3.1 biological molecules Flashcards
what are monomers
small basic units that can form larger molecules (polymers)
what are polymers
large molecules composed of long chains of monomers joined together
examples of monomers
sugars, amino acids etc
what type of sugar is glucose?
hexose sugar (monosaccharide with 6 carbon atoms in each molecule)
examples of polymers
proteins, nucleic acids etc
what is a condensation reaction
it forms a glycosidic bond between two molecules and releases a molecule of water
what shouldn’t you forget to add when writing up a condensation reaction
add the water molecule in the products
how can a chemical bond be broken between two molecules
a hydrolysis reaction (adding water)
what type of bond is formed between the 2 monosaccharides as a molecule of water is released
glycosidic bond
what is the name of the reaction that forms a bond between two molecules and releases a molecule of water in the process
a condensation reaction
what is the name of the reaction that breaks the bond between two molecules
a hydrolysis reaction
monosaccharides
the monomers from which larger cabohydrates are made
example of monosaccharides
simple sugars
disaccharides
formed by a condensation reaction between 2 monosaccharides
polysaccharides
formed by the condensation of many monosaccharides linked by glycosidic bonds
what is maltose made of
alpha glucose molecule + alpha glucose molecule
how is sucrose formed
formed from condensation reaction between alpha glucose molecule and fructose molecule
what is lactose made of
glucose molecule + galactose molecule
draw the structure of alpha glucose
draw the structure of beta glucose
two structural isomers of glucose
alpha glucose
beta glucose
in alpha glucose, what is on the bottom
OH
in alpha glucose, what is on the top
H
in beta glucose, what is on the top
OH
in beta glucose, what is on the bottom
H
differences between fructose and galactose
fructose:
- very soluble
- main sugar in fruits
- sweeter than glucose
galactose:
- not as soluble as glucose
- important in the production of glycolipids and glycoproteins
what is formed in the condensation of alpha glucose
glycogen and starch
what is formed in the condensation of beta glucose
cellulose
what are polysaccharides used for
energy store and as a structural component of cells
structure of starch
mixture of 2 polysaccharides of alpha glucose (amylose and amylopectin)
function of starch
storage (starch is insoluble in water and so doesn’t affect the water potential so this makes it good for storing excess glucose as starch)
iodine test for starch
just add a few drops of iodine solution to a sample that’s in a spotting tile
blue black = presence of starch
2 polysaccharides of alpha-glucose found in starch
amylose
amylopectin
where is starch located in organisms
many parts of plants in the form of small grains
large amounts found in seeds and storage organs
desrcibe structure of amylose
long unbranced chain of alpha glucose
starch is a mixture of..
2 polysaccharides of alpha glucose
structure of cellulose
polysaccharide made up of long unbranched chains of beta glucose molecules
glucose molecules linked by 1-4 glycosidic bonds
describe how structure of amylose relates to its function
angles of the glycosidic bonds (coiled structure) –> makes it compact and it can fit more into a small space
function of cellulose
mainly used in the cell wall for strength (hydrogen bonding between chains gives cellulose molecules high tensile strength, ideal for providing structural support to plant cells)
describe the structure of amylopectin
long, unbranched chain of alpha glucose
structure of glycogen
alpha glucose polysaccharide
containing many 1-6 glycosidic bonds
loads of branches = stored glucose can be released quickly
animals store carbohydrates as glycogen
where is glycogen located in organisms
mainly in liver and some in muscles
what is the purpose of glycogen in animals
animals store excess glucose as glycogen
glycogens structure
lot more side branches and shorter chains compared to amylopectin, but the structure is very similar to it
describe how the structure of amylopectin relates to its function
its side branches allow the enzymes that break down starch to get at the glycosidic bonds easily = glucose can be released quickly
3 reasons why starch is suited for its role
- insoluble in water - doesn’t affect water potential
- compact - lots of it can be stored in small space
- when hydrolysed, alpha glucose can easily be transported and used in respiration
two types of lipids
triglycerides
phospholipids
what is a reducing sugar
sugars that can donate electrons to another chemical e.g benedict’s reagent
i.e all monoaccharides and some disaccharides (maltose and lactose etc)
alpha glucose formed by what type of glycosidic bonds
1,4 + 1,6 glycosidic bonds
triglyceride structure
1 molecule of glycerol and 3 fatty acids attached to it
tails made of hydrocarbons
tails are hydrophobic so they’re insoluble in water
two kinds of fatty acids
saturated
unsaturated
what happens in a condensation reaction between glycerol and a fatty acid
an esther bond is formed between the two molecules
properties of triglycerides
mainly used as energy source molecules- they are good for this because the hydrocarbon tails contain lots of chemical energy. this means that lipids contain twice as much energy per gram as carbohydrates
insoluble in water- fatty tails are hydrophobic so they point inwards, shielding themselves from water with the hydrophilic glycerol heads outwards
emulsion test for lipids
shake substance with ethanol for about 1 minute then pour solution into water
any lipid will show up as a milky emulsion
phospholipids structure
1 molecule of glycerol, 2 fatty acid molecules and a phosphate group
properties of phospholipids
make up bilayer of cell membrane
phospholipid heads are hydrophilic and tails are hydrophobic
causes a double layer to form in their heads
centre of bilayer is hydrophobic
draw the general structure of an amino acid
amino acid + amino acid =
dipeptide
this is a condensation reaction because a water molecule is formed
many amino acids make..
