biological molecules Flashcards
what is a monomer?
small/identical/similar molecules can be joined together through condensation reactions to form larger molecules (polymers)
what is a polymer?
large molecules made from joining 3 or more identical or similar monomers together
condensation reactions:
joins two or more monomer units together with the removal of water molecule and the formation of a chemical bond
anabolic reaction:
condensation reaction
hydrolysis reaction:
the addition of one molecule of water to break the chemical bond between two molecules
catabolic reaction:
hydrolysis reaction
examples of monomers:
monosaccharides (alpha and beta glucose)
amino acids
nucleotides
examples of polymers:
polysaccharides (starch, glycogen, cellulose)
proteins (haemoglobin, enzyme)
polynucleotide/nucleic acid (DNA, RNA)
monomer of carbohydrates:
monosaccharides
what elements do carbohydrates contain?
carbon, hydrogen, oxygen
general formulae of carbohydrate:
ratio of H:O in molecule
(CH2O)n where n is 3 to 7
H:O ratio 2:1
formula of a monosaccharide:
C6H12O6
4 examples of monosaccharide:
alpha glucose
beta glucose
galactose
fructose
how to draw alpha glucose:
penguin - both OH groups down
how to draw beta glucose:
eqyptian
left OH down, right OH up
formula of disaccharide:
C12H122O11
bond formed between disaccharides:
glycosidic bond
how do you form maltose?
and where is it found?
alpha glucose + alpha glucose
found in germinating seeds
how do you form lactose?
and where is it found?
alpha glucose + galactose
found in milk of lactating mammals
how do you form sucrose?
and where is it found?
alpha glucose + fructose
transported in phloem of plants
after digestion of polysaccharides and disaccharides into monosaccharides, what happens?
it is absorbed and used in the body,
e.g respiratory substances during respiration or used to make components or cell membrane
2 types of polysaccharides molecules:
storage or structural
what is the storage molecule in humans?
glycogen
what is the storage molecules in plants?
starch
what is the structural molecules in plants?
cellulose
what is an isomer?
molecules with the same molecular formula but have different arrangement of atoms
starch amylose:
structure and function:
carbon 1:4 glycosidic bond so long linear chains of alpha glucose which coils into a helix,
compact so good for storage,
insoluble so doesn’t affect water potential,
large so doesn’t leave/diffuse out of cell
how do plant cells store glucose?
as starch
(made up of 2 polysaccharides called amylose and amylopectin)
starch amylopectin:
structure and function:
carbon 1:4 and 1:6 glycosidic bonds,
branched chains of alpha glucose with many terminal ends,
so large surface area for rapid hydrolysis by enzymes to release glucose to be used in respiration,
insoluble so doesn’t affect water potential,
large so doesn’t leave/diffuse out of cell
where is glycogen stored?
in liver and muscle cells
glycogen:
structure and function:
long branched chains of alpha glucose,
bonded by carbon 1:4 and 1:6 glycosidic bonds,
more shorter chains, so more highly branched and large surface area,
for rapid hydrolysis by enzymes to release glucose to be used in respiration,
insoluble so doesn’t affect water potential,
large so doesn’t leave/diffuse out of cell
how do animals store excess glucose?
as glycogen
cellulose:
long striaght unbranched chains of beta glucose,
joined together by many weak hydrogen bonds to form microfibrils,
provides rigidity/support/strength to cell wall
many weak hydrogen bonds provide strength in large numbers
every other beta glucose molecule is
rotated 180 degrees so the OH group is adjacent to each other on C1 and C4 to form 1:4 glycosidic bonds
examples of reducing sugars
alpha glucose,
beta glucose,
maltose,
lactose,
fructose,
galactose
examples of non-reducing sugars:
sucrose
what is the test for a reducing sugar
Benedict’s test
Benedict’s test for reducing sugar:
add equal volumes of Benedict’s reagent to sample,
heat to 95 degrees in an electric water bath,
red precipitate shows reducing sugar is present,
what is a precipitate?
solid suspended in solution
Benedict’s test for non-reducing sugar:
complete Benedict’s test and observe a negative result (blue),
add HCl to sugar solution and heat to 95 degrees in an electric water bath to hydrolyse glycosidic bonds,
then neutralise with alkali (sodium hydrogen carbonate),
add equal volumes of Benedict’s reagent and heat to 95 degrees,
red precipitate shows non-reducing sugar is present
what type is the Benedict’s test?
semi-quantitative test
range of colours but no conc of sugars
what type is a colorimeter?
