3.1 Biological Molecules Flashcards
What reaction occurs between two monosaccharides and what molecule is formed?
A condensation reaction occurs and a disaccharide is formed.
What bond is a disaccharide formed through?
A disaccharide is formed through the formation of a glycosidic bond.
What molecule is eliminated in a condensation reaction?
A water molecule.
What is formed if condensation reactions continue to occur?
A long chain called a Polysaccharide which is held together by glycosidic bonds.
What is a Nucleotide and a monomer?
A Nucleotide is a monomer of Deoxyribonucleic acid (DNA), and monomers are the smaller units from which larger molecules are made.
What is formed when two amino acids join together?
What is formed when two monosaccharides join together?
Dipeptide is formed over two amino acids. Disaccharide is formed over two monosaccharides.
What are three examples of monomers?
Nucleotides, Amino Acids and Monosaccharides.
What are polymers?
Molecules made from a large number of monomers joined together.
What is a hydrolysis reaction?
When a chemical bond is broken between two molecules, this involves the use of a molecule of water.
What are the 3 things carbohydrates act as?
Sources of energy, stores of energy & structural units.
What is the ration in which monosaccharides contain carbon, hydrogen, and oxygen?
CnH2nOn
What type of sugar is alpha & beta glucose, and fructose?
They are all hexose sugars.
What type of sugar is B-galactose, deoxyribose and ribose?
Hexose, Pentose, and Pentose.
What is the molecular formula of alpha and beta glucose, and fructose?
C6H12O6
What is the molecular formula of B-galactose, deoxyribose and ribose?
B- C6H12O6
D- C5H4O4
R- C5H10O5
What is the role in the body of alpha and beta glucose?
Alpha is an energy source and component of starch/glycogen.
Beta is also an energy source but a component of cellulose.
What does fructose and beta galactose bond with to form?
Fructose is bonded with glucose to form sucrose.
B-galactose bonds with glucose to form lactose.
What is the role in the body of deoxyribose and ribose?
D- component of DNA.
R- component of ribonucleic acid, ATP and NAD.
What are isomers?
Two or more molecules with the same molecular formula but who differ structurally. (eg beta and alpha glucose.)
What is the difference in structure of beta and alpha glucose?
Beta has hydroxide in the bottom of the structure.
How is maltose made?
Two alpha glucose joined together.
What does A, C, T and G stand for?
Adenine, thymine, cytosine, and guanine.
What is RNA known as?
A polysaccharide.
Why is ribose essential for an athlete to run?
Energy in the form of ATP is needed to contract skeletal muscles to move the bones of the legs and arms.
What is maltose made of?
alpha and alpha glucose.
What is sucrose made of?
alpha glucose and fructose.
what is lactose made of?
beta galactose and alpha glucose.
What are the 3 disaccharides?
lactose, sucrose and maltose.
What are 3 monosaccharides?
glucose, fructose and galactose.
What are 3 polysaccharides?
glycogen, starch and cellulose.
Which polysaccharides are made of alpha glucose monomers?
Glycogen, amylose & amylopectin.
Which polysaccharide is made of beta glucose monomers?
Cellulose.
Which polysaccharides are branched?
Glycogen and amylopectin.
Which polysaccharides are unbranched?
Amylose and cellulose.
Which polysaccharides have 1-6 glycosidic bonds?
Glycogen and Amylopectin, amylase and cellulose do not.
Which polysaccharide isn’t compact?
Cellulose.
Which polysaccharide doesn’t have a spiralled shape?
Cellulose.
Why is a branched polysaccharide (glycogen) easier to break down?
It has many more ends so it is easier to remove glucose monomers by hydrolysis reactions when they are needed for respiration.
Why is starch branched?
70-80% of it is made up of amylopectin which is branched.
Why is a quantitative test better than qualitative?
because it tells us how much of the substance is present instead of just whether or not it is.
What is the ionic equation for the test for reducing sugar?
Cu2+ + e- = Cu+
What is a reducing sugar able to do?
To reduce or give electrons to other molecules.
What do lipids contain? (C,H,O)
Large amounts of carbon & hydrogen and smaller amounts of oxygen.
What are some properties of carbohydrates?
Like monosaccharides they’re polar and so attract water molecules which means they’re soluble in water.
