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BIO1140 > finals review > Flashcards

finals review Flashcards

1
Q

energy

A

capacity to cause change, especially to do work (move matter against an opposing force)

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2
Q

kinetic energy

A

energy associated witht eh relative motion of objects

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3
Q

thermal energy

A

kinetic energy due to the random motion of atoms and molecules (heat)

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4
Q

chemical energy

A

energy available in molecules for release in a chemical reaction

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5
Q

potential energy

A

energy that matter possesses as a result of its location or spatial arrangement

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6
Q

first law of thermodynamics

A

the total amount of energy in the universe must always be the same

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7
Q

what is the ultimate source of energy

A

the sun

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8
Q

what is photosynthesis

A

converts electromagnetic energy in sunlight to chemical-bond energy in organic molecules

ANABOLIC

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9
Q

what is cellular respiration

A

extracts energy from organic molecules (food) by gradual oxidation

CATABOLIC

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10
Q

second law of thermodynamics

A

the degree of entropy (disorder) in the universe can only increase

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11
Q

how do cells not defy the second law of thermodynamics

A

increased order inside cell = increased disorder in cell’s surroundings

free energy (energy that could do work) is dissipated as heat

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12
Q

what is free energy (G)

A

amt of energy available in a molecule to do work in a system when the temp and pressure are uniform

units: joules or kcal/mole

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13
Q

where is free energy stored

A

in the bonds between individual atoms of a molecule

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14
Q

what does free energy cause

A

vibration, rotation and movement of the molecule through space

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15
Q

how can chemical reactions produce disorder

A
  1. reactions can decrease order in the cell (ex. preventing an interaction that prevents bond rotations)
  2. changes of bond energy of reacting molecules can cause heat to be released –> disorders environment
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16
Q

equation for free energy

A

A + B –> C + D

(delta)G = free energy (C + D) - free energy (A + B)

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17
Q

when is G negative

A

if the disorder of the universe increases

a chemical reaction that occurs spontaneously

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18
Q

when is deltaG 0

A

at chemical equilibrium

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19
Q

standard free energy skin

A

gain or loss of free energy as one mole of reactant is converted to one mole of product under “standard conditions”

used to predict the outcome of a reaction

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20
Q

coupled reactions

A

coupling energetically unfavourable reactions with energetically favourable ones makes life possible

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21
Q

exergonic vs. endergonic reactions

A

exergonic: reaction with negative change in free energy

endergonic: reaction with positive change in free energy

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22
Q

exergonic reactions

A

releases energy into its surroundings, SPONTANEOUS

energetically favourable

lower free energy level (more stable)

release free energy in bonds

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23
Q

endergonic reactions

A

require energy, NON-SPONTANEOUS

energetically unfavourable reactions

higher free energy level than substrate

can store energy in molecules

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24
Q

activated carriers

A

store energy as a readily TRANSFERABLE CHEMICAL GROUP or as READILY TRANSFERABLE ELECTRONS

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25
Q

important activated carriers

A

ATP, NADH, NADPH

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26
Q

(t/f) a spontaneous reaction is not necessarily an instantaneous reaction

A

F

highly favourable reactions may not occur unless there are enzymes to speed up the process

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27
Q

what lowers activation energy

A

catalysts

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28
Q

2 metabolic pathways

A

CATABOLIC, ANABOLIC

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29
Q

3 stages food molecules are broken down in

A
  1. in the mouth and gut
  2. in the cytosol
  3. in the mitochondria
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30
Q

most common chemical fuel in cells

A

monosaccharide glucose

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31
Q

what does burning of sugar in nonliving systems generate

A

heat

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32
Q

what catabolic processes harvest the energy in the chemical bonds of glucose? (3)

A
  1. glycolysis
  2. cellular respiration
  3. fermentation
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33
Q

glycolysis

A

begins glucose catabolism

10 enzyme-catalyzed reactions

glucose –> 2 pyruvate +ADP + NADH

ANAEROBIC, without CO2

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34
Q

what does cellular respiration include

A

1 pyruvate –> 3 CO2

includes pyruvate oxidation, citric acid cycle, ETC

AEROBIC

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35
Q

fermentation

A

no O2

converts pyruvate lactic acid OR ethanol into energy (but much less than cellular respiration

NADH gives up electrons in the cytosol, converted back to NAD+ to maintain glycolysis

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36
Q

(t/f) more reduced molecule = more energy stored in covalent bonds

A

T

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37
Q

key electron carrier in redox reactions

A

NADH (Nicotinamide adenine dinucleotide)

NAD+ = oxidized
NADH = reduced

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38
Q

how do cells harvest energy from glucose AEROBICALLY?

A
  • glycolysis
  • pyruvate oxidation
  • citric acid cycle (krebs, tricarboxylic acid cycle)
  • ETC/ATP synthesis
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39
Q

how do cells harvest energy from glucose ANAEROBICALLY?

A
  • glycolysis
  • fermentation
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40
Q

where does glycolysis take place

A

cytoplasm

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41
Q

3 phases of glycolysis

A
  • ENERGY CONSUMING PHASE –> requires ATP
  • CLEAVAGE
  • ENERGY RELEASING PHASE –> produces ATP and NADH
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42
Q

where does cellular respiration take place

A

mitochondria

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43
Q

where does pyruvate oxidation take place

A

mitochondrial matrix

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44
Q

pyruvate oxidation

A

pyruvate is oxidized to an acetate molecule and CO2

creates 1 NADH

acetate then binds to coenzyme A to form acetyl CoA

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45
Q

citric acid cycle

A

starts with Acetyl CoA

8 reactions

acetyl group is oxidized to 2 CO2

creates 2 CO2 + 3 NADH + 1 GTP + 1 FADH2

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46
Q

what does the oxidation of 1 glucose give us

A

6 CO2
10 NADH
2 FADH2
4 ATP (2 from GTP)

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47
Q

what kind of process is oxidative phosphorylation

A

membrane-based process

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48
Q

2 steps of oxidative phosphorylation

A
  • electron transport: electrons from NADH and FADH2 pass through the respiratory chain and create a proton concentration gradient
  • chemiosmosis: protons diffuse back to the mitochondrial matrix and ATP is synthesized
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49
Q

ETC

A

NADH and FADH2 donate their high-energy electrons to the ETC

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50
Q

where does the ETC take palce

A

inner mitochondrial membrane

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51
Q

what happens as electrons pass between carriers?

