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cells, atoms, molecules and membranes Flashcards

atoms, molecules and bonds membrane structure and function membrane transport

1
Q

what are atoms

A

the smallest particles that retain the properties of an element

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2
Q

what are atoms made of

A

sub atomic particles (protons, neutrons, electrons)

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3
Q

atomic number = number of neutrons/protons

A

protons

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4
Q

what are isotopes

A

atoms of an element with the same number of protons but different numbers of neutron, and so different masses

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5
Q

additional neutrons of an isotope makes the atom stable/unstable

A

unstable

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6
Q

what happens when atoms share or exchange electrons with each other

A

they form a bond

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7
Q

under what circumstances do ionic bonds form

A

when the electronegativity difference between the elements involved is large

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8
Q

what is a charged atom or molecule called

A

an ion

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9
Q

what is bond capacity

A

it is known as the atomic valence e.g. Na has atomic valence 1 and chlorine 7

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10
Q

what are the ionic valences of sodium and chlorine

A

Na+ +1

chloride -1

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11
Q

what is a covalent bond

A

the sharing of a pair of valence electrons by two atoms.

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12
Q

do the shared electrons in a bond count as part of each atom’s valence shell

A

yes

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13
Q

under what circumstances does a hydrogen bond form

A

when a hydrogen atom covalently to one electronegative atom is also attracted to another electronegative atom (H bonded to O, N, F)

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14
Q

how are hydrogen bonds shown in biological drawings

A

dotted lines

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15
Q

what are van der waals interactions

A

bonds formed between locally induced dipoles between atoms in close proximity

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16
Q

as an individual bond are van der waals interactions weak or strong

A

weak, however, the combined strength is functionally strong and the interactions are constantly changing

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17
Q

Is water a polar or non polar molecule

A

polar

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18
Q

can water form hydrogen bonds

A

yes (OH group)

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19
Q

what is cohesion

A

the holding together of water molecules by hydrogen bonds

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20
Q

why does water have an unusually high surface tension

A

due to hydrogen bonding between the molecules and the air-water interface and to the water below

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21
Q

what property of water is the reason why some animals can travel across water and why we must measure from the bottom of the meniscus

A

the high surface tension

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22
Q

how does cohesion assist plants

A

helps with the transport of water against gravity

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23
Q

what is adhesion

A

an attraction between different substances e.g. water and plant cell walls

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24
Q

what happens when an ionic compound is dissolved in water

A

each ion becomes surrounded by a sphere of water molecules called a hydration shell

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25
Q

other than ionic compounds what other substances can water dissolve

A

polar molecules (like dissolves like)

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26
Q

what is pH

A

the concentration of H+

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27
Q

what is the pH range that most biological fluids are found in

A

6 to 8

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28
Q

why is CO2 dangerous for our oceans

A

it is dissolved in seawater and forms carbonic acid. This is called ocean acidification

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29
Q

what makes a buffer

A

solutions of a weak acid and its corresponding base, which combine reversibly with H+

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30
Q

explain what happens when the blood is under

  • acidic stress
  • alkaline stress
A

acidic stress - H+ and HCO3- combine to form H2CO3, removing acid
alkaline stress - H2CO3 dissociates to form H+ and HCO3-, adding acid

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31
Q

what are the seven main functional groups in biology

A 
hydroxyl OH e.g. alcohols
carbonyl C=O e.g. ketones and  aldehydes
carboxyl COOH e.g. carboxylic acids
amino NH2 e.g. amino acids, amines 
sulfhydryl SH  e.g. cysteine, thiols 
phosphate PO4 e.g. glycerol phosphate 
methyl CH3 e.g. methylated compounds
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32
Q

what are polymers made of

A

monomers

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33
Q

by what process are biological polymer generally formed by

A

dehydration (removal of water to create an amide bond)

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34
Q

name some common polymers

A

DNA, RNA, proteins, cellulose, keratin, lipids

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35
Q

what are membranes

A

phospholipid polymers of fatty acids, glycerol, phosphate and a terminal amine or alcohol group

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36
Q

what is meant by membranes being amphipathic

A

they have hydrophobic and hydrophilic parts

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37
Q

what is phosphatidyl choline made from

A

choline, a phosphate linkage to glycerol which is esterified with two fatty acids