Are lipids polar?
Non polar so they don’t attract water molecules meaning they are insoluble in water.
What are lipids soluble in?
Alcohol.
What is glycerol?
a 3 carbon molecule with an OH group bonded to each of the 3 carbons.
Why do micro & macro fibrils have high tensile strength?
The glycosidic and hydrogen bonds
Are carbohydrates polar?
Yes.
Carbohydrates can form…
polymers.
Are lipids polar and can they form polymers?
No.
What is an ester bond?
a covalent bond which is formed between a fatty acid with glycerol during a condensation reaction.
What does hydrolysis of a triglyceride produce?
glycerol & three fatty acids
When is the bond saturated?
If the chain has no C-C double bonds.
Monounsaturated?
if there’s a single double carbon bond.
Polyunsaturated?
More than one double carbon bond.
Why are triglycerides an excellent source of energy?
High ratio of energy storing carbon-hydrogen bonds to carbon atoms.
Why doesn’t triglyceride storage affect osmosis in cells or the water potential of them?
They are large non polar molecules and insoluble in water .
How do TG provide a source of water?
When they are oxidised becuase they have a high ratio of hydrogen to oxygen atoms.
What two parts does a phospholipid consist of?
A hydrophilic head,
A hydrophobic tail.
What happens when polar phospholipid molecules are placed in water?
The hydrophilic heads are as close to the water as possible and the hydrophobic tails are as far away from the water as possible.
What is the hydrophilic head made of?
Phosphate.
What is the hydrophobic tail made of?
Two fatty acids.
What happens in an aqueous environment with a phospholipid?
A bilayer forms within a cell surface membrane.
What does the phospholipid structure allow them to form?
Glycolipids by combining with carbohydrates within the cell surface membrane.
What does the R group of an unsaturated fatty acid contain?
at least one double bond between two of the C atoms.
What does a double bond mean?
Fewer hydrogen atoms can be bonded to the molecule.
Why does a triglyceride have lower melting points with more double bonds?
Kinks push the molecules apart slightly which makes the fatty acid more fluid so it has a lower melting point.
What is a gene?
A sequence of bases on DNA molecules that codes for a sequence of amino acids in a polypeptide chain.
How many possible DNA triplets are there?
- 4 cubed.
Why will different bonds form between the side chains in the secondary and tertiary structure of a protein?
R groups of different amino acids will vary in size, charge and polarity.
What elements do amino acids contain?
Carbon, Hydrogen, Nitrogen, Oxygen and Sulphur.
Which amino acid is the only one that holds sulphur in the R group?
Cysteine.
Where do disulphide bridges form?
Between the R groups of cysteine, the same polypeptide chains and adjacent ones.
What bond formed between two amino acids in a CR and what is formed?
Peptide bond, a dipeptide.
What is the primary structure?
A specific sequence of amino acids in a polypeptide chain?
What is the start codon?
AUG.
What does order of the aminos in the primary structure determine?
The shape of the protein molecule through its secondary, tertiary and quaternary structures.
When is the secondary structure formed?
When the chain of aminos coils or folds to form either an alpha helix or a beta pleated sheet.
What holds the coils/folds in place?
Hydrogen bonds.
When is the tertiary structure formed?
When coils/pleats start to fold.
Why will the primary structure of the resulting polypeptide chain be different?
because each gene has a unique base sequence.
What is homogenisation in simple terms?
Breaking up the cells.
Filtration is simply….
getting rid of the big bits
Ultracentrifugation separates the…
organelles.
What 4 key points occur in homogenation?
(Cells mixed with, must be, solution needs to be, use a…)
1) Cells are mixed with a solution.
2) Cells must be ice cold to reduce the amount of enzyme activity which destroys organelles.
3) The solution must be isotonic and have the same concentration as cells because this prevents damage to the organelles through osmosis.
4) Use a buffer solution to maintain correct pH.
What is the result of homogenisation?
Homogenate.
What occurs in filtration?
1) The homogenate solution is passed through a gauze to separate the large cell debris from the organelles.
What is the new filtered solution called?
Supernatant.
What happens in ultracentrifugation?
1) The SN is poured into the tube, put into a centrifuge machine which then spins slowly. Heavy nuclei is flung to the bottom. They form a pellet at the bottom and the rest of the organelles stay in the SN.