A

free energy is released

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52
Q

what do electron transfers cause

A

movement of protons from matrix –> intermembrane space

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53
Q

what does proton pumping generate

A

steep electrochemical proton gradient across inner mitochondrial membrane

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54
Q

chemiosmostic mechanism

A

respiratory chain and ATP synthase produce ATP

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55
Q

what kind of motor is ATP synthase

A

ROTARY motor

–> top part lets in H+, bottom part rotates to expose active sire for ATP so ADP–>ATP

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56
Q

what energy does ATP synthase use to produce ATP

A

energy stored in the electrochemical proton gradient

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57
Q

(t/f) ATP synthase is a reversible coupling device

A

T

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58
Q

what does the inner mitochondrial membrane do

A

converts energy in NADH/FADH2 into phosphate bond of ATP molecules

–> coupled transport across membrane driven by proton gradient

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59
Q

what are fatty acids converted into in the mitochondrial matrix

A

fatty acid oxidation –> fatty acids are broken down into acetyl coA molecules –> enter citric acid cycle

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60
Q

allosteric regulation of glycolysis and citric acid cycle

A
  • changing AMT of active enzyme by regulating its expression
  • changing ENZYME ACTIVITY by covalent modifications
  • substrate availability
  • feedback regulation by building regulatory molecules (METABOLITES)

controls them at early steps –> increases efficiency and prevents excessive build-up of intermediates

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61
Q

how do animals store glucose

A

in the form of glycogen –> provides energy in times of need

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62
Q

where do light reactions take place

A

thylakoid membrane

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63
Q

2 pathways in photosynthesis

A

LIGHT reactions, CARBON-FIXATION reactions (light-independent)

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64
Q

where do carbon-fixation reactions take place

A

stroma

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65
Q

light reactions

A

convert light energy –> chemical energy (AYP, NADPH)

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66
Q

carbon-fixation reactions

A

ATP, NADPH CO2 –> carbs

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67
Q

pigments

A

molecules that absorb light in the visible spectrum
–> certain wavelengths are absorbed –> remaining are scattered/transmitted and make the pigment appear coloured

chlorophyll a, chlorophyll b, beta-carotene
–> most common in plants

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68
Q

photons

A

particles of light/packets of energy

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69
Q

light

A

form of electromagnetic radiation

propagates in waves, but has particle-like behaviours

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70
Q

electromagnetic radiation proportion to wavelength

A

amt of energy in radiation in INVERSLY proportional to wavelength

shorter wavelength = greater energy

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71
Q

(t/f) receptive molecules in plants absorb any wavelength of light

A

F

can only absorb specific wavelengths of light

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72
Q

what happens when a molecule acquires the energy of a photon?

A

raised from ground state to an excited state with higher energy

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73
Q

what do chlorophylls absorb

A

blue and red wavelenghts

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74
Q

chlorophyll structure

A

consists of a complex ring structure and a hydrocarbon tail

–> tail anchors chlorophyll in hydrophobic region of a membrane in thylakoid

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75
Q

chlorophyll a vs b

A

a has CH3 group, b has CHO group

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76
Q

photosystems

A

complex of proteins and pigments

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77
Q

where is the photosystem

A

thylakoid membrane

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78
Q

2 parts of a photosystem

A

antenna system, reaction center

pigments in antenna system absorb light energy –> transfer to chlorophyll a in REACTION CENTER

–> electrons from chlorophyll in reaction center transferred to ELECTRON ACCEPTOR

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79
Q

where are electrons transported through (photosynthesis)

A

thylakoid membrane

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80
Q

how do a pair of photosystems generate ATP and NADPH

A
  • water molecules split to provide electrons for chlorophyll in reaction center of photosystem II
  • protons are transferred from stroma –> interior of thylakoids during electron transport

–> movement of electrons powers production of ATP and NADPH

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81
Q

how is NADPH made from NADP+

A

through photosynthesis in the thylakoid membrane

electrons energy is boosted in photosystem I and transferred to NADP+

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82
Q

carbon fixation

A

uses ATP and NADPH to convert CO2 –> sugar

attaches CO2 to ribulose 1,5 - diphosphate

forms GLYCERALDEHYDE-3-PHOSPHATE

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83
Q

what do you need to form 1 glyceraldehyde-3-phosphate (G3P)

A

3 CO2, 9ATP, 6NADPH

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84
Q

what happens to G3P after its formed

A

some enters glycolysis and is converted to pyruvate

some enters glucohenesis to form glucose

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85
Q

what stimulates the calvin cycle

A

light-induced pH changes in the stroma activate calvin cycle enzymes

–> light induced electron transport reduces disulfide bridges in 4 of the calvin cycle enzymes –> activates them

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86
Q

(t/f) chloroplast’s inner membrane is impermeable to ATP and NADPH

A

T
–> they are used inside chloroplasts for the carbon-fixation cycle
–> resulting sugars are stored in the chloroplasts or exported to the rest of the cell

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87
Q

(t/f) mitochondrial membranes are impermeable to ATP

A

F
–> they are permeable

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88
Q

lyase

A

dissociates molecules, breaks covalent bonds without using water, oxidation, or reduction

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89
Q

ligase

A

joins 2 molecules together, forming covalent bonds

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90
Q

isomerase

A

rearranges bonds of a molecule
–> forms reactant or an isomer

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91
Q

transferase

A

transfers functional group from one molecules to another

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92
Q

hydrolase

A

uses water to cleave molecule, breaks covalent bonds with water

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93
Q

oxidoreductase

A

transfers electrons from one molecules to another, alters oxidation state of reactants

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94
Q

signal transduction

A

the conversion of one type of signal to another

–> receptors convert extracellular signal to intracellular signaling molecules

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95
Q

3 phases of cell signaling

A

RECEPTION, TRANSDUCTION, RESPONSE

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96
Q

endocrine signals

A

LONG RANGE

called hormones

remote signals –> target distant cells, transported by blood

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97
Q

what secretes endocrine signals

A

endocrine GLANDS (pineal, pituitary, parthyroid, thyroid, adrenal, pancreas, ovary, testis)

