biological molecules Flashcards
what is a condensation reaction?
joins two molecules together with the formation of a chemical bond and involves the elimination of a molecule of water.
what is a hydrolysis reaction?
breaks a chemical bond between two molecules and involves the use of a water molecule.
what monomers are used to make larger carbohydrates? name a few and give their symbol form and why they all have the same.
monosaccharides- glucose, galactose and fructose. C6h12o6 for all (they are isomers of each other)
what is a glycosidic bond and how is it formed?
A condensation reaction between two monosaccharides
what is formed by the condensation of two monosaccharides? give 3 examples and what monosaccharides they’re made from.
disaccharides. sucrose (glucose+fructose), maltose (glucose+glucose), lactose (glucose+galactose)
what ratio does hydrogen and oxygen come in, in carbohydrates? give an example
2:1 eg C12H22O11 (can’t really tell how many carbs there will be)
what are polysaccharides? give examples
polymers of monosaccharides e.g. starch, glycogen, cellulose
how would you test for reducing sugars? (any sugar that is capable of acting as a reducing agent)
1) crush up food if needed
2) Add Benedict’s solution
3) heat the solution
4) a positive solution goes from green-yellow-orange-red (red being s strong amount of sugar present)
how does the Benedict’s test work? (2)
the reducing sugar gives an electron to the blue Cu2+ ions making them into red Cu+ ions.
the more reducing the sugar, the more precipitate forms/greater the change.
what are optical isomers?
two or more forms of a compound which have the same structure but are mirror images of each other and typically differ in optical activity
even though a-glucose and b-glucose are optical isomers of each other, they behave differently in the body, why?
the active sites of the enzymes may only be a complementary shape to one version of glucose
what polymers do a-glucose form?
starch and glycogen
what polymers do b-glucose form?
cellulose
in the condensation reaction between glucose+glucose (C6H12O6) why is the formula for maltose C6H22O11
Because 2 hydrogens and 1 oxygen is lost to the water molecule which is also created in the reaction.
what is the main role of starch?
energy storage
how is the structure of starch suited to its main role/function?
1) insoluble- doesn’t affect the movement of water by osmosis
2) compact- allows a lot of carbohydrate to be stored in a small space
3) large and insoluble- doesn’t diffuse out of cells
4) can be hydrolysed- produces a-glucose which is easily transported and readily used in respiration
what is starch? (3)
1) a polysaccharide found in plants in the form of small grains
2) large amounts occur in seeds/storage organs
3) used to store carbohydrates in plant cells
are the chains of glucose in starch branched or unbranched?
can be both.
the unbranched chain will coil up into a helix which makes the molecule compact
what is glycogen? (2)
1) found in animals and bacteria
2) used to store carbohydrates in animals and is stored as small granules mainly in the muscles and liver
how is the structure of glycogen suited to its function?
1) it is insoluble so doesn’t affect the movement of water into the cell by osmosis
2) insoluble- doesn’t diffuse out of cells
3) compact-allows a lot of carbohydrate to stored in a small space
4) more highly branched than starch so has more ends which can be acted on simultaneously by enzymes, therefore it is more rapidly hydrolysed/broken down to produce glucose for respiration
–> important bc animals have a higher metabolic and respiratory rate
what is cellulose? (4)
1) major component of plant cell wall
2) provides rigidity to the plant cell
3) prevents cell from bursting as water enters it by osmosis (exerts an inward pressure)
4) forms dietary fibre
how is the structure of cellulose suited to its function?
1) made up of b-glucose so forms straight, long unbranched chains which run parallel to each other
2) This allows hydrogen bonds to cross link between neighbouring chains adding collective strength
3) these molecules are grouped to form microfibrils which group to form fibres, providing more strength
what elements are triglycerides made of?
carbon, hydrogen and only a little oxygen
The R-group of a fatty acid (RCOOH) may be saturated or unsaturated, what does this mean?
In saturated fatty acids, all the carbon atoms are connected to other C atoms by single bonds
unsaturated fatty acids have one or more double bonds and consequently fewer hydrogens
what are the features of a saturated fatty acid?
