BMR also actually decreases per kg as size goes up (an elephant has a higher BMR than a squirrel. but a squirrel would have a higher BMR per kg)
265
describe the relationship between metabolism, temperature, and age
increased temp = increased metabolism increased age = decreased metabolism
266
what's kinetic energy? what's potential energy?
kinetic: associated with anything with motion e.g. a flagella whipping back and forth potential: found in objects not moving - the object has potential (stored) energy for later use e.g. energy stored within chemical bonds of glucose and glycogen stored in muscles
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what is the formula for gibbs free energy? describe coupling in regards to it
G = deltaH - temperature(deltaS) = change in enthalpy - (temperature x change in entropy) if G is negative, the reaction is spontaneous (exergonic). energy is released if G is positive, then non-spontaneous (endergonic). energy is absorbed chemical reactions can be “coupled" together if they share intermediates. in this case, the overall Gibbs Free Energy change is the sum of the △G values for each reaction. E.G. an unfavorable reaction with a positive △G1 value can be driven by a second, highly favorable reaction (negative △G2 value where the magnitude of △G2 > magnitude of △G1). this principle of coupling reactions to alter the change in Gibbs Free Energy is the basic principle behind all enzymatic action in biological organisms, and is how ATP drives chemical work.
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what is one of the most favourable reactions we can use to drive non-spontaneous reactions?
the breakdown of ATP, an exergonic reaction releasing energy the bonds between the close together, negative phosphate groups of ATP release significant amount of energy when they're broken via hydrolysis NOTE: the formation of ATP from the oxidative phosphorylation of ADP is endergonic, requiring energy
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what is metabolism? what are the (2) different pathways?
sum of all chemical reactions taking place categorized into catabolic (energy releasing) and anabolic (energy consuming) pathways provides the reactions necessary to produce the energy every cell needs metabolism = catabolism + anabolism + energy transfer
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what are the laws of thermodynamics?
1: energy can't be created or destroyed - only transferred and transformed 2: the transfer of energy leads to an increase of entropy over time (for closed systems! -- doesn't apply to organisms that are living systems. our entropy decreases over time at the expense of the environment) 3: as a system approaches absolute zero temperature (0K), entropy approaches a minimum
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how do catalysts lower the activation energy?
stabilize the transition state provide an alternate pathway with a lower activation energy for the reaction
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how do substrates bind to enzymes?
bind via induced fit: the structure of the enzyme's active site changes in response to the enzyme binding to it. the tighter fit brings the chemical groups of the substrate closer together, creating a more favourable environment for the reaction a series of weak interactions NOT strong covalent bonds
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how do enzymes work?
a substrate binds to the active site of an enzyme and is held in place by temporary (non-covalent) bonds while the substrate is bound to the active site, the enzyme catalyzes its conversion into a product molecule the product molecule is released from the active site and a new substrate will bind
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what are zymogens?
aka proenzymes inactive precursor to enzymes; once cleaved, they're able to function e.g. pepsinogen --(low pH)--> pepsin
275
how can enzyme regulation take place? (3)
at the genetic level: genes that produce enzymes can be activated or disabled depending on the needs of the cell at the physical level: enzymes can be stored in vesicles (contents released when cell requires their activity) at the enzyme level: - proenzymes (zymogens) can be cleaved to activate them - can be activated/disabled via chemical modification (e.g. phosphorylation) - can be modified by having another molecule bind to them, altering their level of activity
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what is feedback inhibition (negative feedback)?
when the product of a reaction binds to one of the earlier enzymes in its metabolic pathway, inhibiting its activity the enzyme will no longer function and the product will stop being produced most enzymes are regulated by this type of feedback (prevents too much product from being formed) and it's how the body maintains homeostasis
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what is positive feedback?
a product of the enzyme triggers more product formation -- creating a loop that increases in magnitude over time e.g. labor contractions during birth (oxytocin production)
278
briefly describe cellular respiration and state the formula
cellular respiration is the overall oxidative/combustion, exergonic process (spontaneous) that breaks down (catabolic) glucose in order to derive energy in the form of ATP considered oxidative because glucose is ultimately losing electrons which are used to make ATP C6H12O6 + 6(O2) ——> 6(CO2) + 6(H2O) + energy (heat and ATP) during respiration, high energy H atoms are removed from organic molecules (dehydrogenation)
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in what 2 forms does cellular respiration produce energy?
heat and ATP
280
how is mitochondrial DNA inherited?
exclusively from your mother, since her eggs provides all the mitochondria to the growing embryo
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where can the mitochondria's DNA and ribosomes be found?
in the mitochondrial matrix
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define substrate level phosphorylation and oxidative phosphorylation
substrate level phosphorylation: production of ATP using enzyme catalyzed reactions. direct transfer of phosphate groups to ADP oxidative phosphorylation: ATP produced using energy from redox reactions of the ETC
283
what is external and internal respiration?
external respiration: entry of air into the lungs and subsequent gas exchange between alveoli and blood internal respiration: exchange of gas between blood and the cells.