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98
Q

adrenaline

A

ADRENAL GLAND

derivative of acid tyrosine

increases blood pressure, heart rate, metabolism

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99
Q

cortisol

A

ADRENAL GLAND

steroid, derivative of cholesterol

affects metabolism of proteins, carbs, lipids

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100
Q

estradiol

A

OVARY

steroid, derivative of cholesterol

induces, maintains secondary female characteristics

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101
Q

insulin

A

BETA CELLS OF PANCREAS

protein

stimulates glucose uptake, protein synthesis, lipid synthesis

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102
Q

testosterone

A

TESTIS

steroid, derivative of cholesterol

induces, maintains secondary male sexual characteristics

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103
Q

thyroid hormone (thyroxine)

A

THYROID GLAND

derivative of amino acid tyrosine

stimulates metabolism in many cell types

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104
Q

paracrine signals

A

SHORT RANGE

act locally

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105
Q

synaptic signals

A

SHORT RANGE

act locally

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106
Q

contact-dependent

A

SHORT RANGE

act locally

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107
Q

types of signals

A

endocrine, paracrine, synaptic, contact-dependent

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108
Q

(t/f) each cell responds to an unlimited set of extracellular signals

A

F

cells have different SETS of receptors and SIGNAL TRANSDUCTION pathways that vary

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109
Q

(t/f) the same signal molecules can induce different responses in different target cells

A

T

signal interpretation depends on receptor, intracellular effector proteins, and other signals received by cell

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110
Q

what can chemical signals intruct cells to do

A

intructs cells to survive, grow, divide, or differentiate

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111
Q

fast cell responses to signals

A

change in cell movement, change in cell shape, change in metabolism, secretion

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112
Q

slow cell responses to signals

A

cell differentiation, cell dividion, cell growth

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113
Q

are cell responses involving gene expression fast or slow?

A

SLOW

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114
Q

what do signal molecules bind to (2)

A

membrane or intracellular receptors

–> MOST molecules are large and hydrophilic –> bind to CELL-SURFACE receptors

–> SOME molecules are small and hydrophobic –> cross membrane and biind to INTRACELLULAR receptors

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115
Q

where are intracellular receptors

A

in the cytosol or nucleus

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116
Q

where do steroid hormones bind to

A

INTRACELLULAR receptors

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117
Q

how does NO regulate enzyme activity

A

NO diffuses across the membrane and directly regulates the activity of an intracellular enzyme (guanylyl cyclase)

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118
Q

what does NO trigger

A

smooth muscle relaxation in blood-vessel wall

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119
Q

cell-surface receptors

A

bind the signal and create new intracellular signals

–> each intracellular signaling molecule activates or generates the next signaling molecules (proteins or small messenger molecules)

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120
Q

effector proteins

A

directly affect the behaviour of target cell

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121
Q

extracellular signal is _____ inside the cell

A

AMPLIFIED

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122
Q

(t/f) different extracellular signals are integrated

A

T

–> incoming signal is distributed to effector proteins
–> cross talk occurs between different signaling molecules

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123
Q

general flow of information during cell signaling (4)

A
  1. receptor-ligand binding
  2. signal transduction via second messengeres
  3. cellular responses
  4. changes in gene expression
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124
Q

different ways in which signals can be integrated

A
  1. 1 receptor activates miltiple pathways
  2. different receptors activate the same pathway
  3. different receptors activate different pathways –> 1 pathway affects the other
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125
Q

feedback regulations with extracellular signals

A

feedback regulations inside the cell adjust cellular responses to an extracellular signal (positive or negative)

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126
Q

molecular switches

A

some intracellular signaling proteins act as molecular switches
–> fluctuate between inactive and active state

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127
Q

activated molecular switches

A

stimulate/suppress other proteins in the signaling pathway

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128
Q

what are molecular switches activated by

A

some are activated by phosphorylation

some by G3P binding

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129
Q

molecular switched activated by phosphorylation

A

activated through phosphorylation by protein KINASES (signal in, ATP –> ADP)

inactivated by dephosphorylation by protein PHOSPHATASES (signal out)

SERINE/THREONINE KINASES and TYROSINE KINASES are 2 main types of protein kinases in intracellular signaling pathways

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130
Q

molecular switches activated by GTP binding

A

GTP binding proteins

activated by GTP binding (signal in)
–> GDP out, GTP in

deactivated by GTP hydrolysis (signal out)
–> phosphate out, GTP–>GDP

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131
Q

3 main classes of cell-surface receptors

A
  1. ion-channel-coupled receptors
  2. G-protein-coupled receptors
  3. enzyme-coupled receptors
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132
Q

ion-channel-coupled-receptors

A

responsible for muscle contraction

involves acetylcholin and acetylcholinesterase

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133
Q

g-protein-coupled receptors (GPCRs)

A

MOLECULE SWITCH

largest family of receptors

signals: odorants, light, ions, neurotransmitters, peptides, lipids, amino acids

1/3 drugs work via GPCRs

–>signaling molecules binds to G protein couples receptor –> G protein alpha subunit exchanges GTP –> GDP
–> alpha subunit dissociates from beta and gamma subunits, triggered response
–> GTP hydrolyzed to GDP (switch off)

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134
Q

what does stimulation of GPCRs activate

A

G-protein subunits (20 different types)

–> each type is activated by a set of receptors and activate a set of target proteins

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135
Q

G proteins and ion channels

A

some G proteins directly regulate ion channels

–> acetylcholine signal is transduced to K+ channel opening in pacemaker cells and slows down heartbeat

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136
Q

G proteins and enzymes

A

many G proteins activate membrane-bound enzymes

2 most frequent target enzymes:
- ADENYLYL CYCLASE: produces a second messenger cyclic AMP (cAMP)
- PHOSPHOLIPASE C: prouces second messengers inositol triphosphate and diacylglycerol
–> inositol triphosphate promotes accumulation of another second messenger, cytosolic Ca2+