- stronger intermolecular forces
- solid at RT
- higher melting points
- increase risk of atherosclerosis
What is the role of hydrochloric acid in a test for non-reducing sugar?
acidic environment is necessary for breaking down the disaccharides into monosaccharides
what is a peptide bond?
forms between two amino acids in a condensation reaction
what is a hydrogen bond in proteins?
the weak interaction between side chains of amino acids
what is an ionic bond in proteins?
forms between an amino acid with a positive charge and an amino acid with a negative charge
what is a disulfide bridge?
forms between sulfurs in side chains of amino acids
what is the primary structure of proteins?
the sequence of amino acids in a polypeptide chain joined by peptide bonds which is coded for by the order of bases in a DNA gene
what is the secondary structure of proteins?
the polypeptide folds up into basic shapes (alpha helix, beta sheet, alpha turns)
what is the tertiary structure of proteins?
the polypeptide secondary structures folds up further to give an overall 3-dimensional shape
what is the quaternary structure of proteins? (2)
1) several polypeptide chains
2) they have non-protein prosthetic groups embedded in the protein to help it carry out its function eg haem group
what is a competitive inhibitor?
a molecule with a similar shape to a substrate, which reduces an enzyme’s effectiveness
what is a non competitive inhibitor?
a molecule that reduces an enzyme’s effectiveness without blocking the active site
What is the amount of energy needed to start a reaction called?
activation energy
Which level of protein structure has the most influence on the shape of a protein?
tertiary
what is a phospholipid?
2 fatty acids and 1 phosphate bonded to a glycerol molecule
describe the emulsion test for lipids
1) crush up food if needed
2) add ethanol and shake
3) add water and shake
4) +ve test gives white emulsion
how is the structure of a phospholipid related its properties?
1) polar - in aqueous environments they can form a phospholipid bilayer
2) structure allows them to form glycolipids with carbohydrates - important on the cell surface membrane for cell recognition
how is the structure of a triglyceride related to its properties?
1) high ratio of energy storing carbon-hydrogen bonds to carbon atoms -excellent energy store
2) low mass to energy ratio- good storage molecule as a lot can be stored in a small volume
3) large and non polar- insoluble in water, storage doesn’t affect water potential of cells
what is the difference between dipeptides and polypeptides?
-Dipeptides are formed by the condensation of two amino acids.
-Polypeptides are formed by the condensation of many amino acids.
what are functional proteins? (3) give examples
1) functional proteins possess a biological activity
2) involved in the biological function of a living organism.
3) A functional protein may contain one or more polypeptides.
Eg: Haemoglobin, Insulin, and all the enzymes.
what does the role of hydrogen bonds, ionic bonds and disulfide bridges have in the structure of proteins?
1) these bonds are what hold the R groups/ side chains of amino acids together
2) determine the overall 3D shape of the protein
3) contribute to the folding process of the tertiary structure
how is the primary structure of proteins made?
assembled by ribosomes on the Rough Endoplasmic Reticulum
how will a mutation to a DNA gene affect an enzyme’s functioning?
1) mutation changes the order of nucleotide bases in the gene
2) a different chain of amino acids is coded for which will have different R groups/ side chains
3) This causes different hydrogen bonds to form
4) So the tertiary structure of the protein is also different
5) This causes the active site of the enzyme to be the wrong shape to fit the substrate
what are the basic shapes (alpha helix, beta sheet, alpha turn) in the secondary structure held together by?
by hydrogen bonds between the C=O of one of the peptide bonds and the N-H of a nearby peptide bond
what is the 3D shape of the tertiary structure of proteins held together by?
bonds between the R groups
- can be hydrogen bonds, ionic bonds or disulfide bridges
what is tertiary structure important for? (3)
the correct shape of:
1) enzymes to bind to substrates
2) antibodies to bind to antigens
3) hormone receptors to bind to hormones
describe the biuret test for proteins
1) crush up food if needed
2) add biuret’s reagent
3) +ve result turns from blue to purple
-ve stays blue
name 6 proteins and their functions
1) haemoglobin - loads with oxygen in the alveoli and unloads oxygen in respiring tiessues
2) amylase- catalyses the hydrolysis of glycosidic bonds in starch
3) elastin- elastic protein that allows arteries to stretch and recoil
4) CFTR- Cl- ion channel protein which allows Cl- ions across the cell membrane
5) insulin receptor- binds to insulin, causing cells to take up glucose for storage as glycogen
6) Keratin- tough, hard fibrous protein in nails, skin and hair
what feature makes water important for chemical reactions in the body?
it is a metabolite in many metabolic reactions, including condensation and hydrolysis reactions and photosynthesis
what feature makes water important in terms of maintenance temperature?
give examples
1) has a relatively high heat capacity
2) hydrogen bonding means that water absorbs a lot of heat energy with little temperature rise
3) this buffers changes in temperature
eg cytoplasm and blood plasma absorb heat energy from respiration with little temperature rise
what feature makes water important for cooling? (3) give examples
1) In order to change state a large amount of thermal energy must be absorbed by water to break the hydrogen bonds and evaporate
2) This is an advantage for living organisms as only a little water is required to evaporate for the organism to lose a great amount of heat
3) This provides a cooling effect for living organisms, for example the transpiration from leaves or evaporation of water in sweat on the skin
what feature makes water important for plants and water environments?