2) SN is poured into another tube and centrifuged at a higher speed and the next heaviest organelle goes to the bottom. SN drained off.
3) Process is repeated until all the organisms are separated, each stage has lighter and lighter organelles.
What is the usual order of organelles separated in ultracentrifugation?
Nuclei, chloroplasts, MC, LS, ER and finally ribosomes.
What does the fluid mosaic model suggest?
Bilayer formed of a continuous double layer of PSL.
Why are phospholipids considered fluid?
because they’re constantly moving.
What can pass through the bilayer?
small non polar molecules through the hydrophilic tails. lipid soluble can but water soluble can’t.
What are glycoproteins?
Glycolipids?
Receptor proteins?
proteins with a carbohydrate attached.
lipids with a carbohydrate attached to them.
proteins on the CSM that detect chemicals released from other cells.
What is ATP consisted of?
a pentose sugar (ribose), a nitrogenous organic base (adenosine) and three inorganic phosphate groups.
How does the structure of ATP make it a good source of immediate energy?
The bonds between the phosphate groups have a low activation energy so they can be easily broken. energy is released when bonds are broken.
What is a condensation reaction?
A reaction when monomers combine together by covalent bonds and a molecule of water is removed
describe the structure of starch
chains of alpha glucose monosaccharides linked by glycosidic bonds via condensation reactions
explain how the structure of starch is related to its function
insoluble so it doesn’t affect the plants water potential
large AND insoluble so it cannot diffuse out of the cell
compact so lots is stored in a small space
upon hydrolysis into alpha glucose, it is easily transported and used in respiration
it is branched so has numerous ends, which can be acted on by many enzymes so glucose is released rapidly
describe the structure of glycogen
chains of alpha glucose monosaccharides which is shorter and more branched than starch
explain how the structure of glycogen is related to its function
insoluble so it doesn’t affect water potential
also means it doesn’t diffuse out of cells
compact so lots can be stored in a small space
branched so glucose is released quickly to support the metabolism
describe the structure of cellulose
beta glucose monomers make up straight unbranched chains which are parallel to each other, every other monomer is flipped by 180 degrees
explain how the structure of cellulose is related to its function
the unbranched straight chains form micro and then macro fibrils thanks to the hydrogen bonds, making it strong and rigid to support the cell wall
what is the central carbon atom in an amino acid attached to
an amino group, a carboxyl group, H atom and the R group
where is the water molecule lost in the condensation reaction to form a dipeptide made from
the OH group of the carboxyl and the H atom from the amino group of another
what is the primary structure of a protein
the sequence of amino acids in a polypeptide chain
what is the secondary structure
the coiling or folding of a polypeptide chain into either a beta pleated sheet or an alpha helix
what is the tertiary structure
the specific 3D structure of a protein due to the secondary structure folding once again
what is the tertiary structure maintained by
strong disulphide bridges, ionic bonds which are slightly weaker and Hydrogen bonds which are only strong in mass
what is the quaternary structure
when more than one polypeptide chains link
what are the roles of lipids
to act as a source of energy
waterproofing
insulation
protection
fats vs oils
fats have saturated fatty acids while oils have unsaturated acids, fats are solid at RT but oils are liquid
describe the structure of a triglyceride
3 fatty acids combined with one molecule of glycerol, each acid forms an ester bond with the glycerol molecule via a condensation reaction
explain how the structure of a triglycerides is related to its property
there is a high ratio of C-H bonds to C atoms so good energy source
low mass to energy ratio so lots of energy can be stored in a small volume
they are large and non polar so are insoluble in water which means it doesn’t affect water potential or cause osmosis
high ratio of hydrogen to oxygen atoms so it is an important water source when oxidised
describe the structure of a phospholipid
two fatty acids which are hydrophobic attached to a molecule of glycerol with a phosphate group which is hydrophilic
explain how the structure of a phospholipid is related to its properties
in aqueous environments, they form bilayer within cell surface membranes to form a hydrophobic barrier between the inside and outside of a cell
their structure allows them to form glycolipids by combining with carbohydrates in the CSM
their hydrophilic phosphate heads help to hold the surface of the CSM
compare the structure of a triglyceride to a phospholipid
a phospholipid has two fatty acids but a triglyceride has three
phospholipids have a phosphate group attached to the glycerol molecule but triglycerides do not
both of them are formed from 4 molecules
describe the induced fit model
when a substrate binds to an active site, the site alters shape to fit it more suitably. the enzyme places a strain on the substrate which distorts a bond and lowers the activation energy needed
describe the lock and key model
a substrate will only fit the active site of one particular enzyme
compare the lock and key vs induced fit
lock and key suggest the active site is rigid and only able to bond to the substrate that exactly fits but the induced fit suggest it is more flexible and is complementary to the substrate after the substrate is bound
explain the effect of temperature on enzyme action
an increase in temperature increase the kinetic energy of the molecules. they move around more rapidly and collide more often. this increases the number of effective collisions so the number of enzyme substrate complexes increase which increases rate
describe the graph of the effect of temperature on enzyme action
begins as a rising curve due to the rate increasing, the gradient shallows as H bonds begin to break which changes shape and reduced the number of complexes that can form, then the curve falls as the enzyme is dénaturée because it is so disrupted the substrate no longer fits
explain the effect of pH on enzymes
a change in pH alters the amino acid charges in the active site so the substrate can no longer bind so no E-S complexes can form.