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137
Q

2 principal signal transduction pathways that GPCRs activate

A

cAMP signaling pathway, PHOSPHATIDYLINOSITOL signaling pathway

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138
Q

cAMP signaling pathway

A

adenylyl cyclase (enzyme) generates cAMP from ATP

degraded by cAMP phosphodiesterase

caffeine blocks cAMP phosphodiesterase

ATP –> cAMP –> AMP

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139
Q

cAMP signaling in skeletal muscle cell

A

cAMP can activate a metabolic enzyme like adrenaline in skeletal muscle cell

–> can activate gene transcription
–> effect varies with type of target cell

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140
Q

cAMP signaling in ofactory receptors

A
  1. olfactory cilia have receptors that bind specific odorant molecules
  2. action potentials generated by odorant binding are transmitted to glomeruli in olfactory bulb
  3. neurons in a glomerulus receive input only from receptor cells expressing the same receptor gene
141
Q

phosphatidylinositol signaling pathway

A

triggers rise in intracellular Ca2+

leads to saliva secretion

142
Q

calcium binding

A

changes shape of CA2+ responsive proteins (calmodulin protein)

143
Q

taste perception

A

GPCRs and phosphatidylinositol signaling are involved in taste perception

5 tastes: sweet. salty, sour, bitter, umami
–> sweet, umami, bitter detected by GPCRs

144
Q

GPCRs and light detection

A

GPCRs are responsible for light detection in rod cells in retina

  1. absence of light: Na+ channels kept open by cGMP and create depolarizing dark current
  2. phodopsin obsorbs light energy
  3. activates G protein (transucin) that activates PDE
  4. activated PDE hydrolyzes cGMP, causes Na+ channels to close
    –> cell hyperpokarizes
    –> cGMP –> GMP, GDP –> GTP

light-induced signaling cascade in rod photoreceptor cells greatly amplifies the light signal

145
Q

receptor tyrosine kinases (RTKs)

A

signals binding RTKs are growth factors and hormones

include EGFR, PDGF, FGFR and i insulin receptors

activate multiple intracellular signaling pathways

146
Q

2 signaling pathways activated by RTKs

A

Ras/MAPK signaling, PI3K/AKT signaling

147
Q

interaction domain

A

docked intracellular signaling proteins recognize specific phosphorylated tyrosines on receptor tails by interaction domain

148
Q

activated RTKs

A

unactivated RTK activated bt signal molecule in form of a dimer

recruit a complex of intracellular signaling proteins
–> activation of downstream intracellular signaling pathways

149
Q

what do RTKs activate

A

most activate the monomeric GTPase Ras

150
Q

Ras

A

G protein and molecular switch

151
Q

Ras function in normal cell

A

receptor activation leads to activation of G protein Ras
–> GDP out, GTP in

after stimulation of cell division, returns to inactive
–> GTP hydrolilzes to GDP

152
Q

abnormal Ras function in a cancer cell

A

receptor activation leads to activation of Ras
–> STAYS ACTIVE –> constant stimulation of cell division

153
Q

RTK activate PI 3-Kinase

A

RTks activate PI 3-Kinase (phosphatidylinositol 3-kinase) to produce lipid docking sites in plasms membrane

154
Q

activated AKT

A

promotes cell survival by inhibition of apoptosis

155
Q

AKT

A

stimulated cells to grow in size by activating serine/threonine kinase Tor

156
Q

insulin and RTK

A

insulin binds an RTK, activates both MAPK and PI3K signaling pathways

157
Q

notch receptor

A

transcription regulator

involved in contact-dependent communication

158
Q

cytoskeleton

A

network of protein filaments that extend through the cytoplasm

highly dynamic, continuously reorganized

important for cell shape, interior organization, movement

159
Q

cytoskeleton roles

A
  • supports cell
  • maintains shape
  • holds cell organelles in position
  • moves organelles around in the cell
  • involved with movements of the cytoplasm (cytoplasmic streaming)
  • interacts with extracellular structures –> helps anchor cell in place
160
Q

3 types of protein filaments that make up cytoskeleton

A

MICROFILAMENT (actin), INTERMEDIATE FILAMENT, MICROTUBULE

161
Q

microfilaments

A

polymers of actin proteins

162
Q

actin

A

globular protein

–> bind each other to form helical polymers
–> 2 helical polymers = microfilament
–> REVERSIBLE

has distinct + and - ends
–> permit monomers to interact with each other to form double helix chains

163
Q

microfilaments

A

diameter around 7nm

long, thin and flexible threads

POLARIZED structures

164
Q

microfilament polymerization and depolymerization

A

microfilaments can disappear from cells by breaking down into monomers of actin
–> special actin-binding proteins mediate process

165
Q

actin-binding proteins

A

control organization of actin filaments

166
Q

microfilaments exist as:

A
  • single filaments
  • linear bundles
  • 2D networks
  • 3D gels
167
Q

where are microfilaments highly concentrated

A

cortex

168
Q

microfilament roles (2)

A
  1. determine and stabilize shape
  2. help entire cell or parts of cell move
169
Q

microfilaments in cell shape

A

non-muscle cells: actin filaments are associated with localized changes in cell shape

also involved in cell movement, cytoplasmic movement, cell division, muscle contraction (actin filaments slide against myosin proteins)

170
Q

microfilaments in shape

A

cells that line intestine –> folded into tiny protections (microvilli)
–> SUPPORTED BY MICROFILAMENTS
–> interact with intermediate filaments at base of each microvillus

171
Q

myosin motor proteins

A

actin-dependent movements usually require actin’s association with myosin motor proteins

172
Q

itnermediate filaments

A

tough, ropelike, flexible, good tensile strength

diameter 10nm

made of FIBROUS INTERMEDIATE FILAMENT PROTEINS

permanent structures

173
Q

4 classes of intermediate filaments

A

CYTOPLASMIC
–> keratin filaments (in epithelial cells)
–> vimentin and vimentin-related filaments (in connective-tissue cells, muscle cells, glial cells)
–> neurofilaments (in nerve cells)

NUCLEAR
–> nuclear lamins (in all animal cells)