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38
Q

phospholipids have a hydrophobic head/tail and a hydrophilic head/tail

A

hydrophilic head

hydrophobic tail

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39
Q

membrane phospholipids spontaneously form ……….. and ………… in water

A

monolayers and bilayers

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40
Q

what are simple detergents (soaps)

A

salts of fatty acids which retain amphipathicity and can interact and dissolve other organic compounds

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41
Q

name 4 reasons why the membranes are important

A

they compartmentalize metabolic activities
they separate/protect cellular components
they provide a scaffold for signalling
they are essential for cellular energy generation

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42
Q

what feature of membranes allows for compartmentalization, protection and energy generation

A

immiscibility of water and membranes

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43
Q

the phospholipid bilayer is polar/non-polar

A

non-polar

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44
Q

without other means of transport, the phospholipid bilayer prevents molecules of which nature from passing through into other compartments.

A

polar molecules are unable to pass through

45
Q

what is a limiting factor of membrane dimensions and cell size

A

physical properties in water (diffusion rates)

46
Q

proteins usually carry an excess of positive/negative charge

A

negative

47
Q

under which 2 circumstances does a membrane voltage occur

A
  1. immobile charges are not balanced

2. charge transport id not full balanced

48
Q

what drives diffusion of ions

A

chemical and electrical gradients

49
Q

what does the Nernst equation describe

A

the equilibrium between the chemical and electrical forces on an ion

50
Q

how can the voltage across cell membranes be measured

A

using microelectrodes implanted in cells

51
Q

how can the voltage across membranes of cell organelles be measured

A

using voltage sensitive dyes

52
Q

where are membranes found

A

delimiting all organelles in eukaryotic cells

53
Q

what practice give a static picture of the cell

A

electron microscopy

54
Q

what are the 3 steps in membrane maintenance

A
  1. membrane lipid synthesis
  2. vesicle traffic through the Golgi
  3. membrane and cargo delivery/recovery by endocytosis and exocytosis
55
Q

how does fluorescence work

A
  1. light is absorbed by a pigment
  2. electrons become excited
  3. energy is released in the form of light as the electron falls back to ground state (lowest empty electron shell)
56
Q

why can chloroplasts be considered autonomous

A
  1. they are endosymbiont progenitors suggested by double membranes
  2. they undergo independent division/replication
57
Q

why can chloroplasts not be considered autonomous

A

because they interact via structures called stromules

58
Q

what type of molecules does the membrane have high permeability for

A

small hydrophobic molecules and gases e.g. oxygen

59
Q

are membranes permeable to water

A

their permeability to water is limited, hence, why aquaporin channels are employed

60
Q

how permeable is the membrane to ions and large solutes e.g. glucose

A

very low permeability

61
Q

what are 4 roles of transport proteins

A
  1. create a passage for hydrophilic substances
  2. create a filter
  3. provide opportunity for energy coupling
  4. provide possibility for regulation
62
Q

transport proteins create a hydrophobic/hydrophilic pore

A

hydrophilic - like dissolves like so the hydrophilic substance that are usually repelled by the membrane are able to diffuse through

63
Q

what kind of transport is aquaporin an example of

A

facilitated diffusion

64
Q

what are the two types of forces that drive the movement of molecules across membranes

A
  1. chemical gradient - concentration gradient

2. electrical gradient - charge gradient (only relevant for ions)

65
Q

what is cation

A

a positively charged ion

66
Q

what is anion

A

a negatively charged ion

67
Q

what is the combine force of electrical and chemical gradients called

A

electrochemical gradient

68
Q

what is the electrochemical gradient

A

• The net driving force for the movement of a molecule resulting from the combination of the chemical and electrical gradient.

69
Q

what are the differences between passive and active transport

A

active transport
- requires energy
- moves substances against the electrochemical gradient
passive transport
- doesn’t require energy
- moves substances down the electrochemical gradient

70
Q

what are the 2 types of transport proteins for active transport

A

pumps

cotransport systems

71
Q

what are the 2 types of transport for passive transport

A

channels

carriers

72
Q

give 2 examples of energy coupling pumps

A

ATPases

Bacteriorhodopsin

73
Q

how does ATPase work

A

transport is coupled with the hydrolysis of ATP

74
Q

what is the bacteriorhodopsin pump driven by

A

light

75
Q

how does the sodium potassium pump work

A

2 K in 3 Na out

conformational changes driven by phosphorylation and dephosphorylation

76
Q

name 3 pumps that are driven by conformational changes

A

sodium potassium pump
proton pump
calcium pump

77
Q

what is the role of the calcium pump

A

to maintain calcium concentration in the cytoplasm

78
Q

what is the role of proton pumps and how do they work

A

the pump keeps the inside of the cell less acidic than the outside
It does this by using TAP to move protons out of the cell. The additional hydrogen ions make the extracellular fluid more acidic.

