topic 1 - biological molecules Flashcards
monomers
smaller units from which larger molecules are made
polymers
molecules made from a large number of monomers joined together in a chain
how many bonds can each carbon atom form?
4 covalent bonds
the molecules of life all contain….
carbon, hydrogen and oxygen
carbohydrates, lipids, proteins & nucleic acids are…
the four main groups of carbon-based molecules that are common to all life forms
carbohydrates: uses
-respiratory substrates
-energy for cells
-structure
lipids: uses
-respiratory substrates
-form bilayer
-sometimes make up hormones
proteins: uses
-main component of many cellular structures
-form enzymes and chemical messengers
nucleic acids: uses
-form polymers (DNA and RNA) which make up the genetic material of organisms
-they code for the sequence of amino acids which make up all proteins
how many amino acids build up protein
20
condensation reaction
joins two monomers together with a covalent bond and produces a water molecule
hydrolysis
breaks the covalent bond between two monomers and involves the use of a water molecule
what elements are common to all the molecules of life?
carbon, hydrogen, nitrogen, oxygen, phosphorous, sulfate
which molecule forms part of the plasma membrane?
phospholipids
what are monosaccharides?
individual sugar molecules (monomers) that make up disaccharides and polysaccharides
hexose sugar
A sugar made up of 6 carbons.
pentose sugar
a sugar made up of 5 carbons
how many isomers can glucose form?
two:
a-glucose
b-glucose
difference between structure of alpha and beta glucose:
alpha:
h over oh
beta:
oh over h
how are disaccharides formed?
formed when two monosaccharides join through a condensation reaction forming a glycosidic bond between the two OH groups
glucose + glucose
maltose (reducing)
glucose + galactose
lactose (reducing)
glucose + fructose
sucrose (non reducing)
when is a polysaccharide formed?
when more than two monosaccharides are joined together by condensation reaction
what is starch made from?
the monosaccharide alpha glucose
structure of starch:
mixture of two polysaccharides: amylose and amylopectin
structure of amylose
-long unbranched forms
-coiled
-1-4 glycosidic bonds
structure of amylopectin
long branched chain due to 1-6 glycosidic bonds
properties of amylose
coiling makes it compact and stores more in a smaller space
properties of amylopectin
branches increase surface area for enzymes to hydrolyse glycosidic bonds allowing glucose to be released quickly
uses of starch:
plants → starch to store excess glucose
-too large to leave cells and insoluble (doesn’t dissolve in water) so it doesn’t affect water potential)
-starch can be hydrolysed to release glucose for respiration
monosaccharide of glycogen
alpha glucose
structure of glycogen
-a long, branched chain with lots of side branches (more than amylopectin)
-1-6 glycosidic bonds
properties of glycogen
-lots of branches increase surface area for enzymes to hydrolyse glycosidic bonds allowing glucose to be released quickly
-compact molecule, good for storage
uses of glycogen
-animals store excess glucose as glycogen in muscles and in the liver.
-glycogen is an energy store as it can be hydrolysed to release glucose quickly when needed for respiration e.g during exercise
monosaccharide of cellulose
beta glucose
structure of cellulose
-long unbranched straight chains
-1-4 glycosidic bonds
-cellulose chains are linked together by hydrogen bonds between the glucose molecules in each chain to form thicker fires called microfibrils
properties of cellulose
-hydrogen bonds between the cellulose chains make the microfibrils very strong but still flexible allowing them to provide support
uses of cellulose
-major structural component in the cell walls of plants
-provides support and allows cells to become turgid
one way starch molecules are adapted for their function in plant cells
insoluble so that they don’t affect water potential
what is the group of carbohydrates?
hydroxyl
one advantage of storing starch rather than glucose in potato cells
plants use starch to store excess glucose, it’s insoluble, so potato cells save space and don’t affect water potential
most common disaccharides
maltose
lactose
fructose
where is maltose found?
in germinating seeds
where is lactose found?
in mammalian milk
where is fructose found?
used to transport sugar around plants
are lipids polymers?
no
which two types of lipids do we look at?