174
Q

intermediate filament roles

A
  • create strong durable network in cytoplasm
  • support the nuclear envelope (nuclear lamina)
  • gives mechanical strength (filaments extend across cytoplasm from one cell-cell function to another –> distributes mechanical stress in epithelial tissue)
175
Q

nuclear lamina

A

just beneath the inner nuclear membrane

intermediate filaments form a meshwork

supports, strengthens nuclear envelope

176
Q

microtubules

A

made of tubulin dimers
–> each dimer consists of 2 subunits (alpha tubulin and beta tubulin)
–> each microtubule consists of 13 protofilaments of tubulin

long, hollow, straight cylinders

25nm in diameter

more rigid than the other 2

POLAR
–> + and - end grow at their + end

177
Q

what happens when microtubules are stretched

A

they rupture

178
Q

where do microtubules grow out of

A

centrosomes
–> each microtubule grows and shrinks independently of its neighbors

array of microtubules anchored in a centrosome is constantly changing
–> new tubules grow, old tubules shrink

179
Q

dynamic instability in growing microtubules

A

dynamic instability: switching back and firth between polymerization and depolymerization

leads to rapid remodeling of microtubule organization

important for microtubule function

180
Q

dynamic instability

A

driven by GTP hydrolysis
–> tubulin dimers hydrolyze their bound GTP

GTP-tubulin attaches to GTP cap(plus end) –> rapid growth –> loss of GTP cap –> GDP tubulin is released –> catastrophic shrinkage –> GTP cap restablished

181
Q

microtubule binding proteins

A

stabilize microtubules

microtubule will persist only if both its ends are protected from depolymerization
–> - end protected by centrosome
–> + ends are initially free but stabilized by binding to specific proteins

182
Q

microtubule roles (2)

A
  1. form rigid internal skeleton for some cells
  2. act as framework along which motor proteins can move structures within the cell
183
Q

microtubule tracks

A

microtubules provide tracks for movement of cytoplasmic material
–> motor proteins use them to transport vesicles, macromolecules, and organelles

184
Q

types of motor proteins that use microtubules

A

KINESINS (towards - end), DYNEINS (towards + end)

185
Q

microtubules in a dividing cell

A

microtubules distribute chromosomes in a dividing cell

186
Q

microtubules in positioning

A

help position organelles in a eukaryotic cell

–> kinesin motor protein pulls endoplasmic reticulum outward along microtubules
–> dynein motor proteins pull golgi apparatus inward along the microtubules to its position near centrosome

187
Q

microtubules in cilia and flagella movement

A

microtubules allow cilia/flagella movements

cilia/flagella –> movable appendages on eukaryotic cells
–> cilia move fluid across cell surface
–> epithelial cells lining human respiratory tract has huge numbers of beating cilia
–>flagella: propel sperm cells, much longer than cilia

188
Q

cilia and flagella (microtubules)

A

microtubules are arranged in different patterns

eukaryotic cilia and flagella –> 9 doublet microtubules are arranged in a ring around a pair of single microtubules (“9+2” array)

189
Q

what causes the movement of a cilium/flagellum

A

produced by ciliary dynein movement between 2 microtubules

190
Q

nucleotides

A

building blocks of nucleic acids

4 nucleotides = 1 nucleic acid

composed of a base, sugar, and a phosphate group

191
Q

growth of nucleic acid

A

5’ –> 3’ direction

nucleotides link to each other to make nucleic acids

192
Q

how are DNA strands held together

A

held together with hydrogen bonds
–> purine and pyrimidines bases form H bonds (complementary base pairing)

van der waals forces occur between adjacent bases on the same strand

193
Q

(t/f) 2 strands of DNA are parallel

A

F
–> 2 strands run antiparallel, opposite directions

each sugar-phosphate backbone has a free 5’ phosphate and a free 3’ hydroxyl
–> each end has one of each

194
Q

what does the coiling of DNA strands create

A

coiling of DNA strands creates 2 grooves
–> outer edges of nitrogenous bases are exposed in major and minor grooves
–> base pairs in DNA can interact with other molecules

195
Q

3 models for DNA replication

A
  • semiconservative
  • conservative
  • dispersive replication
196
Q

what kind of replication is DNA replication

A

semiconservative

197
Q

semiconservative replication

A

produce daughter molecules with both an original and newly synthesized DNA strand

198
Q

conservative replication

A

produce daughter molecule with either 2 original/2 newly synthesized DNA strands

199
Q

dispersive replication

A

produce daughter molecules with a mix of both original and newly synthesized DNA in each strand

200
Q

how does DNA synthesis proceed

A

replication proceeds by complementary base-pairing (C-G, A-T)

synthesis occurs in 5’ - 3’ direction

201
Q

4 nucleotides (deoxyribonucleoside triphosphates)

A

dATP, dTTP, dCTP, dGTP (dNTPs)

202
Q

ori

A

regions where DNA replication starts

203
Q

DNA replication with a single ori

A
  1. ori sequence binds the pre-replication complex
  2. replication bubble consists of 2 replication forks that move away from one another during elongation
204
Q

multiple ori

A

replication forks move away from each other during elongation

205
Q

replication forks

A

2 Y-shaped junctions that replication origin creates when DNA unwinds

206
Q

RNA primers

A

DNA synthesis begins with the synthesis of short sequences of RNA –> RNA primers

synthesized by primase (RNA polymerase)

207
Q

DNA polymerase

A

elongates RNA primer

208
Q

DNA helicase

A

uses energy from ATP hydrolysis to unwind/seperate strands

209
Q

single-stranded binding proteins

A

bind to the unwound strands to keep them from reassociating into a double helix

210
Q

sliding DNA clamp

A

increases efficiency of DNA polymerization

keeps DNA polymerase stably bound to DNA to many nucleotides can be added for each binding event

211
Q

leading strand vs. lagging strand

A

leading strand is synthesized continuously

lagging strand is synthesized as fragments (Okazaki fragments)

212
Q

DNA ligase

A

joins Okazaki fragments together

213
Q

telomerase

A

replicates the ends of eukaryotic chromosomes
–>uses an RNA template (made by primer) to extend telomere

–> binds to template strand –> adds additional telomere repeats to template strand –>completion of lagging strand by DNA polymerase

214
Q

2 types of cell division

A

MITOSIS, MEIOSIS

215
Q

Xeroderma pigmentosum

A

extremely sensitive to sunlight

develop skin cancers after exposure to UV in sunlight

1/250K

216
Q

mutations

A

permanent changes in DNA squence
–> most are harmful

could be in somatic cells or in germline

217
Q

chromosomal mutations

A

mutations can alter large sequences of DNA
–> 4 types: deletions, duplications, inversions, translocations