quantitative test
increasing conc of sugars will produce increasing mass of precipitates
how to make Benedict’s test quantitative?
filter, dry and weight precipitate
how does a colorimeter work?
measures the intensity of light transmitted through a solution,
increased precipitate = reduced transmission
absorbance and transmission are indirectly proportional
how to calibrate a colorimeter?
add distilled water and set absorption to 0
rules for using a colorimeter:
samples should always be shaken before tested,
zero the colorimeter before use,
use same absorbance/transmission filter,
use same volume for reducing
test for starch:
add potassium iodide to sample,
turns from orange to blue/black shows starch is present
describe how to use a calibration curve to find concentration of an unknown solution
make upseveral known concentrations of a reducing sugar,
carry out benedict’s test on each one,
use a colorimeter to measure the absorbance/transmission of each one,
plot curve of absorbance on y axis, known conc. on X
read off from absorbance of unknown conc. Using curve
two types of lipids:
triglyceride and phospholipid
what is a lipid?
a macromolecule
how is triglycerides formed?
condensation reaction of one molecule of glycerol and three molecules of fatty acids
joined by 3 ester bonds
and loss of 3 water molecules
what is triglyceride used primarily as?
a storage molecule
the whole molecule of a triglyceride is..
hydrophobic
saturated fatty acids:
melting point and state at room temp?
no double bonds between carbon atoms within hydrocarbon chains,
high MP and solid at room temp
straight chain molecules with many contact points
saturated fatty acids are found in
animal fats
unsaturated fatty acids:
melting point and state at room temp?
double bonds between carbon atoms within hydrocarbon chains,
low MP and liquid at room temp
kinked molecules with fewer contact points
unsaturated fatty acids are found in
plant oils
what are phospholipids used for?
primary component of all membranes
what are phospholipids made from?
condensation reaction between one molecule of glycerol, one molecule of phosphate and 2 fatty acid molecules
what is the charge of phosphate group?
negative charge (polar)
what is the charge of fatty acids?
no charge (non-polar)
phospholipid heads
hydrophilic,
are water facing,
in contact with water on both sides
attracts water - soluble
fatty acid tails:
hydrophobic,
face inwards away from water
repels water - insoluble
properties of phospholipids:
form bilayer in cell membrane
form a double layer with heads
membrane acts as barrier
allowing diffusion of non polar/ small molecules
centre of bilayer is hydrophobic so water soluble substances cannot easily pass through
tails = waterproofing
properties of triglycerides:
low energy to mass ratio so good energy store,
insoluble in water so doesn’t affect water potential,
slow conductor of heat, so thermal insulator,
less dense than water,
high H:O ratio so good source of water,
hydrocarbon chain contains a lot of chemical energy, which is released when broken down,
protects organs by storing around them
emulsion test for lipids:
crush/grind sample
add ethanol and shake
then add water and shake
cloudy white emulsion shows lipid is present
what is the bond and monomer of proteins?
peptide bond,
amino acids
what groups does the amino acid contain?
amine group,
variable side chain,
carboxyl group
R groups can be
positive
negative
hydrophilic
hydrophobic
primary structure of protein:
number and sequence of amino acids in a polypeptide chain
only peptide bonds
secondary structure of protein:
coiling/folding of polypeptide chains due to weak hydrogen bonds into alpha helixes and beta pleated sheets,
only bond between O atoms on carboxyl group and H atoms on amine group,
weak hydrogen bonds provide strength in large numbers
tertiary structure of protein:
further folding of polypeptide chain into specific 3D complex shape held together by ionic bonds, disulphide bridges and weak hydrogen bonds
ionic bonds
disulphide bridges
weak hydrogen bonds
ionic bonds between oppositely charged R groups,
disulphide bridges between S atoms on cysteine amino acids
weak hydrogen atoms between H and O
quaternary structure of protein:
two or more polypeptide chains joined together
haemoglobin - 4 polypeptide chain, globular, spherical chain, functional proteins
collagen - 3 polypeptide chain, fibrous, rope like strands twisted, structural proteins
dipeptides:
condensation of two or more amino acids, with removal of molecule of water and formation of peptide bond
polypeptides:
condensation of 3 or more amino acids
protein:
increasing the temperature
increases the kinetic energy of the molecules making them vibrate more, this breaks the weak hydrogen bonds in secondary and tertiary structure
protein:
changing the pH of environment
breaks ionic bonds between R groups in the tertiary structure
as bonds break, specific tertiary structure is lost
= denaturation - permanent change
biuret test for protein:
add equal volumes of biuret solution to sample in test tubes,
if protein is present, changes from blue to purple
(enzymes are proteins = positive result)