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what (4) major steps make up cellular respiration?
glycolysis pyruvate decarboxylation (links glycolysis and krebs cycle) (once for each pyruvate) krebs cycle electron transport chain
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what is glycolysis? where does it take place?
decomposition of glucose into pyruvate in the cytosol the purpose is to produce pyruvate (which will be used in the citric acid cycle) and ATP takes place in the cytosol
286
describe the formula of glycolysis
glucose + 2NAD + 2ADP -> 2 pyruvate + 2ATP + 2NADH + 2H2O reactants: glucose, NAD, ADP products: pyruvate, ATP, NADH, and water it takes the 6-carbon glucose and produces 3 2-carbon pyruvate
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which step of cellular respiration produces the most ATP?
electron transport chain (ETC)
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describe the (2) important steps of glycolysis
using ATP, hexokinase phosphorylates glucose to glucose 6-phosphate, which is important as this step is irreversible because glucose can’t diffuse out of the cell due to the negative charge it now has. since it can't leave, it can be immediately usable for energy LATER IN THE PROCESS, phosphofructokinase (PFK), using ATP, adds a 2nd phosphate, to convert fructose 6-phosphate to fructose 1,6-bisphosphate, which is irreversible and commits the glucose to glycolysis. this is the rate limiting step
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is glycolysis aerobic or anaerobic?
glycolysis can occur under both conditions as it does not require oxygen, thus, ANEROBIC
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how is ATP produced in glycolysis?
ATP is produced via substrate level phosphorylation, which involves the direct transfer of a phosphate group via enzyme, to ADP (no extraneous carriers needed) the energy for ATP formation comes from the coupled reaction
291
what is the importance of phosphofructokinase adding a 2nd phosphate to fructose 6-phosphate, converting it to fructose 1,6-bisphosphate? how does phosphofructokinase regulate glycolysis?
commits the glucose to glycolysis the PFK step of glycolysis is the major regulatory point of glycolysis and is a point of allosteric regulation that controls the overall rate of glycolysis an example of negative feedback. when ATP in the cell is high, phosphofructokinase is inhibited and prevents glycolysis from moving forward. when ATP is low, phosphofructokinase is used in abundance, and the cell is free to use glycolysis to make more ATP it is also the rate limiting step of glycolysis
292
describe the steps of pyruvate decarboxylation
pyruvate becomes acetyl CoA, while producing 1 NADH and 1 CO2 (net: 2 NADH and 2 CO2 since 2 pyruvate formed in glycolysis) reaction is catalyzed by PDC enzyme (pyruvate dehydrogenase complex)
293
where does pyruvate decarboxylation take place?
mitochondrial matrix but in prokaryotes, it takes place in the cytoplasm
294
describe krebs cycle (fate of pyruvate that is produced in glycolysis) and its steps
in the krebs cycle, acetyl CoA merges with oxaloacetate to form citrate, and the cycle continues with 7 intermediates 3 NADH, 1 FADH2, 1 ATP (via substrate level phosphorylation) and 2 CO2 are produced per pyruvate molecule. Each glucose molecule forms two pyruvate in glycolysis, so the cycle turns two times, creating a net of 6 NADH, 2 FADH2, 2 ATP (technically GTP), and 4 CO2. The CO2 produced here is the CO2 animals exhale during breathing
295
where does the krebs cycle take place?
mitochondrial matrix but it takes place in the cytosol for prokaryotes
296
where does the electron transport chain (ETC) take place?
in the inner membrane/cristae of the mitochondria (the folds increase surface area for more ETC action) ETC is embedded into the membrane and the membrane can host multiple so more space = more ETC = more ATP produced in prokaryotes, this process takes place in the cellular membrane
297
what are the (2) other names for krebs cycle?
citric acid cycle tricarboxylic acid cycle
298
what is aerobic respiration?
aerobic pathway of cellular respiration organic compounds and oxygen react in a combustion reaction that produces energy
299
why are muscle cells abundant in mitochondria?
mitochondria are responsible for synthesizing very large amounts of ATP for cells to survive. the higher energy needs of a cell are, the more mitochondria it will have since muscle cells (like cardiac and skeletal) require lots of energy to move, they will have many mitochondria.
300
what is the purpose of pyruvate decarboxylation?
to synthesize acetyl-CoA
301
how is ATP produced in the citric acid cycle?
ATP is produced via substrate level phosphorylation, which involves the direct transfer of a phosphate group via enzyme, to ADP (no extraneous carriers needed)
302
describe the important steps of the citric acid cycle?
first, acetyl-CoA merges with oxalacetate forming citrate this citrate will go thru multiple steps, progressively being turned into different intermediates. during this process, electrons are stripped away and used to form different products at the end, oxalacetate is reformed and the cycle can repeat NOTE: this cycle happened twice per glucose!! 1 glucose -> 2 pyruvates -> 2 acetyl CoA
303
what is produced in the citric acid cycle?
NAD, ATP, FADH2, CO2 note that we technically get 2 acetyl-CoA from glucose so this cycle happens twice
304
where does the CO2 that animals exhale come from?
citric acid cycle
305
what is the purpose of NADH and FADH2?
coenzyme nucleotide molecules that function as high energy electron carriers during glycolysis and the citric acid cycle, electrons are removed from glucose and transferred, converting NAD+ and FAD to NADH and FADH2. these electrons are eventually used to create ATP in the ETC
306
what is the electron transport chain?
a series of proteins embedded in the inner membrane of the mitochondria IN ANAEROBIC CELLULAR RESPIRATION, the electron transport chain is found in the cellular membrane in this process, the proteins pass high energy electrons through the chain, ultimately allowing the production of ATP
307
what are the steps of the electron transport chain (ETC)?