218
Q

point mutations

A

mutations affecting a single, or few DNA base pairs

219
Q

difference effects of mutations on protein activity

A
  1. normal allele
  2. no effect
  3. loss of function
  4. gain of function
  • wild type
  • silent mutation
  • missense mutation
  • nonsense mutation
  • loss of stop mutation
  • frame shift mutation
220
Q

2 most frequent chemical reactions that create serious DNA damage

A

DEPURINATION: leads to base pair deletion
DEAMINATION: leads to transition mutations (GC –> AT)

221
Q

chemical mutagens

A

mutations can be induced by chemical reagents

ex. alkylating agents, base analogs, acridines, deaminating agens, hydroxylating agents

222
Q

alkylating agents

A

induce transitions, transversions, frameshifts, chromosome aberrations

223
Q

acridine dyes

A

induce frameshift mutations

224
Q

nitrous acid

A

induces transition

225
Q

mutations and radiation

A

mutations can be induced by radiation

–> UV radiation induces thymine dimers
–> x-rays and gamma-rays cause single/double stranded breaks in DNA

226
Q

DNA proofreading

A

DNA polymerase has a proofreading activity

–> removes mispaired base

227
Q

mismatch repair mechanism

A

repairs mispaired bases
–> restores original sequence –> decreases error rate even further

228
Q

base excision repair mechanism

A

removes modified bases

229
Q

nucleotide excision repair mechanism

A

repair thymine dimers

230
Q

nonhomologous end joining

A

double-strand DNA breaks can be repaired by nonhomologous end joining

–> nuclease processes DNA end –> DNA ligase joins ends

231
Q

homologous recombination

A

double-strand DNA breaks can be repaired

special nuclease processes broken ends –> double-strand break accurately repaired using undamaged DNA as template

232
Q

APC (anaphase promoting complex)

A

loss of normal tumor suppressor gene APC –> small growth forms on colon wall –> benign, precancerous tumor grows
–> activation of oncogene RAS –> class II adenome (benign) grows –> loss of tumor suppressor gene DCC –> class III adenoma grows
–> loss of tumor suppressor gene P53 –> carcinoma (malignant tumor) develops

233
Q

sickle-cell anemia

A

disease caused by a single nucleotide change

234
Q

transcription

A

RNA synthesis of an RNA strand complementary to one strand of DNA

235
Q

translation

A

protein synthesis

236
Q

messenger RNA (mRNA)

A

code for proteins

237
Q

ribosomal RNAs(rRNAs)

A

form core of ribosome’s structure and catalyze protein synthesis

238
Q

microRNAs(miRNAs)

A

regulate gene expression

239
Q

transfer RNAs (tRNAs)

A

serve as adaptors between mRNA and amino acids during protein synthesis

240
Q

other noncoding RNAs

A

used in RNA splicing, gene regulation, telomere maintenance, and many other processes

241
Q

RNA polymerase enzyme

A

responsible for transcription

1 RNA polymerase in prokaryotes, 5 in eukaryotes

242
Q

5 kinds of RNA polymerase and their products

A

RNA polymerase I(nucleolus): ribosomal RNAs, excluding 55rRNA
II (nucleus): nuclear pre-mRNAs
III (nucleus): tRNAs, 55 rRNA, and other small nuclear RNAs
IV (nucleus(plant)): small interfering RNAs(siRNAs)
V (nucleus(plant)): some siRNAs plus noncoding [antisense] transcripts of siRNA target genes

243
Q

3 steps of transcription

A
  1. initiation: RNA polymerase binds to the promoter and starts to unqind the DNA strands
  2. elongation: RNA polymerase moves along the DNA template strant from 3’ - 5’ and produces the RNA transcript by adding nucleotides complementary to the DNA template
  3. termination: when RNA polymerase reaches termination site, RNA transcript and polymerase are released from template
244
Q

promotor

A

signal to start transcription in a DNA sequence
–> guides RNA polymerase

DNA sequences that indicate 2 things:
- transcription initiation site
- template DNA strand

245
Q

terminator

A

signal to stop transcription in a DNA sequence

246
Q

general transcription factors

A

recruit RNA polymerase to the promoter in eukaryotes

247
Q

what do specific transcription factors do

A

increase or decrease gene transcription efficiency

248
Q

what is the transcription initiation site indicated by

A

+1

5’ –> 3’ = downstream (+2, +3, +4, +5)
3’ –> 5’ = upstream (-1, -2, -3, -4)

NO ZERO

249
Q

pre mRNA processing

A

5’ capping
3’ polyadenylation
splicing

eukaryotic mRNA is processed before translation

250
Q

5’ capping`

A

a “cap” of modified GTP is added

251
Q

3’ polyadenylation

A

a poly “A” tail is added

252
Q

introns

A

eukaryotic protein-coding genes are interrupted by noncoding sequences (INTRONS)

253
Q

exons

A

coding regions

254
Q

splicing

A

process of intron removal from pre-mRNA
–> various mRNAs and proteins can be produced by alternative premRNA splicing

  1. small nuclear ribonucleoprotein (snRNPs) bind to pre-mRNA near both 5’ donor and branch point
  2. binding of snRNPs recruits many proteins
  3. a cut is made between the upstream exon and the intron
  4. after first cut at 5’ end, intron forms a closed loop
  5. free 3’ OH group at end of the cut reacts with 5’ phosphate
  6. downstream exon is cleaved at the intron junction and spliced to the upsream exon
    –> after all introns are removed, mature mRNA is exported to the cytosol for translation
255
Q

(t/f) transcription and translation occur simultaneously in prokaryotes

A

T

256
Q

where are mature eukarytotic mRNAs exported

A

exported from the nucleus to the cytoplasm for translation

257
Q

codon

A

every 3 ribonucelotides (triplet code)

specifies amino acids

genetic code contains 64 codons

258
Q

initiation codon and 3 stop codons

A

initiation: AUG

3 stop codons:
UAA, UAG, UGA

259
Q

which aminoacids are encoded by single codons

A

tryptophan, methionine

–> almost all amino acids are specified by 2, 3, 4 different codons

260
Q

exceptions to the universal genetic code

A

UGA (normal: termination): altered–>Trp, comes from human and yeast mitochondria
CUA (n: Leu): altered –> Thr, from yeast mitochondria