-triglycerides
-phospholipids
components of triglycerides
a glycerol molecule and three fatty acid chains
bonds of triglycerides
ester bond
properties of triglycerides
-the fatty acid chains are hydrophobic (repel water) which makes lipids insoluble in water
-they bundle together as insoluble droplets because the tails face inwards, and the glycerol heads shield them from the water
-the hydrocarbon fatty acid chains can be saturated or unsaturated
(triglycerides are entirely hydrophobic)
-non-polar, hydrophobic molecules
components of phospholipids
a glycerol molecule, a phosphate group and two fatty acid chains
bonds of phospholipids
ester bond
properties of phospholipids
-the phosphate group is hydrophilic (attracts water)
-the fatty acid chains are hydrophobic (repel water)
-this allows phospholipid to form bilayers which make up membranes in and around cells
saturated fatty acids
-don’t have any double bonds between their carbon atoms
-the fatty acid has all the hydrogens it can hold
unsaturated fatty acids
-have double bonds between carbon atoms which means they contain fewer hydrogen atoms
-the double bond also causes the chain to bend
-unsaturated fatty acid chains can contain one (mono) or many (poly) carbon double bonds
phospholipid bilayer
-phospholipid heads are hydrophilic and their tails are hydrophobic
-when placed in water they form a double layer with the heads facing outwards towards the water and their tails facing inwards away from the water
-the centre of the bilayer is therefore hydrophobic so water soluble substances cannot easily pass through
-this creates a barrier, allows separation of solutions and can create different conditions either side of the membrane
four roles of lipids
-hormones
-insulation
-energy reserve
-cushion vital organs
what are proteins?
polymers made up of monomers known as amino acids
components of amino acids:
amino group (H^2n)
carboxylic group (COOH)
variable group (R)
what is the only difference between each amino acid?
the variable R group/side chain
what happens when two amino acids join in a condensation reaction?
-a dipeptide forms
-a water molecule is produced
-the peptide bond forms between the amine group of one amino acid and the carboxyl group of the other
what is more than two amino acids joined together?
polypeptide
how can dipeptides and polypeptides be broken down?
hydrolysis
how many levels can … have?
single chain polypeptides
→
three (primary, secondary and tertiary)
primary structure (chain of amino acids)
-the number and sequence of amino acids in the polypeptide chain can determine the 3D shape or tertiary structure and can affect the shape of the active site in enzymes
secondary structure:
-hydrogen bonds form between amino acids in the chain, this causes it to coil into an a-helix or fold into a-pleated sheet
-the many hydrogen bonds make these structures stable
tertiary structure
the 3D shape of the polypeptide chain:
-creates a specific shape due to the sequence of amino acids in the chain -hydrogen bonds, ionic bonds and disulphide bridges (covalent bonds) form between R groups
-a change to the sequence of amino acids would affect the tertiary structure as these bonds would form in different places
-all enzymes, antibodies and some hormones have tertiary structure
quartenary structure
(+ example)
-if proteins are made of more than one polypeptide chain, then they are joined together to create quaternary structure
-antibodies and haemoglobin are examples of these
what are enzymes?
biological catalysts
-increase rate of reaction by lowering the activation energy of the reaction they catalyse
-3D tertiary structured globular proteins whose shape is determined by the primary sequence of amino acids
what are enzymes specific to?
the substrates that they bind to
what happens when enzymes and substrates bind?
they form an enzyme substrate complex
induced fit model
when an enzyme’s structure is altered so that the active site of the enzyme fits around the substrate that it has binded to
how does temperature affect the rate of enzyme controlled reactions?
-temperatures cause reactions to speed up
-molecules move more quickly as they have more kinetic energy
-increased kinetic energy results in a higher frequency of successful collisions between substrate molecules and the active sites of the enzymes which leads to more frequent enzyme-substrate complex formation
(at very high temperatures, the enzyme denatures)
how does pH affect the rate of enzyme controlled reactions?
-pH affects the enzymes shape as it can disrupt the bonds in the tertiary structure of the enzyme
-all enzymes work at different optimum pH’s, at pH’s that aren’t these, the enzymes don’t work at their best
how does enzyme concentration affect the rate of enzyme controlled reactions?
-the rate of reaction increases as enzyme concentration increases as there are more active sites for substrates to bind to
-however increasing the enzyme concentration beyond a certain point has no effect on the rate of reaction as there are more active sites than substrates so substrate concentration becomes the limiting factor
how does substrate concentration affect the rate of enzyme controlled reactions?
-as concentration of substrate increases, rate of reaction increases as more enzyme-substrate complexes are formed
-beyond a certain point the rate of reaction no longer increases as enzyme concentration becomes the limiting factor
competitive inhibitors
-compete with the substrate for the active site
-the inhibitor molecule has a similar shape to the substrate molecule
-they block the active site so the substrate cannot bind, and no ES complexes are formed
non competitive inhibitors
-non competitive do not bind to the active site
-the inhibitor molecule can bind to a site on an enzyme that is not the active site (allosteric site)
-binding of the inhibitor to the alternative site results in a change in shape of the active site
-the enzyme is no longer able to bind to its substrate
how to reverse the effects of a competitive inhibitor
increasing the concentration of the substrate, the substrate will out-compete the inhibitor for the active sites
can you reverse the effects of a non competitive inhibitor?
no, increasing the concentration of the substrate will not affect the rate of reaction because they cannot bind to the active site
what does ATP consist of?
ribose, adenine and three phosphate groups
when is energy released from ATP?
when ATP is hydrolysed to form ADP and a phosphate molecule
what is the process of releasing energy from ATP hydrolysed with?