polypeptides
primary structure in a protein
primary structure:
chain of amino acids (polypeptide bonds).
this polypeptide chain forms the primary structure.
primary structure of a protein determines its shape and the function
if a single amino acid is incorrect, the whole protein can be useless and wont carry out its main function
secondary structure in a protein
secondary structure (alpha helix):
the amino acids that make up a polypeptide have both -C=O groups on either side. The hydrogen of the -NH group has an overall positive charge, O in -C=O has a negative charge.
These two groups therefore readily form weak bonds - hydrogen bonds.
this causes chain to twist into 3d shape - alpha helix
tertiary structure in a protein
alpha helix from secondary structure can be twisted and folded even more to give a more complex 3D protein.
quaternary structure
large proteins often form complex molecules containing a number of large individual polypeptide chains that are linked in various ways
there may also be non-protein (prosthetic) groups associated with the molecules.
biuret test for proteins
test solution needs to be alkaline, so first you add a few drops of sodium hydroxide solution
then add some copper (II) sulphate solution
protein present = purple
protein functions
structural: main component of body tissues. e.g muscle, skin, ligaments, hair etc
catalytic: enzymes are proteins, catalysing many biochemical reactions
signalling: many hormones and receptors are proteins
immunological: all antibodies are proteins
fibrous proteins
collagen: main component of connective tissues such as ligaments etc
keratin: main component of hard structures such as hair etc
silk: forms spiders’ webs and silkworms’ cocoons
globular proteins
transport proteins: haemoglobin. myoglobin etc
enzymes: lipase DNA polymerase
hormones: oestrogen and insulin
what reactions can enzymes catalyse
anabolic (building up) reactions
catabloic (breaking down) reactions
specificity of enzymes
the active site of an enzyme binds the substrate molecule of a biochemical reaction and is critical to its specificity and catalytic activity
location of enzyme action
intracellular:
DNA replication
some occur on membrane
synthesis of ATP by ATPase during respiration occurs across inner membrane of mitochondria
extracellular:
digestion - involves extracellular action of enzymes such as pepsin and amylase; breaks down food particles into small molecules such as peptides and disaccharides
describe the lock and key theory
- the active site shape is very precise and is maintained by the tertiary structure of the enzyme
the substrate molecule fits exactly into the active site like a key fitting into a lock
this forms an enzyme-substrate complex
this enables the reaction to take place more easily
the complex only exists for a fraction of a second until the products are formed and then once they’re formed, they leave the site and the enzyme is free to take part in another reaction
induced fit model of enzyme action
induced fit theory proposes that the active site is not initially an exact fit for the substrate molecule.
as the substrate moves into the active site, forces between the molecules distort the enxyme and its active site so it envelopes the substrate (enzyme substrate complex is formed)
role of hydrogen bonds, in the structure of proteins
are numerous but easily broken
role of ionic bonds in the structure of proteins
formed between any carboxyl and amino groups that aren’t involved in forming peptide bonds.
weaker than disulfide bonds and are easily broken by changes in pH
role of disulfide bridges in the structure of proteins
fairly strong and therefore not easily broken
effect of temperature on enzyme reaction
- increase in temperature increases kinetic energy of molecules
- molecules move around more rapidly and collide with each other more often
this means that the enzyme and substrate molecules come together more often in a given time. - the more effective collisions=more enzyme-substrate complexes being formed, rate of reaction increases
at around 60C, enzyme is disrupted so it denatures.