NOTE: this is oxidative phosphorylation first, NADH and FADH2 ferry electrons to the ETC and drop them off (converting back to NAD+ and FAD -- they are oxidized!! -- and go back to glycolysis/CAC to repeat their process) to other electron carriers/proteins as electrons pass through the proteins of ETC, protons (H+ ions) are pumped across the inner mitochondrial membrane and into the intermembrane space, establishing an electrochemical gradient. the intermembrane space has a high proton concentration (high pH - acidic) while the mitochondrial matrix has a low proton concentration note that as the electrons move through, they slowly lose energy due to the pumping of protons. the movement of electrons throughout the ETC is a highly exergonic reaction which is coupled with the endergonic pumping of protons against the gradient in the final step of the ETC, electrons are transferred from a protein to oxygen gas (O2). which then combines with hydrogen ions in the mitochondrial matrix to form water. oxygen is the final electron acceptor, NOT water. water is the final PRODUCT ATP synthase forms ATP from ADP via oxidative phosphorylation (powered by the series of redox reactions from the acceptance and transfer of electrons). the build up of protons (H+ ions) in the intermembrane space goes against the desired balance. the protons wish to even out and move down the electrochemical gradient into the mitochondrial matrix (chemiosmosis). these protons move down through ATP synthase which uses the flow of protons (proton motive force) to create ATP from ADP -- like using wind for energy!
308
between NADH and FADH2, which has more energy? when is this seen?
NADH has more energy than FADH2 and is able to "pump" more protons across the membrane. NADH pumps 3 protons for every 2 protons FADH2 pumps.
309
in the ETC, how are protons able to be continuously pumped against the concentration gradient?
the movement of electrons throughout the ETC is a highly exergonic reaction which is coupled with the endergonic pumping of protons against the gradient note that as the electrons move through, they slowly lose energy due to the pumping of protons
310
what is the final electron acceptor in the ETC?
in the final step, electrons are transferred from a protein to oxygen gas (O2). which then combines with hydrogen ions in the mitochondrial matrix to form water. oxygen is the final electron acceptor, NOT water water is the final PRODUCT
311
what is proton motive force?
promotes movement of protons across membranes downhill the electrochemical potential -- providing energy that can be used to power other reactions OR its energy can either be used right away to do work, like power flagella, or be stored for later in ATP
312
what is chemiosmosis?
movement of ions across a selectively permeable membrane, down their electrochemical gradient
313
what is the total yield for 1 glucose molecule going through aerobic cellular respiration? why is there a discrepancy in numbers of the total of all the individual processes of respiration and the actual total?
glycolysis: 2 ATP & 2 NADH - 2ATP for NADH to be transported into the cytosol pyruvate decarboxylation: 2 NADH citric acid cycle: 2 ATP & 6 NADH & 2 FADH2 electron transport chain: 34 ATP total: 36 ATP (38 - 2)
314
how is ATP produced in the electron transport chain? describe the steps
via oxidative phosphorylation, series of redox reactions where electrons are transferred and accepted etcc ATP synthase forms ATP from ADP via oxidative phosphorylation (powered by the series of redox reactions from the acceptance and transfer of electrons). the build up of protons (H+ ions) in the intermembrane space goes against the desired balance. the protons wish to even out and move down the electrochemical gradient into the mitochondrial matrix (chemiosmosis). these protons move down through ATP synthase which uses the flow of protons (proton motive force) to create ATP from ADP -- like using wind for energy!
315
what's the key difference between aerobic and anaerobic cellular respiration?
in anaerobic respiration, the last electron acceptor is not oxygen! some alternatives: SO4, NO3, S, etc. -- as long as it's not oxygen
316
what is fermentation? how's it different from respiration?
anaerobic process that isn't respiration. there's no citric acid cycle or ETC fermentation allows for the regeneration of NAD+ without needing CAC or ETC. this is done thru the partial breakdown of glucose. note that, respiration is the complete breakdown of glucose
317
what are the steps of alcohol fermentation?
this is after glycolysis turns glucose into 2 pyruvate molecules pyruvate is converted to acetaldehyde and CO2 acetaldehyde and NADH (from glycolysis) is converted to ethanol and NAD+ --- acetaldehyde acts as the final electron acceptor, becoming ethanol. ethanol is the final product the NAD+ is replenished, allowing more glycolysis to take place note that these fermentation steps do not produce any ATP
318
which organisms generally partake in alcohol fermentation?
yeast and some bacteria
319
what are the steps of lactic fermentation?
this is after glycolysis turns glucose into 2 pyruvate molecules pyruvate and NADH is converted to lactate and NAD+ ---- the NAD+ is replenished, allowing more glycolysis to take place note that these fermentation steps do not produce any ATP
320
which organisms generally partake in lactic fermentation?
human muscle cells, fungi, bacteria
321
what happens to lactate in humans following lactic fermentation?
the lactate is transported from the muscle cells to the liver where it's converted back to glucose via the cori cycle. the glucose is sent back to the muscle cells to use as energy
322
out of all human cells, why does lactic fermentation occur in muscle cells?
muscles turn to this process when we we have low oxygen availability due to physical exertion - to continue generating ATP
323
what are the two types of fermentation?
alcohol and lactic
324
where does fermentation occur?
in the cytosol -- where glycolysis takes place
325
why do prokaryotes ultimately gain more ATP from aerobic respiration than eukaryotes? what's the ATP difference?