ATP hydrolase
where does the energy in ATP come from?
the bonds between the phosphate molecules
why is energy released quickly from
ATP?
-the bonds between phosphate molecules are very unstable and have a low activation energy
-the breaking of these is quick and releases a considerable amount of energy
why is ATP more desirable than glucose?
-ATP is an immediate source of energy
-ATP can be broken down in a single step to release a manageable quantity of energy
why isn’t ATP stored in large quantities?
it can easily be reformed from ADP in seconds
(ATP can’t be stored)
how is ATP used?
-in metabolic processes (respiration)
-for movement
-in active transport
what is water a major component of?
all cells
why is water a polar molecule?
-there is an uneven distribution of charge within the molecule
-the hydrogen atoms are more positive than the oxygen atom causing one end of the molecule to be more positive than the other
what part does water play in metabolic reactions?
-it is a metabolite in metabolic reactions (eg: condensation and hydrolysis)
water has a high…? what does this mean?
-it has a high heat specific capacity
-this is because water molecules stick together with hydrogen bonds meaning that a lot of energy is required to break these bonds
-this helps to minimise temperature fluctuations in living things therefore it acts as a buffer
what does water having a relatively high latent heat of vaporisation mean?
hydrogen bonding means that it requires a lot of energy to evaporate 1 gram of water, meaning evaporation of water provides a cooling effect with little water loss
is water a solvent, solute or solution?
solvent, it aids diffusion
cohesion tension theory
1) hydrogen bonds between water molecules result in cohesion
2) water moves from the roots to the leaves because of a gradient
3) this gradient is present due to the constant loss of water from the leaves by transpiration and the constant uptake of water at the roots by osmosis
4) the evaporation of water into the air spaces in the leaves creates tension in the xylem tissue which is transmitted all the way down the plant because of the cohesive nature of water molecules
5) the cohesive force results in a continuous column of water with high tensile strength
6) adhesive force stops the water column from pulling away from the walls of the xylem vessels
what colour is benedict’s solution?
blue
what does benedict’s reagent contain?
copper (II) sulfate ions
what happens to copper (II) sulfate ions in the presence of a reducing sugar?
copper (I) oxide forms
property of copper (I) oxide that relates to benedict’s test
copper (I) oxide is not soluble in water, so it forms a precipitate
method of benedict’s test:
1) heat a sample in a test tube with benedict’s
2) if a reducing sugar is present, a coloured precipitate will form
how much benedict’s should be used and why?
an excess of benedict’s solution is used so that there is more than enough copper (II) sulfate present to react with any sugar present
colour range for benedict’s test:
a colour scale from blue (no reducing sugar), through green, yellow and orange (low to medium concentration of reducing sugar) to brick-red (a high concentration of reducing sugar)
benedict’s test equipment
benedict’s
test tube
bunsen burner or water bath
non reducing sugar example
sucrose
test for non reducing sugars
-add dilute hydrochloric acid to the sample and boil in a water bath
-neutralise the solution with an alkali (sodium hydrogencarbonate)
-use a suitable indicator to see when the solution has been neutralised, and then add a little more sodium hydrogencarbonate
-carry out the benedict’s test as normal
why is excess sodium hydrogen carbonate added?
the conditions need to be slightly alkaline for the benedict’s test to work
why is acid added?
will hydrolyse any glycosidic bonds present in any carbohydrate molecules
test for starch
1) add a few drops of iodine to the sample
2) blue-black colour is produced
what does DNA stand for?
deoxyribonucleic acid
what does RNA stand for?
ribonucleic acid
similarities of DNA and RNA:
-nucleic acids
-needed to build proteins
-found in all living cells
what is the function of dna?
-to store genetic information (the instructions an organism needs to grow and develop)
what is the function of rna?
to transfer genetic information from the DNA to the ribosomes
what is a nucleotide?
a type of biological molecule
what is a nucleotide made up of?
-a pentose sugar
-a nitrogenous base
-a phosphate group
why are nucleotides important?
they’re the monomers that make up DNA and RNA
what makes up a DNA nucleotide?
-a deoxyribose sugar
-a phosphate group
-an organic base (varies)
what are the four DNA bases?