effect of pH on enzyme action
- a change in pH alters the charges on the amino acids that make up the active site. as a result, the substrate can no longer attach to the active site so the enzyme substrate complex cannot be formed
- depending on how significant the change in pH is, it may cause the bonds maintaining the enzyme’s tertiary structure to break. active site therefore changes
effect of enzyme concentration on rate of reaction
there is more substrate than the enzyme’s active sites can cope with.
if you increase the enzyme concentration, some of the excess substrate can now be acted upon and the r.o.r will increase
effects of substrate concentration on the rate of enzyme action
at low substrate concentration, the enzyme molecules have only a limited number of substrate molecules to collide with and therefore the active site of enzymes aren’t working fully
as more substrate is added, the active sites gradually become more filled until they are working as fast as they can
DNA
deoxyribonucleic acid
RNA
ribonucleic acid
DNA structure
- double helix made up of two strands of nucleotides. each strand is joined together by hydrogen formed between complementary bases
- each nucleotide is made up of a pentose sugar (deoxyribose), phosphate group, nitrogen base (adenine, thymine, guanine and cytosine) and are joined as a result of condensation reactions.
- the bond formed between them is called a phosphodiester bond.
- long chain
RNA structure
- polymer made up of nucleotides formed by condensation
- phosphodiester bonds between nucleotides
- each nucleotide formed from a pentose sugar (always ribose), phosphate group, nitrogen base (adenine, guanine, cytosine and uracil)
- short polynucleotide chain
-ribosomes are made up of proteins and another type of RNA
role of DNA
- material responsible for passing information from cell to cell
how is the DNA molecule adapted to carry out its function
- stable structure so most mutations are repaired
- two separate strands are joined together by hydrogen bonds which allows them to separate during DNA replication
- large molecule so carries a lot of genetic information
role of RNA
RNA transfers genetic information from DNA to ribosomes for protein synthesis.
similarities and differences of DNA and RNA
-DNA has deoxyribose whereas RNA has ribose
- DNA is double stranded whereas RNA is single stranded
- DNA has thymine whereas RNA has uracil
- DNA carries genetic information whereas RNA transfers genetic information
- DNA is a long polynucleotide chain whereas RNA is a short polynucleotide chain
- DNA has hydrogen bonds whereas RNA doesn’t
- both contain phosphodiester bonds
- both contain the sugar phosphate backbone
which method is used for DNA replication
semi-conservative
process of semi conservative DNA replication
- enzyme DNA helicase breaks down the hydrogen bonds between base pairs of DNA
- As a result, DNA double strands unwind and separate
- now that the strands have been split, each exposed polynucleotide strand has complementary nucleotides bind by specific base pairing.
- nucleotides are joined together in a condensation reaction by the enzyme DNA polymerase to form the ‘missing’ polynucleotide strand on each of the two original polynucleotide strands of DNA
- each of the new DNA molecules contains half of the original DNA that has been saved and built into each of the new DNA molecules
experiment for evidence of semi conservative replication
- used 2 isotopes of nitrogen: heavy nitrogen (15N) and light nitrogen (14N) (because DNA contains nitrogen - nitrogenous base)
- one sample of bacteria was grown in a nutrient broth containing light nitrogen (N14)
- one was grown in a broth with heavy nitrogen (N15).
- the bacteria took up the nitrogen to make new nucleotides so it was incorporated into their DNA.
- a sample of DNA was taken from the batches of bacteria and spun in a centrifuge
- DNA from heavy nitrogen bacteria settled lower down the centrifuge tube than the DNA from the light nitrogen bacteria
- then bacteria that had been grown in the heavy DNA broth were taken out and put into a broth containing light nitrogen
- bacteria was left for one round of DNA replication and then a sample was taken and spun again in centrifuge
- if replication was conservative, the original heavy DNA would settle at the bottom and the new light DNA made would settle at the top.