AUA(n:Ile): a –> Met, from human mitochondria
AGA (n:Arg): a –> termination, from human mitochondria
AGG (n:Arg): a –> termination, from human mitochondria

UAA(n: termination): a –> Gln, from paramecium, tetrahymena, stylonychia
UAG (n: termination): a –> Gln, from paramecium

261
Q

transfer RNAs

A

serve as translators for protein synthesis in ribosomes

tRNAs bind amino acids, bind mRNA, and interact with ribosomes
–> at least one tRNA for each amino acid

262
Q

where are unusual bases found

A

tRNA

263
Q

(t/f) the number of tRNA molecules = codons

A

F
–> there are less tRNA molecules than codons

264
Q

wobble pairing

A

enables one tRNA to recognize multiple codons
–> enables a more flexible H bonding

allows 30 different tRNA types to accommodate 61 codons

265
Q

tRNA attachment

A

1 tRNA for 1 aminoacyl-tRNA (amino acid)

  1. enzyme activates amino acid –> catalyzes reaction with ATP to form phosphate ion and high energy AMP amino acid
  2. –> enzyme catalyzes reaction of the activated amino acid with correct tRNA
  3. specificity of enzyme ensures the correct amino acid and tRNA acid are together
  4. charged tRNA delivers appropriate amino acid to join elongating polypeptide production of translation
266
Q

aminoacyl-tRNA synthases

A

charge tRNAs

267
Q

aminoacylation/charging

A

addition of an amino acid to the corresponding tRNA

268
Q

ribosome

A

workbench for translation

269
Q

aminoacyl-tRNA

A

A site –> where the charged tRNA anticodon binds to the mRNA

270
Q

peptidyl-tRNA

A

P site –> where the tRNA carrying the growing peptide chain resides

271
Q

Exit (tRNA)

A

E site –> where the uncharged tRNA resides

272
Q

translation initiation

A

prokaryotes: involves recognition of Shine Dalgarno sequence

eukaryotes:recognition of the 5’ cap

273
Q

translation elongation

A

involves peptide bond formation

274
Q

translation termination

A

involves encountering a stop codon

  1. release factor binds to complex when a stop codon enters A site
  2. release factor disconnects polypeptide from tRNA in P site
  3. remaining components seperate
275
Q

stop codons

A

bing release factors
–> allows hydrolysis of the bond between polypeptide chain and tRNA in P side

276
Q

polysome formation

A

increases rate of protein synthesis

277
Q

polysome

A

(polyribosome)

assemblage of mRNA, ribosomes, and their growing polypeptides

278
Q

what happens after translation

A

proteins are modified
–> post-translational modifications are required for a new protein to become fully functional

279
Q

post-translational processing (3)

A

phosphorylation: added phosphate groups alter shape of protein

glycosylation: adding sugars is important for targeting and recognition

proteolysis: cleaving the polypeptide allows the fragments to fold into diff shapes

280
Q

proteins reach final cellular destination

A
  1. signal peptide binds to a signal recognition particle –> halts translation –> complex binds to receptor protein in membrane of RER and translation resumes
  2. signal sequence is removed by an enzyme in lumen of RER
  3. polypeptide continues to elongate until translation terminates
  4. ribosome is released –> protein folds inside RER
281
Q

what guides proteins to its final destination

A

signal sequences guide proteins to their destination

282
Q

how do proteins enter the mitochondria

A

protein translocators

283
Q

how do selected proteins enter the nucleus

A

some proteins enter the nucleus through nuclear pores
–> nuclear localization signal of prospective nuclear proteins are recognized by nuclear import receptors (transport receptor)

284
Q

where do proteins go during their synthesis

A

ER (endoplasmic reticulum)
–> ER signal sequence guides a ribosome to the ER membrane
–> enter via protein translocator
–> ER signal recognition particle and its receptor direct a ribosome to the ER membrane

membrane proteins remain in the ER lipid bilayer

285
Q

where do soluble proteins go

A

cross the ER membrane and enters the lumen

286
Q

where is Na+ most abundant

A

OUTSIDE the cell

287
Q

where is K+ most abundant

A

INSIDE the cell

288
Q

voltage difference

A

small excesses of positive or negative charge on 2 sides of the plasma membrane

289
Q

membrane potential

A

the vooltage difference across the membrane

290
Q

transporters

A

transfer small organic molecules/inorganic ions

291
Q

channels

A

form tiny hydrophilic pores, allow substances to pass by diffusion

292
Q

passive vs active transport

A

passive: downhill movement, requries no energy
active: uphill movement, requires energy

293
Q

3 types of proteins for active transport:

A
  • uniporter: transports 1 substance in 1 direction
  • symporter: transports 2 diff substances in the same direction
  • antiporter: transports 2 diff substances in opposite directions
294
Q

3 types of endocytosis

A

receptor-mediated endocytosis: specific uptake of large molecules

pinocytosis: nonspecific uptake of extracellular fluid

phagocytosis: nonspecific uptake of large undissolved particles

295
Q

exocytosis

A

release of large/small molecules
–> vesicle fusion with cell membrane
–> secretory vesicles fuse with plasma membrane and release its content into extracellular space

296
Q

ATP-driven Na+ transporters

A

use energy supplied by ATP to expel Na+ and bring in K+
–> high Na+ conc outside cell represents a huge nstore of energy

primary active transport: Na+–K+ pump moves Na+ to create a gradient of Na+
secondary AT: Na+, moving with concentration gradient drives transport of glucose against its concentration gradient

297
Q

ATP-driven Ca2+ transports

A

keep cystolic Ca2+ concentration low
–> binds to a variety of proteins in the cell and alters their activities
–> influx of Ca2+ into cell = intracellular signal
–> triggers cell processes like muscle contraction, fertilization, nerve cell communication

298
Q

K+ leak channels

A

responsible for resting membrane potential
–> plasms membrane mostly permeable to K+ moving out of cell

299
Q

leak channels

A

always open

300
Q

voltage-gates ion channels

A

controlled by changes in coltage across membrane

301
Q

ligand-gates ion channels

A

controlled by binding of molecule

polar substance more concentrated on outside –> binding of stimulus molecule –> pore opens –> polar substance diffuses