1) strong cohesion between water molecules due to H bonding
2) this supports continuous columns of water in the xylem vessels of plants
3) produces surface tension layer which is a microhabitat for pondskates and waterboatmen
what is water? (3)
1) a polar molecule
2) oxygen atoms are slightly negative, hydrogen atoms are slightly positive
3) hydrogen bonds form between water molecules
why is it important that water is transparent?
1) aquatic plants get light for photosynthesis
2) aquatic animals can see to find food
why is it important that water is hard to compress?
1) in synovial joints, compression forces are absorbed by synovial fluid
2) also in cerebrospinal fluid around the brain
what is the lock and key model for enzymes specificity?
enzyme’s active site acts as the lock and is a complementary shape (due to the enzyme’s tertiary structure) to the substrate which acts as the key
what do enzymes do?
lower the activation energy for the reaction it catalyses through forming enzyme substrate complexes
what is the induced-fit model of enzyme action? (2)
1) The enzyme’s active site changes shape slightly to mould around the substrate
2) the substrate also changes shape slightly
what do the properties of an enzyme relate to? (2)
1) the tertiary structure of its active site
2) its ability to combine with complementary substrate(s) to form an enzyme-substrate complex
how do enzymes catalyse reactions? (5)
1) enzyme and substrate bind to form an ES complex with the active site moulded around the substrate by induced fit
2) this lowers the activation energy for the reaction by providing an alternative reaction pathway
3) this is achieved by holding reactants in the correct orientation to react
4) bonds in the substrate that need to be broken are put under strain by the induced fit
5) charged amino acids in the active site help the movement of electrons
what causes the specificity of enzymes? (3)
1) each enzyme has a unique tertiary structure
2) the active site of the enzyme is a complementary shape to its substrate
3) so the enzyme and substrate bind to form an ES complex in an ‘induced fit’ manner with the enzyme moulded around the substrate
why is the specificity of enzymes important (2)? give an example
1) it means that one enzyme will not bind to a ‘wrong’ substrate as it would not be a complementary shape to the active site, therefore wouldn’t form an enzyme substrate complex
2) this allows many different reactions to occur at the same time and in the same area of the cell, without interfering with each other
e.g
the many reaction steps in respiration in the matrix of mitochondria that are all catalysed by different enzymes
why is it important to calculate initial rate of reaction from a graph?
the initial rate is the rate at the start of the experiment before the substrate(s) start to get used up
how do you calculate rate of reaction from a graph?
draw a tangent to the curve and calculate the gradient (rise/run)
what happens if pH is brought away from enzyme activity? (2)
1) rate of reaction decreases but this is reversible if enzyme is brought back to optimum pH
2) this is because charged amino acids in the active site lose their charge and can’t act as catalysts
what happens at more extreme pH values in terms of enzyme activity? (5)
1) hydrogen bonds get broken
2) tertiary structure is destroyed
3) enzyme gets denatured
4) active site loses its shape
5) no enzyme-substrate complexes can be made
how does an increase in temperature affect enzyme activity up to optimum temp?
1) rate of reaction increases
2) because enzyme and substrate molecules have more kinetic energy and move faster
3) so they collide more often forming more enzyme substrate complexes
how does temperature affect enzyme activity past optimum temp? (5)
1) above optimum temperature rate of reaction decreases rapidly
2) because enzymes are denatured
3) hydrogen bonds break and tertiary structure is destroyed
4) active site loses shape and so is no longer a complementary shape to the substrate
5) no enzyme substrate complexes can be made
what are ‘reaction progress’ graphs?
