cells, atoms, molecules and membranes Flashcards
atoms, molecules and bonds membrane structure and function membrane transport
what are atoms
the smallest particles that retain the properties of an element
what are atoms made of
sub atomic particles (protons, neutrons, electrons)
atomic number = number of neutrons/protons
protons
what are isotopes
atoms of an element with the same number of protons but different numbers of neutron, and so different masses
additional neutrons of an isotope makes the atom stable/unstable
unstable
what happens when atoms share or exchange electrons with each other
they form a bond
under what circumstances do ionic bonds form
when the electronegativity difference between the elements involved is large
what is a charged atom or molecule called
an ion
what is bond capacity
it is known as the atomic valence e.g. Na has atomic valence 1 and chlorine 7
what are the ionic valences of sodium and chlorine
Na+ +1
chloride -1
what is a covalent bond
the sharing of a pair of valence electrons by two atoms.
do the shared electrons in a bond count as part of each atom’s valence shell
yes
under what circumstances does a hydrogen bond form
when a hydrogen atom covalently to one electronegative atom is also attracted to another electronegative atom (H bonded to O, N, F)
how are hydrogen bonds shown in biological drawings
dotted lines
what are van der waals interactions
bonds formed between locally induced dipoles between atoms in close proximity
as an individual bond are van der waals interactions weak or strong
weak, however, the combined strength is functionally strong and the interactions are constantly changing
Is water a polar or non polar molecule
polar
can water form hydrogen bonds
yes (OH group)
what is cohesion
the holding together of water molecules by hydrogen bonds
why does water have an unusually high surface tension
due to hydrogen bonding between the molecules and the air-water interface and to the water below
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
the high surface tension
how does cohesion assist plants
helps with the transport of water against gravity
what is adhesion
an attraction between different substances e.g. water and plant cell walls
what happens when an ionic compound is dissolved in water
each ion becomes surrounded by a sphere of water molecules called a hydration shell
other than ionic compounds what other substances can water dissolve
polar molecules (like dissolves like)
what is pH
the concentration of H+
what is the pH range that most biological fluids are found in
6 to 8
why is CO2 dangerous for our oceans
it is dissolved in seawater and forms carbonic acid. This is called ocean acidification
what makes a buffer
solutions of a weak acid and its corresponding base, which combine reversibly with H+
explain what happens when the blood is under
- acidic stress
- alkaline stress
acidic stress - H+ and HCO3- combine to form H2CO3, removing acid
alkaline stress - H2CO3 dissociates to form H+ and HCO3-, adding acid
what are the seven main functional groups in biology
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
what are polymers made of
monomers
by what process are biological polymer generally formed by
dehydration (removal of water to create an amide bond)
name some common polymers
DNA, RNA, proteins, cellulose, keratin, lipids
what are membranes
phospholipid polymers of fatty acids, glycerol, phosphate and a terminal amine or alcohol group
what is meant by membranes being amphipathic
they have hydrophobic and hydrophilic parts
what is phosphatidyl choline made from
choline, a phosphate linkage to glycerol which is esterified with two fatty acids
phospholipids have a hydrophobic head/tail and a hydrophilic head/tail
hydrophilic head
hydrophobic tail
membrane phospholipids spontaneously form ……….. and ………… in water
monolayers and bilayers
what are simple detergents (soaps)
salts of fatty acids which retain amphipathicity and can interact and dissolve other organic compounds
name 4 reasons why the membranes are important
they compartmentalize metabolic activities
they separate/protect cellular components
they provide a scaffold for signalling
they are essential for cellular energy generation
what feature of membranes allows for compartmentalization, protection and energy generation
immiscibility of water and membranes
the phospholipid bilayer is polar/non-polar
non-polar
without other means of transport, the phospholipid bilayer prevents molecules of which nature from passing through into other compartments.