function of DNA:
holds genetic information in all living organisms cells
structure of DNA:
phosphate group attached to carbon 5 of
deoxyribose sugar
nitogrenous organic base
adenine, thymine, guanine, cytosine
double helix structure with 2 polynucleotide chains joined together by many weak hydrogen bonds between complementary base pairings
function of RNA:
transfers genetic information from DNA to the ribosome where translation occurs to make protein
structure of RNA:
phosphate group attached to carbon 5 of
ribose sugar
nitogrenous organic base
adenine, uracil, guanine, cytosine
nucleotide forms a single strand
shorter than most DNA polynucleotide chains
polynucleotide:
3 or more identical/similar nucleotides by covalent bonds to form a larger polymer/polynucleotide chain by condensation reactions
forms a phosphodiester bond between the phosphate group of the nucleotide to the 3rd carbon of the next nucleotide
there is a covalent bond and makes sugar phosphate backbone of nucleic acid very strong and stable
what are purines
adenine and guanine
what are pyrimadines
thymine cytosine and uracil
dna consists of 2 anti parallel strands:
each end of the molecule is labelled with a 3’ end and a 5’end indicating when carbon is involved in phosphodiester bond
on the complementary strand, top is 3’end and bottom is 5’end
DNA polymerase only has a complimentary end to the
5’end of the molecule
process of semi conservative replication:
DNA helicase attaches and moves along the DNA molecule,
unwinding the DNA and breaking hydrogen bonds between complementary bases,
the strands separate - each strand acts as a template,
DNA polymers joins adjacent nucleotides via condensation reactions forming phosphodiester bonds in a 5’ end to 3’ end direction,
the new DNA molecule contains an original and new strand that is identical to original strand
adaptations of DNA:
long/large molecule
stores a lot of information
adaptations of DNA:
helical/coiled structure
so compact
adaptations of DNA:
base sequence
allows info to be stored
codes amino acids and therefore proteins
adaptations of DNA:
double stranded
replication can only occur semi conservatively,
as each strand acts as a template
adaptations of DNA:
hydrogen bonds between bases are weak
allows for easy strand separation for semi conservative replication
adaptations of DNA:
many weak hydrogen bonds
so DNA is a strong/stable molecule
adaptations of DNA:
sugar phosphate backbone and double helix
provides strength and stability,
protects the bases,
protects the hydrogen bonds in between bases
adaptations of DNA:
complimentary base pairings
allows for accurate replication/identical copies are made
ATP - adenine triphosphate
3 phosphate groups
ribose sugar
nitrogenous organic base adenine
2 uses of ATP:
provides energy for active transport/muscle contraction/protein synthesis
- phosphorylation of molecules to lower activation energy, make substrate more reactive, activates enzymes by altering tertiary structure
why is ATP useful?
releases relatively small amounts of energy,
releases energy instantaneously,
phosphorlaytes other compounds making them more reactive,
can be rapidly resynthesised,
is not lost from/does not leave cell
ATP condensation ADP + Pi -> ATP
catalysed by ATP synthase,
produces H2O
requires energy to add Pi to ADP creating a high energy bonds
(occurs during photosynthesis and respiration)
ATP hydrolysis ATP -> ADP + Pi
catalysed by ATP hydrolase
requires H2O
bond between 2nd and 3rd Pi breaks releasing small manageable energy
water as a solvent:
polar molecules dissolve in solvent = universal solvent
major component of cytoplasm as it allows chemical and enzymes to dissolve so chemical reactions can occur,
can dissolve other substances like gases urea ammonia
water
high specific heat capacity
requires a lot of heat energy to heat because of hydrogen bonds,
higher heat capacity in water than air = more energy required to heat water than air,
habitats in H2O resist fluctuations in temp,
so organisms enzymes always have optimum temp to work,
organisms mainly made of water so can maintain a consistent body temp,
water
latent heat of vapourisarion
takes a lot of heat energy to break H bonds,
lots of body heat required to evaporate all amounts of sweat = lowers body temp
water as metabolite
water is used and produced in many chemical reactions,
hydrolysis reaction and photosynthesis reactions use water,
condensation reaction and respiration reactions produce water,
chemical reactions take place in aqueous medium
and enzymes and substrates dissolve so can react
water
cohesion and surface tension:
water molecules stick together by weak bonds = cohesion,
provides surface tension at an air water surface so small organisms can be supported,
allows water to be pulled up narrow tubes - xylem
other properties of water:
when water freezes, it becomes less dense,
ice forms habitats for animals,
insulates the water below and stops freezing,
not easily compressed so provide support in plants, hydro skeleton in worms
light can penetrate through in plants underwater so plants can photosynthesise
where are inorganic ions found?