79
Q

proton gradients and other gradients can be used to drive what

A

the active transport of other molecules

80
Q

what do co-transport systems do

A

they couple the downward movement of one ion (driver) to the uphill movement of another solute (substrate)

81
Q

what is symport

A

when the driver ion and substrate of a co-transport system move in the same direction (piggyback)

82
Q

what is antiport

A

when the driver ion and substrate of a co-transport system move in the opposite direction (revolving door)

83
Q

although passive transport doesn’t require energy input it relies on what

A

previously established electrochemical gradients

84
Q

for passive transport what is the difference between a channel and a carrier

A
  • a channel provides an aqueous pore for the passage of ions
  • a carrier undergoes a conformational change that exposes ion binding sites to different sides of the membrane
  • both pathways facilitate movement down the electrochemical gradient
85
Q

are ion channels selective

A

yes, K channels have a 100fold higher permeability for K than for Na

86
Q

are ion channels gated

A

yes, they can open and close in response o specific stimuli e.g. voltage, chemical or ligands

87
Q

how can you measure how single channel proteins gate

A

using a method called patch lamp

88
Q

name 3 types of chemical bond

A

covalent
ionic
hydrogen

89
Q

what is the equation for finding pH

A

pH= -log[H+] OR pOH= -log[OH-]

the pH + pOH = 14

90
Q

what are the three major biological polymers and list their monomers

A

carbohydrates - sugars
nucleic acids - nucleotides
proteins - amino acids

91
Q

what is potential energy

A

the energy that matter possesses because of its location or structure

92
Q

what are valence electrons

A

the outermost electrons of an atom

93
Q

what are the main emergent properties of water

A

cohesion - hydrogen bonds hold water molecules together
adhesion - clinging of water to another substance by hydrogen bonding
high surface tension - a measure of how difficult it is to stretch or break the surface of a liquid
moderation of temperature by water - moderates air temperature by absorbing heat from air that is warmer and releasing stored heat to air that is cooler
high specific heat capacity - due to this water will change its temperature less than other substances when it absorbs or loses a given amount of heat (due to its hydrogen bonds)
High heat of vaporization - due to hydrogen bonds
Floating of ice on liquid water - less dense as solid than liquid. Ice is lattice shape so the molecules have more space between them and are less dense. More hydrogen bonds in ice compared to liquid water. Liquid water molecules can sit closer together due to lack of hydrogen bonds - more densely packed

94
Q

what is kinetic energy

A

the energy of motion

95
Q

what does temperature represent

A

the average kinetic energy of molecules

96
Q

what is thermal energy

A

kinetic energy associated with the random movement of atoms or molecules

97
Q

what is thermal energy transfer defined as

A

heat

98
Q

what is the specific heat capacity

A

the amount of heat that must be absorbed or lost for 1g of a substance to change its temperature by 1 C

99
Q

what is the hydration shell

A

the sphere of water molecules surrounding each dissolved ion

100
Q

what is a base

A

a proton acceptor, electron donor

101
Q

what is an acid

A

a proton donor, electron acceptor

102
Q

what is a buffer

A

a substance that minimizes changes in pH by accepting hydrogen ions from solution when they are in excess and donating them when they have been depleted

103
Q

what is a buffer generally made from

A

a weak acid and its alkali salt e.g. ethanoic acid and sodium ethanoate
a weak base and its acidic salt e.g. ammonia and ammonium chloride

104
Q

what characterizes the function of a molecule

A

its shape and size

105
Q

what are hydrocarbons

A

organic molecules consisting only of carbon and hydrogen

106
Q

what are structural isomers

A

molecules that contain the same components but they differ in spacial arrangement e.g. cis/trans isomerism

107
Q

what are enantiomers

A

isomers that are mirror images of each other due to having chiral centres

108
Q

why is the concept of enantiomers important in the pharmaceutical industry

A

because in most cases only one enantiomer is biologically active. The different enantiomers are often not equally effective in medicines

109
Q

what is a functional group

A

a chemical group that is directly involved in reactions

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