A - adenine
T - thymine
C - cytosine
G - guanine
what makes up a RNA nucleotide?
-ribose sugar
-a phosphate group
-one of four different bases
what are the four RNA bases?
A - adenine
U - uracil (replaces thymine)
C - cytosine
G - guanine
what is a polynucleotide?
-a polymer of nucleotides
-both DNA and RNA nucleotides form polynucleotides
how do nucleotides join up?
via a condensation reaction between the phosphate group of one nucleotide and the sugar of another
what bond is between nucleotides
a phosphodiester bond (consisting of the phosphate group and two ester bonds)
what is the sugar phosphate backbone?
the chain of sugars and phosphates
two DNA polynucleotide strands join together by…
hydrogen bonding between the bases
what is complementary base pairing?
each base can only join with one particular partner
what are the base pairs?
A-T
C-G
how does the distribution of bases work?
% of C = % of G
% of A = % of T/U
how many hydrogen bonds are between A-T?
2 hydrogen bonds
how many hydrogen bonds are between C-G?
3 hydrogen bonds
how is the double helix structure formed?
two antiparallel polynucleotide strands twist
structure of RNA
-RNA is made from a single polynucleotide chain
-shorter than most DNA polynucleotides
when and why does DNA copy itself?
DNA copies itself before cell division so that each new cell has the full amount of DNA.
the concept of semi-conservative replication and what it means
one strand in each new DNA molecule is from the original DNA molecule
↳ this means that there’s genetic continuity between generations of cells
steps of semi conservative replication:
1) the enzyme DNA helicase breaks the hydrogen bonds between bases, the helix unwinds to form two single strands
2) each original single strand acts as a template for a new strand. free DNA bases are attracted to their complementary exposed bases on each original template strand
3) condensation reactions join the nucleotides of the new strands together catalysed by the enzyme DNA polymerase. hydrogen bonds form between the bases on the original and new strands
4) each new DNA molecule contains one strand from the original DNA molecule and one new strand
which two structural forms do nucleotides occur in?
purines and pyrimidines
what is a purine (+ examples)
double ring structure
(adenine and guanine)
what are pyrimidines? (+ examples)
single ring structure
(cytosine, thymine, uracil)
the ends of DNA
each DNA polynucleotide strand is said to have a 3’ end and a 5’ end (these numbers relate to which carbon on the pentose sugar could be bonded with another nucleotide)
-the strands are antiparallel: one is known as the 5’ to 3’ strand and the other is known as the 3’ to 5’ strand
what did the simplicity of RNA mean?
many scientists doubted that it carried the genetic code
what are the components of ribosomes?
RNA and proteins
properties of the RNA in ribsomes
the rRNA in ribsomes catalyses the formation of peptide bonds between amino acids
where is mRNA in the ribsome?
mRNA sits between the two subunits
watson & crick
-two scientists who worked together to confirm the double-helix structure of DNA in 1953
-came up with the theory of semi-conservative DNA replication
meselson and stahl’s experiment
1) two samples of bacteria were grown, one in a nutrient broth with light nitrogen, one in a broth with heavy nitrogen. as the bacteria reproduced, they took up nitrogen from the broth to help make nucleotides for new DNA, so the nitrogen gradually became part of the bacteria’s DNA
2) a sample of DNA was taken from each batch of bacteria, and spun in a centrifuge. the DNA from the heavy nitrogen bacteria settled lower down the centrifuge tube than the DNA from the light nitrogen bacteria
3) then the bacteria grown in the heavy nitrogen broth were taken out and put in a broth containing only light nitrogen. the bacteria were left for one round of DNA replication, and then another DNA sample was taken out and spun in the centrifuge
4) the DNA settled out in the middle, showing that the DNA molecules contained a mixture of heavy and light nitrogen. the bacterial DNA had replicated semi-conservatively in the light nitrogen
what is the emulsion test for?
lipids
emulsion test steps:
1) add ethanol and shake
2) next, pour the entire solution into a test tube containing water
3) check for formation of a milky white emulsion
why does emulsion form?
-lipids are insoluble in water, so they will not mix with the water
-any lipids present in your sample will float to the top and form a milky white emulsion
-the greater the concentration of lipids in your sample, the more apparent the milky colour will become
what is the biuret test for?
proteins
first step of the biuret test:
(+ explanation)
make the solution alkaline
-to properly test for proteins, your test solution needs to be alkaline
-add a few drops of sodium hydroxide to your solution
second step of the biuret test:
add copper (II) sulfate
third step of the biuret test:
(+ explanation)
observe the colour change of your test solution
blue = no protein present in your sample
purple = protein is present