in extracellular fluid and in cytoplasm
function of H+ ions and OH- ions
affects acidity of solution
H+ used in respiration to provide energy to make ATP
H+ used in photosynthesis to provide energy to make ATP
function of Fe2+/Fe3+
structural component of Hb
to allow transport of O2 to respiring tissues
function of sodium ions:
used in co transport of glucose and amino acids from lumen of small intestine into intestinal epithelial cell
also used in nervous conduction
function of phosphate ions:
component of phospholipid, ATP, DNA, RNA
function of nitrates NO3 -
and nitrites NO2 -
taken up plant roots from soil
used in making amino acids
function of chloride:
used in regulating water potential in small intestine
what are enzymes?
globular proteins soluble - act as biological catalysts
which increase rate of reaction but remain unchanged (not used up)
how do enzymes increase rate of reaction?
(products can only form when all bonds are broken which required activation energy)
by lowering activation needed for reaction
stresses/distorts/weakens bonds in substrate when forming an enzyme substrate complex
- allows reaction to work at lower temp
enzyme have a
specific tertiary structure which is specifically complementary shaped active site to substrate
which allows substrate to bind and form enzyme substrate complex
lock and key model:
active site is rigid and doesn’t change shape,
substrate binds to active site,
substrate fits exactly into active site - they are complementary,
products are formed and no longer fit in active site so are released,
enzymes free to take part in another reaction
induced fit model:
substrate enters enzyme active site and binds to form enzyme substrate complexes,
binding of substrate induced a change in shape of active site,
change in shape of specific 3D structure stresses/distorts bonds within substrate molecules
which lowers activation energy of reaction,
when substrate leaves, active site returns to original shape
effect of temperature on enzymes:
at optimum temp:
optimum temperature increases KE of enzyme and substrate = more likely to collide successfully = rate of reaction increases = more enzyme substrate complexes form per second
effect of temperature on enzymes:
above optimum temp:
above temp = atoms vibrate faster within amino acid structure of enzyme = more KE = weak hydrogen bonds and ionic bonds between R groups of amino acids to break = change in specific tertiary structure = change in active site = denatured as no longer complimentary and cannot catalyse anymore reactions
effect of pH on enzymes:
change from optimum =
change on thr charge on R groups of amino acids and ionic bond in tertiary broken = active site changes shape
= substrate can no longer fit
= less/no enzyme substrate complexes formed and rare of reaction decreases
= denatured enzymes
describe and explain the effect of substrate concentration on enzyme action:
as substrate conc increases, the rate of reaction increases then plateaus
when substrate conc is low, the rate of reaction is low as there is less collisions = fewer enzyme substrate complexes form per second, substrate is limiting factor
the rate of reaction shows no further increase even when the substrate conc increases as the enzyme active sites are all saturated, enzyme conc is now limiting factor
effect of enzyme concentration on enzyme action:
LOW ENZYME CONC:
too few enzyme molecules to allow all substrate molecules to find an active site at one time,
all enzyme active sites are saturated,
enzyme conc is limiting factor,
MEDIUM ENZYME CONC:
twice as many enzyme molecules available,
twice as many ESC can form per second,
enzyme conc is limiting factor,
HIGH ENZYME CONC:
addition of further enzyme molecules has no effect on as there are already enough active sites for all available substrate conc,
no increase in rate of reaction,
all substrate has been converted to product
process of product formation:
- initial rate of reaction is high, because lot of substrate molecules,
soa lot of enzyme substrate complexes can form, therefore a lot of product formed (initially) - rate of product formation plateaus
because no substrate is left for reaction so fewer ESC form
what is an inhibitor?
substances which decrease the rate of reaction
how does a competitive inhibitor work?
- similar structure to substrates,
- bind to active site and prevent substrate from binding temporarily,
- fewer enzyme substrate complexes form per second
- reduce rate of reaction so fewer products are formed per second,
- longer for all substrates to eventually form products
how does a non-competitive inhibitor work?
- bind to a site on enzyme away from active site - allosteric site,
- causes a conformational change to shape of active site so substrate cannot bind,
- binding can be temporary or permanent,
- if detached from one enzyme it is free to bind to another enzyme,
- fewer enzyme substrate complexes formed-> rare of reaction decreases
so fewer product formed.
same effect as reducing total no. of enzymes