302
Q

mechanically gated ion channels

A

controlled by a physical stimuli
ex. light, sound waves, pressure

303
Q

action potential

A

rapid change in membrane potential
–> travels along axon, jump along myelinated axons

304
Q

depolarization

A

neuron stimulation shifts membrane potential from -70mV to a less negative value
–> causes voltage gated Na+ channels to open

305
Q

synapses

A

neurons connect to their target cels
–> separated by pre and postsynaptic cells and synaptic cleft

306
Q

what kind of channels are neurotransmitter receptors

A

ligand-gated ion channels

307
Q

what happens at a synapse

A

chemical signal is converted into an electrical signal

308
Q

what ion channel is responsible for muscle contraction

A

ligand-gated ion channels
–>acetylcholine is the ligand responsible for Na+ ion channel activity in neuromuscular junction

309
Q

phospholipid

A

have hydrophilic head and 2 hydrophobic tails

310
Q

what links the hydrophilic head and hydrophobic tail

A

glycerol

311
Q

what is the most common phospholipid in biological membranes

A

phosphatidylcholine

312
Q

saturated vs unsaturated fats

A

hydrocarbon tail WITH double bond = UNSATURATED
–> unsaturated is MORE FLUID, bilayers with shorter fatty acid chains are more fluid

313
Q

amphipathic

A

molecules with both hydrophilic and hydrophobic parts

314
Q

cholesterol

A

controls membrane fluidity

315
Q

2 kinds of membrane proteins

A

integral: extend through bilayer
–> can be removed only by disrupting the bilayer with detergents
–> usually crosses the bilayer as an alpha helix

peripheral: interact with integral membrane proteins/phospholipids

316
Q

transmembrane protein

A

integral protein that extends all the way through the bilayer
–> hydrophilic R groups in exposed parts of protein interact with aqueous environments
–> hydrophobic R groups interact with hydrophobic core of membrane

317
Q

which proteins can move laterally in the lipid bilayer

A

plasma membranes can move laterally in the lipid bilayer

318
Q

how can cells restrict the movement of its membrane proteins

A
  • bind meshwork of proteins inside cell (cell cortex)
  • bind extracellular matric molecules
  • bind proteins on surface of another cell
  • be restricted by diffusion barriers
319
Q

membrane domains

A

functionally specialized regions that can confine proteins to localized areas on the membrane

320
Q

cell cortex

A

framework of proteins that support the cell membrane

321
Q

carbohydrates on the cell surface

A

all the carbs on the glycoproteins, proteoglycans, and glycolipids is located on the outside of the membrane
–> coating is called the carbohydrate later/glycocalyx
–> function in cell recognition and adhesion

322
Q

desmosomal adhesion

A

cell structure specialized for cell-cell adhesion

localized spot-like adhesions

randomly arranged on the lateral sides of the cell

tissues faced with mechanical stress

323
Q

tight junctions

A

protein complex between 2 cells that create a seal to prevent any leakage of content through cell membranes

324
Q

gap junctions

A

allow intracellular flow of ions and molecules between cytoplasms

325
Q

bright field microscopy

A

light passes directly through cells
–> little contrast and details not distinguished

326
Q

phase-contrast microscopy

A

contrast is increased by emphasizing differences in refractive index
–> enhances light and dark regions in cell

327
Q

differential interference-contrast microscopy

A

2 beams of polarized light are used
–> looks as if cell is casting a shadow on one side

328
Q

stained bright gield microscopy

A

stain enhances contrast, reveals details not otherwise visible

329
Q

fluorescence microscopy

A

natural substance in cell or fluorescent dye that binds to a specific cell material is stimulated by a beam of light

330
Q

confocal microscopy

A

fluorescent materials are used
–> adds system of focusing both stimulating and emitted light so that a single place through cell is seen
–> sharper 2D image

331
Q

transmission electron microscopt (TEM)

A

beam of electrons is focused on the objects by magnets
–> objects appear darker if they absorb electrons
–> objects detected on fluorescent screen if electrons pass through

332
Q

scanning electron microscopy (SEM)

A

electrons are directed to the surface of the sample where they cause other electrons to be emitted

333
Q

cytoplasm

A

everything inside the cell except for the nucleus

334
Q

cytosol

A

fluid cytoplasm

335
Q

prokaryotic vs eukaryotic cell

A

prokaryotic cell has no nucleus or membrane enclosed compartments

336
Q

gram positive vs gram negative bacteria

A

+ = thick peptidoglycan layer, no lipid membrane
- = thin peptidoglycan layer, have outer lipid membrane

337
Q

nuclear pores

A

protein-lined channel in nuclear envelope that regulate the transportation of molecules between the nucleus and cytoplasm

338
Q

endoplasmic reticulum

A

RER: site of protein synthesis
SER: sire of glycogen degradation, lipid/steroid synthesis, calcium ion storage

339
Q

golgi apparatus

A

site of protein modification and osrting

add carbs to proteins

sort proteins to destination

340
Q

lysosomes

A

site of macromolecule digestion

primary lysosomes bud from golgi apparatus

contain digestive enzymes to digest proteins, polysaccharides, nucleic acids, and lipids

interior is acidic

341
Q

mitochondria

A

site of energy transformation

most likely ancient aerobic prokaryote engulfed by a pre-eukaryotic cell (endosymbiosis)

342
Q

chloroplasts

A

sites of photosynthesis

343
Q

chromoplasts

A

make/store red, yellow, and organde pigments
–> esp in flowers and fruits

344
Q

leucoplasts

A

store starch

345
Q

peroxisomes/glyoxysomes

A

accumulate toxic peroxides like H2O2
–> safely broken down in peroxisomes

glyoxysomes: same but in plants

346
Q

vacuols

A

storage compartment in platns

347
Q

what are plant vacuols involved in

A
  • supports plant body
  • reproduction
  • digestion
  • storage
348
Q

where does protein synthesis take place

A

ribosomes

349
Q

eukaryotic cell evolution

A
  1. ancient prokaryotic cell w no internal membranes
  2. cell membrane folds inward
  3. further membrane infoldings form ER –> surrounds nucleoid and forms nuclear envelope

BIO1140 (2 decks)

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