polar molecules are unable to pass through
what is a limiting factor of membrane dimensions and cell size
physical properties in water (diffusion rates)
proteins usually carry an excess of positive/negative charge
negative
under which 2 circumstances does a membrane voltage occur
- immobile charges are not balanced
2. charge transport id not full balanced
what drives diffusion of ions
chemical and electrical gradients
what does the Nernst equation describe
the equilibrium between the chemical and electrical forces on an ion
how can the voltage across cell membranes be measured
using microelectrodes implanted in cells
how can the voltage across membranes of cell organelles be measured
using voltage sensitive dyes
where are membranes found
delimiting all organelles in eukaryotic cells
what practice give a static picture of the cell
electron microscopy
what are the 3 steps in membrane maintenance
- membrane lipid synthesis
- vesicle traffic through the Golgi
- membrane and cargo delivery/recovery by endocytosis and exocytosis
how does fluorescence work
- light is absorbed by a pigment
- electrons become excited
- energy is released in the form of light as the electron falls back to ground state (lowest empty electron shell)
why can chloroplasts be considered autonomous
- they are endosymbiont progenitors suggested by double membranes
- they undergo independent division/replication
why can chloroplasts not be considered autonomous
because they interact via structures called stromules
what type of molecules does the membrane have high permeability for
small hydrophobic molecules and gases e.g. oxygen
are membranes permeable to water
their permeability to water is limited, hence, why aquaporin channels are employed
how permeable is the membrane to ions and large solutes e.g. glucose
very low permeability
what are 4 roles of transport proteins
- create a passage for hydrophilic substances
- create a filter
- provide opportunity for energy coupling
- provide possibility for regulation
transport proteins create a hydrophobic/hydrophilic pore
hydrophilic - like dissolves like so the hydrophilic substance that are usually repelled by the membrane are able to diffuse through
what kind of transport is aquaporin an example of
facilitated diffusion
what are the two types of forces that drive the movement of molecules across membranes
- chemical gradient - concentration gradient
2. electrical gradient - charge gradient (only relevant for ions)
what is cation
a positively charged ion
what is anion
a negatively charged ion
what is the combine force of electrical and chemical gradients called
electrochemical gradient
what is the electrochemical gradient
• The net driving force for the movement of a molecule resulting from the combination of the chemical and electrical gradient.
what are the differences between passive and active transport
active transport
- requires energy
- moves substances against the electrochemical gradient
passive transport
- doesn’t require energy
- moves substances down the electrochemical gradient
what are the 2 types of transport proteins for active transport
pumps
cotransport systems
what are the 2 types of transport for passive transport
channels
carriers
give 2 examples of energy coupling pumps
ATPases
Bacteriorhodopsin
how does ATPase work
transport is coupled with the hydrolysis of ATP
what is the bacteriorhodopsin pump driven by
light
how does the sodium potassium pump work
2 K in 3 Na out
conformational changes driven by phosphorylation and dephosphorylation
name 3 pumps that are driven by conformational changes
sodium potassium pump
proton pump
calcium pump
what is the role of the calcium pump
to maintain calcium concentration in the cytoplasm
what is the role of proton pumps and how do they work
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.
proton gradients and other gradients can be used to drive what
the active transport of other molecules
what do co-transport systems do
they couple the downward movement of one ion (driver) to the uphill movement of another solute (substrate)
what is symport
when the driver ion and substrate of a co-transport system move in the same direction (piggyback)
what is antiport
when the driver ion and substrate of a co-transport system move in the opposite direction (revolving door)
although passive transport doesn’t require energy input it relies on what
previously established electrochemical gradients
for passive transport what is the difference between a channel and a carrier
- 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
are ion channels selective
yes, K channels have a 100fold higher permeability for K than for Na
are ion channels gated
yes, they can open and close in response o specific stimuli e.g. voltage, chemical or ligands
how can you measure how single channel proteins gate
using a method called patch lamp
name 3 types of chemical bond
covalent
ionic
hydrogen
what is the equation for finding pH
pH= -log[H+] OR pOH= -log[OH-]
the pH + pOH = 14
what are the three major biological polymers and list their monomers
carbohydrates - sugars
nucleic acids - nucleotides
proteins - amino acids
what is potential energy
the energy that matter possesses because of its location or structure
what are valence electrons
the outermost electrons of an atom
what are the main emergent properties of water
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
what is kinetic energy
the energy of motion
what does temperature represent
the average kinetic energy of molecules
what is thermal energy
kinetic energy associated with the random movement of atoms or molecules
what is thermal energy transfer defined as
heat
what is the specific heat capacity
the amount of heat that must be absorbed or lost for 1g of a substance to change its temperature by 1 C
what is the hydration shell
the sphere of water molecules surrounding each dissolved ion
what is a base
a proton acceptor, electron donor
what is an acid
a proton donor, electron acceptor
what is a buffer
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
what is a buffer generally made from
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
what characterizes the function of a molecule
its shape and size
what are hydrocarbons
organic molecules consisting only of carbon and hydrogen
what are structural isomers
molecules that contain the same components but they differ in spacial arrangement e.g. cis/trans isomerism
what are enantiomers
isomers that are mirror images of each other due to having chiral centres
why is the concept of enantiomers important in the pharmaceutical industry
because in most cases only one enantiomer is biologically active. The different enantiomers are often not equally effective in medicines
what is a functional group
a chemical group that is directly involved in reactions