NADH does not need to be transported into the mitochondrial matrix for prokaryotes the transportation of NADH requires the consumption of 2 ATP. note that pyruvate doesn't require ATP to be transported as its symport with protons so, prokaryotes gain 38 ATP and eukaryotes gain 36 ATP
326
what other macromolecules can be used as an energy source when glucose has been used up?
other carbohydrates lipids proteins (lowk a last resort)
327
what is glycogenesis? describe how it works
occurs when we have more than the necessary amt of glucose glucose monomers are linked together to form the polymer, glycogen -- first, an ATP is used to turn glucose to glucose-6-phosphate. then a bunch of other steps... lastly, we have our branched polymer of glycogen
328
where can glycogen be found?
generally in the liver and in skeletal muscles as they can store large amounts. but technically all cells can store glycogen stored for later use
329
how are other carbohydrates like fructose and galactose used in metabolism?
they are converted to glucose-6-phosphate which can then be used in glycolysis and other metabolic pathways such as glycogenesis
330
what is glycogenolysis?
occurs when we are lacking in glucose glycogen is broken down into glucose-6-phosphate which can be used in glycolysis
331
what is gluconeogenesis?
when other biological macromolecules such as lipids and proteins are converted into glucose AKA conversion of non-carbohydrate precursors into glucose
332
where does gluconeogenesis mainly occur?
liver and kidneys remember that gluconeogenesis is the conversion of non-carbohydrate precursors into glucose
333
how is carbohydrate metabolism regulated?
via two hormones produced by the pancreas: insulin and glucagon
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what role does insulin play in carbohydrate metabolism?
insulin is released when blood glucose levels are too high. what insulin does: - cells will uptake glucose and make use of the glucose, producing ATP (promotes glycolysis). insulin activates the phosphofructokinase enzyme to promote glycolysis - excess glucose made into glycogen (promotes glycogenesis)
335
what role does glucagon play in carbohydrate metabolism?
glucagon is released when blood glucose levels are too low what glucagon does: - glycogen is broken down into glucose for energy (promotes glycogenolysis) - inhibits glycogenesis (to produce energy) and glycolysis (to conserve energy). it inhibits the phosphofructokinase enzyme to inhibit glycolysis note that glycolysis is only inhibited in certain organs so organs that actually need it more have energy (like the brain)
336
how are proteins able to be used for energy?
proteins are broken into amino acids which are then converted in various molecules that can enter the citric acid cycle at various points, such as acetyl-CoA, pyruvate, oxaloacetate (depends on the amino acid) first, remove the amino group from the amino acid through a process called deamination. this amino group will now exists as ammonia which is then converted into urea (more harmless than ammonia which is toxic when accumulated)
337
what is the purpose of breaking down nucleic acids?
different components can be "salvaged" to form new nucleotides and certain parts can be excreted in urea
338
how does a lipid, such as triglyceride able to be used for energy?
note that triglyceride is a glycerol carbon backbone connected to 3 fatty acid chains first, the triglyceride must be broken down into its components. the enzyme lipase splits apart the glycerol backbone and fatty acids the glycerol is phosphorylated to G3P, an intermediate is glycolysis. it enters the glycolysis cycle like this fatty acids in the blood combine with the protein, albumin which carries them throughout the bloodstream. in the mitochondrial matrix, fatty acids are broken down for energy in a process called beta-oxidation. every time we break down a fatty acid, we take two of its carbons and combine it with another molecule to form acetyl-CoA. with each acetyl-CoA we produce, we also get 1 NADH and 1 FADH2 (-1 FADH2 per double bond from the total). this process repeats! we can get lots of ATP this way but note that 1ATP is used for activation of the fatty acid chain
339
what is beta oxidation? where does it take place?
fatty acids are broken down for energy in a process called beta-oxidation. every time we break down a fatty acid, we take two of its carbons and combine it with another molecule to form acetyl-CoA. with each acetyl-CoA we produce, we also get 1 NADH and 1 FADH2 (-1 FADH2 per double bond from the total). this process repeats! we can get lots of ATP this way but note that 1ATP is used for activation of the fatty acid chain takes place in the mitochondrial matrix of eukaryotes and cytosol of prokaryotes
340
what does the brain use for energy when there's no glucose?
ketones, a byproduct from the breakdown of fatty acids in the liver these ketones can enter the citric acid cycle where they will produce ATP
341
how many calories do fats and carbohydrates and proteins store? what does this mean?
fats are 9 calories/gram, whereas carbohydrates and proteins are 4 calories/gram fats store more energy than carbohydrates per carbon - their carbons are in a more reduced state -- this explains the amount of calories for the macromolecules
342
briefly describe photosynthesis and state the formula
captures energy from sunlight and converts it into chemical energy -- organisms that partake in this process are called photoautotrophs plants take in CO2 and water and convert it into glucose and O2 6(CO2) + 6(H2O) ——> C6H12O6 + 6(O2)
343
what are chloroplasts?
photosynthesis takes place in chloroplasts which is found in plants and photosynthetic protists/bacteria it contains a molecule called chlorophyll (found in proteins called photosystems embedded in the thylakoid membrane) that captures energy from sunlight and uses it the energy to make glucose from water and CO2
344
describe the structure of chloroplasts
outer membrane intermembrane space inner membrane stroma: similar to the cytoplasm of cells. where all of the internal structures of the chloroplast are suspended in stroma lamellae: connects thylakoid thylakoid: membrane bound structures that look like flattened discs. the inside is called thylakoid lumen (some parts of photosynthesis take place in here). stacked thylakoids are called granum
345
what's chlorophyll? how does it capture energy from sunlight?
embedded in the photosystems of the thylakoid membrane in chloroplasts. chlorophyll contains a porphyrin ring centered around Mg it captures energy from sunlight and uses it the energy to make glucose from water and CO2 photons from the sunlight hit electrons in the chlorophyll molecule and excites the electrons to a higher state which begins the photosynthesis process
346
what are the (2) sets of reactions that make up photosynthesis?