the change may also cause bonds in the tertiary structure to break so the active site changes shape
explain the effect of enzyme concentration on rate of reaction
at low enzyme concentration, there are too few enzymes for all the substrates to find an active site at one time. At intermediate enzyme concentration, all substrate molecules can occupy an active site, so the rate is at maximum as all active sites are filled. at high enzyme concentration, there is no affect as all available substrates have already bound to active sites, substrates are the limiting factor.
explain the effect of substrate concentration on the rate of reaction
at a low substrate concentration, there are too few substrate to act occupy all the active sites. At a higher substrate concentration, all available active sites can be occupied at one time, so the rate reaches maximum. At high substrate concentration, all active sites have already been occupied so there is no affect as there are none available.
describe the features of a competitive inhibitor
they have a similar shape to the substrate
compete for available active sites
if the substrate concentration is increased, the effect of an inhibitor is decreased
describe the features of a non competitive inhibitor
attaches to the allosteric site and alters the shape of the enzyme so the substrate cannot occupy the active site and no E-S complexes can be formed
an increase in substrate concentration does not decrease the effect of inhibitors as they aren’t competing for the same site
what is a phosphodiester bond
the bond between the deoxyribose sugar of one mono nucleotide and the phosphate group of another
describe the base pairs
adenine pairs with thymine or uracil
guanine pairs with cytosine
why is DNA a relatively stable molecule
the phosphodiester backbone protects the more chemically reactive bases inside the double helix
how is DNA adapted to its function
two strands are only joined by weak hydrogen bonds which allow them to separate during replication
they are large so they can hold lots of genetic information
what is the 5 and 3 carbon atom attached to
the 5’C attached to the phosphate group and the 3’C attached to the hydroxyl group
why can nucleic acids only be synthesised in the 5’-3’ direction?
DNA polymerase can only attach nucleotides to the hydroxyl group on the 3’C
what are the 4 things needed for semi conservative replication
the 4 types of nucleotides and their complementary bases present
both strands of DNA to act as a template for nucleotide attachment
DNA polymerase
a source of chemical energy
describe the steps of semi conservative replication
DNA helicase breaks the hydrogen bonds linking base pairs of DNA
The double helix separates into two strands and unwinds
Free nucleotides bind to exposed bases via complementary base pairing
DNA polymerase joins nucleotides together via a condensation reaction
describe the bonds between the phosphate groups on ATP
they are very unstable so there is a low activation energy and the bonds are easily broken
what is the equation for the hydrolysis of ATP
ATP + H2O ——> ADP + Pi + E
what is hydrolysis of ATP catalysed by
ATP hydrolase
in which organisms is an inorganic phosphate added to ADP to reform ATP
in chlorophyll containing plant cells during photosynthesis
in plant or animals cells during respiration
in “ when phosphate groups are transferred from donor molecules to ADP
why is ATP a better immediate energy source than glucose
each ATP molecule releases less energy than each glucose so energy is released in much smaller, more manageable quantities
the hydrolysis of ATP to ADP is a single reaction which releases immediate energy but the breakdown of glucose is a long series of reactions so the energy release is longer
what is ATP used in
metabolic processes, movement, AT, secretion (to form lysosomes) and activation of molecules (Pi released can phosphorylate other compounds to make them more reactive which decreases the activation energy in enzyme catalysed reactions.)