- if replication was semi conservative, the new bacterial DNA molecules would contain one strand of old DNA with heavy nitrogen and one strand of new DNA containing light nitrogen
- so DNA would settle out in the middle of the tube, rather than the top or the bottom
structure of ATP
adenine, ribose, 3 phosphate groups
role of enzymes in hydrolysing ATP
hydrolysis of ATP to ADP and Pi is catalysed by the enzyme ATP hydrolase and can be used to phosphorylate (cause an organic compound to take up/combine with phosphoric acid or a phosphorus containing group) compounds often making them more reactive, or provide energy to energy requiring cellular reactions
role of enzymes in synthesising ATP
conversion of ATP to ADP is a reversible reaction and therefore energy can be used to add an inorganic phosphate to ADP to re-form ATP
ATP is resynthesised from ADP and Pi by the enzyme ATP synthase, during photosynthesis or respiration
reversible reaction of the hydrolysis of ATP
ATP + water —-> ADP + Pi + E
adenosine triphosphate + water —> adenosine diphosphate + inorganic phosphate + energy
synthesis of ATP from ADP involves the addition of a phosphate molecule to ADP. it occurs in three ways:
- in chlorophyll-containing plant cells during photosynthesis (photophosphorylation)
- in plant and animal cells during respiration (oxidative phosphorylation)
- in plant and animal cells when phosphate groups are transferred from donor molecules to ADP
what energy requiring processes in cells is ATP used for
- metabolic processes: ATP provides the energy needed to build up macromolecules from their basic units e.g making starch from glucose or polypeptides from amino acids
- movement: ATP requires energy for muscle contraction. in muscle contraction, ATP provides the energy for the filaments of muscle to slide past one another and therefore shorten the overall length of a muscle fibre
- active transport: ATP provides the energy to change the shape of carrier proteins in plasma membranes. this allows molecules or ions to be moved against a concentration gradient
- secretion: ATP is needed to form the lysosomes necessary for the secretion of cell products
-activation of molecules: the inorganic phosphate released during the hydrolysis of ATP can be used to phosphorylate other compounds in order to make them more reactive e.g. the addition of phosphate to glucose molecules at the start of glycosis
importance of water
makes up about 80% of cell’s contents and has several function:
- its a metabolite in lots of metabolic reactions e.g condensation
- its a solvent. most metabolic reactions take place in solution
- helps with temp control
- has a high heat capacity
- has a large latent heat of vapourisation
- water molecules are cohesive and adhesive which helps transport of substances
properties of water linked to the polar nature of the molecule
- although the molecule has no overall charge, the oxygen atom has a slight negative charge whilst the hydrogen atoms have a slight positive one.
- the water molecule has both a positive and negative pole and therefore described as dipolar
- different poles attract so therefore the pole of one water molecule will be attracted to the negative pole of another water molecule. this force is called a hydrogen bond.
water as a metabolite
many metabollic reactions involve a condensation or hydrolysis reaction
water as a solvent
- polar nature of water means by changing the water molecules orientation around the ions, it is able to dissolve them
- this means organisms can take up useful substances (mineral ions) dissolved in water and then easily transport them around the body
water’s latent heat of vapourisation
- water evapourates when the hydrogen bonds are broken
- allows water molecules on the surface of water to escape as a gas
- takes energy to break the hydrogen bonds so a lot of energy is used when it evapourates
- this means it has a high latent of vapourisation
- useful in organisms as it can be a way of cooling without losing a lot of water
water’s specific heat capacity
- lots of energy used to break hydrogen bonds between water molecules
- water inside organisms stay at a relatively constant temperature and so helps maintain internal body temperature
water’s cohesive and adhesiveness
adhesive: water molecules are attracted to ‘stick’ to unlike molecules e.g glass
cohesive: water molecules ‘stick’ to each other
- this means water is great for transporting substances
- also gives water a high surface tension. this is why sweat forms droplets and some insects walk on water
important features of water to living organisms
- evapouration allows organisms to cool down and therefore control their temperatures
- its not easily compressed and therefore provides support, e.g - the hydrostatic skeleton of animals such as the earthworm and turgor pressure in herbaceous plants
- it is transparent and therefore aquatic plants can photosynthesise and also light rays can penetrate the jelly like fluid that fills the eye so it can reach the retina
what is meant by inorganic ions
an ion that doesnt contain carbon
where do inorganic ions occur
occur in solution in the cytoplasm and body fluids of organisms, some in high concentrations and others in very low concentrations
specific roles of hydrogen ions
- they perform a range of functions depending on its properties
- important in determining the pH of solutions and therefore functioning of enzymes.
specific roles of iron ions
- they perform a range of functions depending on its properties
- component of haemoglobin where they play the role in the transport of oxygen
specific roles of sodium ions
- they perform a range of functions depending on its properties
- important in co-transport of glucose and amino acids across plasma membranes
specific roles of phosphate ions
- they perform a range of functions depending on its properties
- components of DNA and of ATP