light dependent reactions: cyclic and non-cyclic photophosphorylation light independent (dark) reactions aka calvin cycle: doesn't require photons
347
what are the (2) important photosystems of light dependent reactions? what are their other names? briefly describe the two different photosystems and what they produce
photosystem I - 680nm photosystem II - 700nm their second set of names comes from the approximate wavelengths they absorb photosystem II captures energy and starts the process of high energy electron transfer. primarily used to generate ATP photosystem I gets electrons after they've been passed through photosystem II. it boosts them with energy again to eventually produce NADPH
348
describe the steps in the process of non-cyclic photophosphorylation (a light dependent reaction)
the photons from the sunlight excite the electrons (gained through photolysis) found in photosystem II, boosting them to a higher energy level excited electrons passed to primary electron acceptor primary electron acceptor will pass electron through the electron transport chain (ETC) as the electron is passed, the energy from this process is used to pumps protons (H+ ions) from the stroma into the thylakoid lumen, against the concentration gradient. this establishes an electrochemical gradient ATP synthase catalyzes the reaction of ADP to ATP using the flow of protons going down the gradient (proton motive force/chemiosmosis). note that 3 H+ ions produce 1ATP the electrons that passed through the ETC arrive at photosystem I in a low energy state as it's energy was used up as it moved from acceptors and moving protons against the gradient. photons hit photosystem I, exciting the electrons. the electron is passed to an acceptor at the start of another ETC. as the electrons travels down the ETC, it combines with a molecule called NADP+ and H+ (from photolysis), forming NADPH
349
in the non-cyclic photophosphorylation, how much ATP is produced per 2 electrons going down the ETC?
2 electrons phosphorylate 1.5 ATP
350
in the cyclic photophosphorylation, how much ATP is produced per 2 electrons going down the ETC?
1 ATP
351
what is the purpose of the light dependent reactions of photosynthesis?
non-cyclic photophosphorylation produces: ATP to be used in the light independent (dark) reactions and NADPH that will help power the formation of glucose in the dark reactions. cyclic photophosphorylation produces: more ATP (dark reactions require more ATP than NADPH)
352
what is the overall formula of the light dependent reactions of photosynthesis?
H2O + ADP + Pi + (NADP+) + light → ATP + NADPH + O2 + (H+)
353
what is the overall formula of the light independent reactions of photosynthesis?
6CO2 + 18ATP + 12NADPH → 18ADP + 18 Pi + 12(NADP+) + 1 glucose (or 2 G3P)
354
what's photolysis? what's the purpose of it?
the splitting of water by light during photosynthesis. water splits into hydrogen ions, electrons, and oxygen. the hydrogen ions are used in the concentration gradient, the electrons are stored in the photosystems to be used in the light dependent reaction, and the oxygen is given off by plants into the atmosphere (what we breathe in) occurs in the thylakoid lumen
355
where does photolysis occur?
thylakoid lumen
356
where does non-cyclic photophosphorylation, a light dependent reaction occur?
thylakoid lumen, it passes electrons to the thylakoid membrane
357
where does cyclic photophosphorylation, a light dependent reaction occur?
stroma lamellae
358
describe the steps in the process of cyclic photophosphorylation (a light dependent reaction)
note that only photosystem I is used in this process -- REMEMBER THAT photosystem I gets its electrons from the ETC that feeds into it (direction of photosystem II).... photons from sunlight excite the electrons residing in photosystem I the electrons then get passed back to the (beginning of??) ETC that pumped H+ ions across the membrane until it's back at photosystem I, while also pumping H+ ions across repeats
359
where does the calvin cycle take place?
in the stroma
360
what is the purpose of the calvin cycle of photosynthesis?
to convert CO2 into glucose
361
what's carbon fixation?
taking carbon from an inorganic source and converting it into an organic compound e.g. taking CO2 from the atmosphere and converting it into glucose in the calvin cycle
362
what (3) phases make up the calvin cycle?
carbon fixation: in this situation, carbon from CO2 is used to produce an organic compound reduction: using the ATP and NADPH generated from the light dependent reactions regeneration: recycling intermediates to regenerate RuBisCo, an enzyme
363
what is the most abundant enzyme on earth?
RuBisCO -- essential for carbon fixation
364
describe the steps in the calvin cycle
enzyme, RuBisCo combines CO2 and ribulose biphosphate (RuBP) forming an organic compound --- this is carbon fixation!! the 6-carbon compound we formed into 2 phosphoglycerate (PGA) using ATP and NADPH, the PGA molecules are phosphorylated into G3P. the now ADP and NADP+ go into non-cyclic photophosphorylation some G3P is converted back to the ribulose bi-phosphate (to allow the calvin cycle to continue again) and some G3P is converted to glucose in order to make ONE molecule of glucose, we need to calvin cycle to occur 6 times. out of the 12 G3P produced, 10 is used to reform ribulose biphosphate and 2 used to form glucose
365
what are the products of the calvin cycle?
glucose and regeneration of ribulose biphosphate in order to make ONE molecule of glucose, we need to calvin cycle to occur 6 times. out of the 12 G3P produced, 10 is used to reform ribulose biphosphate and 2 used to form glucose
366
what is photorespiration?
when O2 is used instead of CO2 in the calvin cycle, producing a useless byproduct, a 2-carbon molecule (photosynthesis produces 3-carbon molecules). this byproduct can be broken down by peroxisomes O2 competitively inhibits RuBisCo
367
what can competitively inhibit RuBisCo?
oxygen! both O2 and CO2 can bind to RuBisCo CO2 is preferred, O2 is not! CO2 leads to calvin cycle O2 leads to photorespiration
368
what are the types of photosynthesis? what plants partake in each?