why is water dipolar
the oxygen has a slight negative charge and the hydrogen atoms have a slight positive charge
where do hydrogen bonds form
between the positive pole of one water molecule and the negative of another
explain the specific heat capacity of water
due to its hydrogen bonding, water molecules stick together so it takes more energy to separate them. this causes a higher boiling point than expected so it also takes more energy to heat a given mass of water. this also means a higher specific hear capacity.
what does water act as
a buffer to sudden temperature changes which helps to keep aquatic environments stable and organisms stable
describe the latent heat of vaporisation of water
its hydrogen bonding means lots of energy is required to evaporate 1g of water
the energy from body heat is used to evaporate water so it causes an effective means of cooling
explain the cohesion/surface tension of water
the cohesion (tendency to stick together) is a large force and allows water to be pulled up through a tube.
the surface tension (where water meets air the molecules are pulled back into the body of water instead of trying to escape it) means water acts like a skin and is strong enough to support small organisms
what are two other properties of water
it is not easily compressed so provides support for organisms
it is transparent so aquatic plants can photosynthesis and light rays can reach the retina
describe the test for reducing sugars
add 2cm3 of a food sample to a test tube
add equal volume of benedict’s reagent
heat in a gently boiling water bath for 5 minutes
if a reducing sugar is present it will turn orange brown
explain how the reducing sugar test works
the sugar reduces soluble alkaline copper II sulphate to insoluble brick red copper I oxide precipitate
describe the test for non reducing sugars
add 2cm3 of a food sample in liquid form to 2cm3 of benedict’s reagent to a test tube
place in a water bath for 5 minutes and if there’s no colour change it means there is no reducing sugar present
add another 2cm3 to the same volume of dilute HCl and place in a water bath for 5 minutes
slowly add sodium hydrogen carbonate to neutralise HCl
test with pH to check it is alkaline
re test by heating with 2cm of benedict’s reagent and it will turn orange brown due to the reducing sugars produced by hydrolysis
explain the test for non reducing sugars
the HCl is used as it hydrolyses disaccharides into monosaccharides, sodium hydrogen carbonate needed to neutralise the acid because benedict’s reagent doesn’t work in acidic conditions
describe the test for starch
mix a 2cm3 food sample with 2 drops of iodine solution
shake the tube and if a blue black colouration occurs it shows the presence of starch
describe the test for lipids
add ethanol to a sample and mix with water, if lipids are present then a white milky emulsion forms
describe the test for proteins
put the sample in a test tube and add equal volume of sodium hydroxide at room temperature
add a few drops of very dilute (0.05%) copper II sulphate solution and mix.
if there are no proteins present, the solution stays blue, and purple if present.
Describe the optimum temperature
The temperature at which an enzyme works best and therefore the temperature at which a reaction involving that enzyme will occur at its’ maximum rate.
how is the tertiary structure affected when temperature is raised above optimum
The precise 3D shape of a protein held in place by bonds between the amino acid will be disrupted by the vigorous vibrations.
What is the issue of increasing the temperature above the optimum
Causes the enzyme molecules to vibrate more vigorously which starts to disrupt the structure of the protein.
which bases are purine and pyrimidine
adenine and guanine are purine, thymine, cytosine and uracil are pyrimidine.
describe the structure of purine and pyrimidine bases
purine bases have a double ring structure but pyrimidine have a single ring structure.
how many hydrogen bonds are formed between adenine and thymine, guanine and cytosine?
A-T = 2
C-G = 3
what shape is a DNA molecule
a double helix with two polynucleotide chains held together by hydrogen bonds between specific complementary base pairs.
what is the lagging strand
as the dna polymerase enzyme can’t move continuously, it has to repeatedly stop and start again, synthesising short fragments (okazaki) later joined by DNA ligase
what are the 4 activated or phosphorylated deoxyribonucleotides?
atp, ctp, ttp, gtp
why is the leading strand continuously replicated
it is synthesised in the same direction as the growing replication fork.