C2 = photorespiration - an "accidental" process; all plants C3 = normal photosynthesis; all plants ---------- different versions of photosynthesis that prevents/mitigates certain problems C4: mitigates photorespiration by spatial separation; corn and sugarcane CAM: mitigates water loss by temporal separation; cactus and pineapple (found in locations with higher temps)
369
what is C4 photosynthesis?
it prevents photorespiration by physical separation of the light and dark reactions of photosynthesis NOTE THAT IN C3 RESPIRATION, THE CALVIN CYCLE OCCURS IN THE MESOPHYLL CELLS. in C4 respiration, RuBisCo is found in the bundle sheath cell, so the calvin cycle only occurs there oxygen can't reach the bundle sheath cells, thus, unable to competitively inhibit RuBisCo only occurs in plants that follow Kranz anatomy. has the following layers from outside to inside: mesophyll cells, bundle sheath cells, vascular tissue (veins)
370
describe the steps of C4 photosynthesis
first, PEP carboxylase combines CO2 with PEP (instead of RuBP), forming oxalacetate (a 4-carbon compound) which is then converted to malate. this occurs in a mesophyll cell (one of the outer cells). the malate is then moved to a bundle sheath cell (a layer deeper). the malate is converted into 2 products: CO2 and pyruvate the pyruvate is shuttled back to the mesophyll cell and converted back to PEP the CO2 in the bundle sheath cell undergoes the calvin cycle to produce glucose glucose can be shuttled to the vascular tissue for transport for plant cells that need it
371
what's the main drawback of C4 photosynthesis?
the use of extra ATP to pump 4C compounds (malate) to bundle sheath cells
372
what's the hatch and slack pathway?
aka the C4 photosynthesis pathway explains that little presence of oxygen reduces competition while RuBisCo is deciding to fix either carbon dioxide or oxygen
373
what is CAM (crassulacean acid metabolism) photosynthesis? why does this process exist (explain the problem this tries to prevent)?
prevents water loss from plants by temporal separation (day and night) plants have stomata, pores found on the bottom of leaves, that serve as the site of gas exchange. it's how CO2 enters and O2 leaves. usually, the stomata are always open to allow the plant to continuously take in CO2 to produce glucose. BUT, if these are open, water can also leave the plant through the stomata. in CAM photosynthesis, the stomata is open at night and closed during the day.
374
describe the steps in the process of CAM photosynthesis
in CAM photosynthesis, the stomata is open at night and closed during the day so at night, CO2 enters. rather than going through the calvin cycle right away (we can't bc no sunlight!!), PEP carboxylase combines CO2 with PEP, forming maleic acid. the maleic acid is then stores in the plant cell's vacuole for later. when it's daytime, the plant closes the stomata to prevent water loss (especially during higher temperatures) the plant moves maleic acid out of its storage and converts it back into malate and then CO2 and PEP with the use of 1ATP. the CO2 then goes through the calvin cycle to produce glucose.
375
what's the role of carotenoids in photosynthesis?
main function is to absorb light energy in the blue-green and green regions of the electromagnetic spectrum that chlorophyll cannot absorb effectively. allows carotenoids to broaden the range of light wavelengths that can be utilized for photosynthesis. carotenoids also help protect the plant from damage caused by excessive light energy. acts as antioxidants, neutralizing harmful free radicals produced during photosynthesis. helps prevent damage to the plant's cells and tissues.
376
what results in the orangeness seen in leaves as they age?
as leaves age, chlorophyll breaks down to extract valuable components like Mg2+, and carotenoids become visible
377
what (2) processes make up cell division?
nuclear division: dividing the genetic material and nucleus cytokinesis: dividing the cytoplasm (happens near the end of anaphase)
378
where on sister chromatids linked together?
in a constricted region called the centromere
379
how many chromosomes are in a human diploid? haploid
diploid: 46 haploid: 23
380
what are homologous chromosomes?
a pair of chromosomes that are similar in length, gene position, and centromere position. carry genetic information for the same shape but are not identical one inherited from the mother, and one from the father humans have 23 pairs but in a male, the X and Y sex chromosomes are technically not considered to be homologous
381
what's miotic spindle?
full set of spindle fibers during cell division the spindles attach to the chromosomes and separates them
382
how do spindle fibers attach to the chromosomes?
they attach to the protein, kinetochore, which adheres to the centromere the kinetochore serves as an anchor point for spindle fibers, allowing them to change the position of the chromosomes during cell division
383
what are the (5) different phases of mitosis? just list them
prophase prometaphase metaphase anaphase telophase cytokinesis, a separate process also occurs around the end of anaphase
384
what are the (5) different phases of mitosis? describe what happens during each
prophase - chromatin condenses into chromosomes - nucleolus disappears (where ribosomes are made) -- nucleus still intact - miotic spindles begin to form as the centrosomes it emerges from are slowly pushed to opposite ends prometaphase - nuclear membrane breaks down and disappears - chromosomes condense further - kinetochore proteins are attached to each chromatid - miotic spindle fiber continues to develop, some of it has even attached to the kinetochores metaphase - chromosomes are lined up across the middle of the cell -- "metaphase plate" - centrosomes have reached opposite ends of the cell - miotic spindle is fully developed and fibers are attached to all chromosomes via kinetochores anaphase - shortest step of mitosis - begins when miotic spindle begin to shorten, pulling the sister chromatids apart. each chromosome pulled to opposite end of the cell (important to note, once the sister chromatids are separate, each chromatid is considered a chromosome) telophase (cytokinesis, a separate process also occurs around the end of anaphase) - nucleolus redevelops and 2 new nuclear membranes develop - chromosomes decondense into chromatin - spindle fibers disassemble
385
what happens during prophase and prometaphase of mitosis?
PROPHASE chromatin condenses into chromosomes nucleolus disappears (where ribosomes are made) -- nucleus still intact miotic spindles begin to form as the centrosomes it emerges from are slowly pushed to opposite ends ------------------ PROMETAPHASE nuclear membrane breaks down and disappears chromosomes condense further kinetochore proteins are attached to each chromatid miotic spindle fiber continues to develop, some of it has even attached to the kinetochores
386
what happens during metaphase of mitosis?
chromosomes are lined up across the middle of the cell -- "metaphase plate" centrosomes have reached opposite ends of the cell miotic spindle is fully developed and fibers are attached to all chromosomes via kinetochores
387
what happens during anaphase of mitosis?
begins when miotic spindle begin to shorten, pulling the sister chromatids apart. each chromosome pulled to opposite end of the cell (important to note, once the sister chromatids are separate, each chromatid is considered a chromosome) this is the shortest step of mitosis
388
what happens during telophase of mitosis?
nucleolus redevelops and 2 new nuclear membranes develop chromosomes decondense into chromatin spindle fibers disassemble
389
differentiate between cytokinesis in an animal and plant cell
animal cell - a structure called a cleavage furrow forms. it's a contractile ring made of actin and myosin filaments - the ring gradually tightens and gets smaller, pinching the cell into two separate cells - the actin and myosin filaments are shortening plant cell - a structure called a cell plate (made of vesicles from golgi bodies) forms in the middle. it extends and fuses with the cell wall, separating the cell into two cells
390
when karyotyping be performed during mitosis?
during metaphase considered to be the most convenient time as chromosomes are fully developed and lined up, making them easy to separate
391
what are the (8) different phases of meiosis? describe what happens during each
prophase I - nucleolus and nucleus disassembles - chromatin condenses into chromosomes - meiotic spindle begins to form and centrosomes begin to move towards opposite ends - homologous chromosomes pair up (synapsis). they sit on top of each other in a structure called tetrad. crossing over occurs at the chiasmata (where they swap segments) - microtubules from the meiotic spindle begin to attach to the kinetochores of the homologous chromosomes metaphase I - paired homologous chromosomes are lined up across the metaphase plate (independent assortment) - kinetochores of chromosome are attached to microtubules emerging from the meiotic spindle anaphase I - homologous chromosomes within the tetrads will uncouple and be pulled apart to opposite sides of the cell in a process called disjunction - note that sister chromatids are still paired together in their chromosomes telophase I - nuclear envelope redevelops - chromosomes decondense - each nucleus will have half the number of chromosomes that we started out with so we now have 2 haploids (note that the chromosomes are still in their duplicated state and not separated!!) depending on the species, interphase may occur here in between meiosis I and meiosis II prophase II - nucleus and nucleolus disassembles - chromosomes condense - meiotic spindle develops and starts to attach to the chromosomes metaphase II - chromosomes line up across the metaphase plate - meiotic spindle has fully formed and is attached to every chromosome at the kinetochore - note that we have half the number of chromosomes than we did in metaphase I and that the sister chromatids are no longer identical to one another due to crossing over anaphase II - microtubules of the meiotic spindle shortens and the sister chromatids of each chromosome are pulled apart to opposite ends of the cell. as soon as they are apart, each chromatid is now considered a chromosome telophase II - nucleolus and nucleus reforms - chromosomes decondense back into chromatin - spindle fibers disappear
392
what's the synaptonemal complex?
protein structure that temporarily forms between homologous chromosomes; gives rise to tetrad with chiasmata and crossing over
393
differentiate between quiescent and senescent
quiescent is reversible in the G0 phase of the cell cycle senescent is permanently in the G0 phase of the cell cycle
394
what happens during prophase I of meiosis?
nucleolus and nucleus disassembles chromatin condenses into chromosomes meiotic spindle begins to form and centrosomes begin to move towards opposite ends homologous chromosomes pair up. they sit on top of each other in a structure called tetras. crossing over occurs at the chiasmata (where they swap segments) microtubules from the meiotic spindle begin to attach to the kinetochores of the homologous chromosomes
395
what happens during metaphase I of meiosis?
paired homologous chromosomes are lined up across the metaphase plate (independent assortment) kinetochores of chromosome are attached to microtubules emerging from the meiotic spindle
396
what happens during anaphase I of meiosis?
homologous chromosomes within the tetrads will uncouple and be pulled apart to opposite sides of the cell in a process called disjunction note that sister chromatids are still paired together in their chromosomes
397
what's disjunction?
homologous chromosomes within the tetrads will uncouple and be pulled apart to opposite sides of the cell during anaphase
398
what happens during telophase I of meiosis?
nuclear envelope redevelops chromosomes decondense each nucleus will have half the number of chromosomes that we started out with so we now have 2 haploids (note that the chromosomes are still in their duplicated state and not separated!!)
399
what happens during prophase II of meiosis?
nucleus and nucleolus disassembles chromosomes condense meiotic spindle develops and starts to attach to the chromosomes
400
what happens during metaphase II of meiosis?
chromosomes line up across the metaphase plate meiotic spindle has fully formed and is attached to every chromosome at the kinetochore note that we have half the number of chromosomes than we did in metaphase I and that the sister chromatids are no longer identical to one another due to crossing over
401
what happens during anaphase II of meiosis?
microtubules of the meiotic spindle shortens and the sister chromatids of each chromosome are pulled apart to opposite ends of the cell. as soon as they are apart, each chromatid is now considered a chromosome
402
what happens during telophase II of meiosis?
nucleolus and nucleus reforms chromosomes decondense back into chromatin spindle fibers disappear
403
how does meiosis give rise to genetic diversity? (3)
crossing over (during prophase I) - creates unique chromosomes that aren't identical to the parents they come from independent assortment (during metaphase I) - the mix of which chromosomes in a homologous pair gets separated to which end of the cell is random random joining of gametes - the combination of which sperm fertilizes which egg - NOTE: joining of gametes is random, but some sperm cells contain genetic material that gives them a competitive advantage - so they all aren’t “equally” competitive
404
what's the interphase?
sequence of events that occurs before the cell undergoes cell division this is where cells spend the majority of their time
405
what are the (3) separate phases of the cell's interphase? what happens during these phases?
G1: cell grows in size. increases protein synthesis to prepare for cell division (e.g. DNA polymerase used in S) - most cell growth is here S (synthesis): duplicates genetic material, forming sister chromatids. also duplicates centrosomes. cell also grows here G2: cell continues to grow in size and synthesizing proteins. the cell will also replicate its organelles during this phase. cell checks to see if mitosis can proceed
406
what's G 0? (the phase outside of the cell cycle)
"resting phase" cells are still active and functional. they aren't dividing or preparing to divide nerve cells and muscle cells are often found in this phase
407
differentiate between quiescent or senescent
quiescent is temporarily in the G0 phase and can reenter the cell cycle when they need to divide. senescent is permanently in the G0 phase due to damage or degradation.
408
why do our cells divide instead of just growing bigger?
there are functional limitations to what a cell can do when it passes a certain size due to the - surface to volume ratio - genome to volume ratio
409
why is the surface to volume ratio important for a cell's function?
a smaller surface to volume ration (when the cell becomes bigger in size) leads to difficulties in cellular exchange a large cell has a large volume which means it needs tons of nutrients and oxygen, so it needs a larger surface area to be able to facilitate its needs this also applies to getting rid of waste
410
why is the genome to volume ratio important for a cell's function?
as a cell grows larger in volume, the genome amount doesn't change. our genome is used to express genes and produce proteins. the larger a cell is, the more processes that need to be regulated
411
what are some exceptions to the genome/surface to volume ratio rule of cells?
skeletal muscles remain in the G0 phase and don't divide. they're even capable of growing larger with exercise. the skeletal muscle cells don't follow this limitation bc - they have multiple nuclei (large genome to volume ratio) - long and cylindrical (large surface area to volume ratio)
412
what are the (5) ways in which the cell cycle can be regulated?
cell cycle checkpoints: to make sure the cell is ready to divide density dependent inhibition: stops cells from dividing when overcrowded anchorage dependence: makes sure cells are firmly attached to a surface to be able to divide --- so a cell that comes loose and is traveling thru your lymphatic vessel or thru your blood can't divide cyclin-dependent kinases (CDK’s): a CDK enzyme activates proteins that regulate the cell cycle via phosphorylation. CDK’s are activated by protein cyclins, which vary in type and concentration throughout each phase of the cell cycle growth factors: a secreted biologically active molecule that can affect the growth of cells. definition has become expanded to include secreted molecules that promote or inhibit mitosis or affect cellular differentiation. the plasma membrane contains receptors for growth factors note that cancer cells can "defy" the last 4 methods of regulation
413
when are the (3) regulation checkpoints in the cycle? what do they check for?
end of G1 phase (before the cell enters S) aka restriction checkpoint makes sure the cell is ready to replicate it's DNA by checking: - if the cell has proper nutrients to go thru cell division - if it has necessary cell products to replicate its DNA - if the cell has grown sufficiently large and if its DNA is intact and error-free and undamaged --------------------------- end of G2 phase (before the cell enters mitosis) checks to see if the DNA replicated properly: DNA has been duplicated and that the DNA is error-free and undamaged if there's any issues, the cell can pause here and make any repairs necessary or finish the DNA duplication --------- metaphase (mitosis) aka M checkpoint aka spindle checkpoint checks that each of the sister chromatids is attached to a spindle fiber, if so, anaphase is triggered. if not attached, mitosis halts until all are chromosomes are properly attached to spindle fibers
414
what happens if the cell fails one of the cell cycle checkpoints?
the cell can either permanently enter the G0 phase and stop dividing or go thru apoptosis (cell death)
415
what happens if there are regulations for cell division?
the cell goes thru uncontrolled cell division eventually leading to cancer
416
describe the development of a cancer cell
a normal cell divides only when it's supposed to but it can develop mutations that disrupt our ability to regulate cell division, which allows the cell to divide uncontrollably --- increasing the amount of mutated cells --- leading to large dangerous masses of cells called tumors
417
differentiate between malignant and benign tumors
malignant is when the uncontrollably dividing mutated cells have broken loose and spread to other tissues -- this process is called metastasis benign is localized
418
define metastasis
when the uncontrollably dividing mutated cells have broken loose and spread to other tissues -- this is called a malignant tumor
419
what's p53?
a tumor supressing gene -- like Rb limits cell division --> prevents tumors from forming if the one of the p53 gene gets mutated, it becomes easier for the cell to divide uncontrollably. if both copies get mutated, the ability to stop cell proliferation has been impaired and cancer is likely to develop
420
what do cancer drugs do?
the main goal is to limit the amount of cell division ------------ many drugs work by inhibiting mitosis directly e.g. disrupting the ability of miotic spindle to form and disassemble during the cell cycle --further division no longer possible
421
what are the (3) names used to categorize cells based on how they divide?
labile: constantly dividing and replenishing themselves - e.g. skin cells quiescent: cell do not divide; but can be stimulated when needed - e.g. liver cells fixed/permanent cells: little to no capacity to divide - e.g. cardiac muscle cells
422
how does fluorescence microscopy, a type of optical microscopy work?
use of a fluorescent marker to tag certain structures. we then shine light to excite the fluorescent probe. assist in visually locating protein expression within a cell can be used on living organisms