product concentration and time
how does substrate concentration affect enzyme activity? (4)
1) rate of reaction increases
2) because there are more collisions between enzyme active sites and substrate molecules
3) more enzyme substrate complexes are formed
4) at high substrate concentration no further increase in reaction rate occurs and product can’t be made any faster because all active sites are saturated
how does enzyme concentration affect rate of reaction? (3)
1) rate of reaction increases
2) because there are more collisions between enzyme active sites and substrate molecules
3) more enzyme substrate complexes are formed
what is enzyme concentration like in cells (2)
1) enzyme concentration is usually very low as enzymes can perform millions of reactions in a second
2) cells do increase enzyme concentration when they need to by doing more protein synthesis
what are competitive inhibitors? (4)
1) similar shape to the substrate/ complementary shape to active site
2) binds to active site
3) reduces no. of enzyme substrate complexes
4) inhibition can be overcome by increasing substrate concentration
what are non competitive inhibitors? (5)
1) not a similar shape to the substrate
2) bind to enzyme away from the active site
3) changes shape of the active site
4) no enzyme substrate complexes can form
5) inhibition can not be overcome by adding lots of substrate
what is the function of DNA? (2)
1) holds genetic information
2) responsible for passing this info. from cell to cell and generation to generation
what is each nucleotide made out of?
a deoxyribose sugar, a nitrogen-containing organic base and a phosphate group
what are the 4 organic bases?
adenine, thymine, guanine, cytosine
what is a DNA molecule?
a double helix with two polynucleotide chains held together by hydrogen bonds between specific complementary base pairs.
how are 2 DNA strands joined together?
hydrogen bonds
how many hydrogen bonds are between G & C?
3
how many hydrogen bonds are between A & T?
2
list the 2 pairs of complementary bases
adenine and thymine
guanine and cytosine
what features makes DNA a chemically stable molecule? (2)
1) phosphodiester backbone which protects the more chemically reactive organic bases inside the double helix from being corrupted by outside chemical and physical forces
2) hydrogen bonds link the organic base pairs forming bridges between the phosphodiester uprights
the 4 different bases occurring in any order allows…
DNA to code for proteins
how is DNA adapted to its function of storing the genetic code? (6)
1) it is a very long/large molecule so a lot of genetic information can be coded
2) 4 different nucleotide bases, order of these makes up the genetic code
3) the phosphodiester backbone is on the outisde, so the base pairs on the inside are protected from UV and chemical damage
4) the bases are joined by many hydrogen bonds so the 2 strands are held together in a stable molecule
5) individually hydrogen bonds are weak so the 2 strands can be separated during DNA replication
6) A+T and G+C only hydrogen bond to each other so DNA replication can be very accurate with few mutations
what is DNA made up of?
nucleotides which have 3 basic components
how are the deoxyribose sugar, phosphate group and organic base joined?
as a result of condensation reactions to form a single nucleotide/ mononucleotide
what happens when two mononucleotides join? (3)
1) join through a condensation reaction between the deoxyribose sugar of one mononucleotide and the phosphate group of another
2) A condensation reaction between two nucleotides forms a phosphodiester bond.
3) new structure is a dinucleotide
what is a polynucleotide?
the continued linking of mononucleotides
what is the function of RNA? (2)
1) transfers genetic information from DNA to the ribosomes
2) or involved in protein synthesis
what is the structure of RNA?
a relatively short polynucleotide chain in which the pentose sugar is always ribose and the organic bases are adenine, guanine, cytosine and uracil.
what is the structure of DNA? (2)
1) In DNA the pentose sugar is deoxyribose and the organic bases are adenine, thymine, guanine, and cytosine.
2) made up of two strands of polynucleotides which are extremely long and joined together by hydrogen bonds between certain bases
how can DNA be thought of as a ladder structure? (2)
1) the phosphate and deoxyribose molecules alternate to form the uprights
2) the organic bases pair together to form the rungs
how do bases attach to each other?
hydrogen bonds
adenine is said to be… to thymine
complementary
why is DNA described as a double helix? (3)
1) ladder-like arrangement of the two polynucleotide chains are twisted
2) the uprights of phosphate and deoxyribose wind around one another to form a double helix
3) they form the structural backbone of the DNA molecule
what differs between one DNA molecule and another?
the proportions and sequence of each of the four bases
why is complementary base pairing important?
A+T and G+C only hydrogen bond to each other so DNA replication can be very accurate with few mutations
what is stage 1 of DNA replication?
template is a double stranded DNA molecule in interphase
what is stage 2 of DNA replication? (3)
1) DNA helicase unwinds the DNA double helix
2) by breaking the hydrogen bonds between the complementary organic base pairs on the two antiparallel polynucleotide strands
3) to form two single polynucleotide DNA strands
what is stage 3 of DNA replication? (2)
1) Each single polynucleotide DNA strand acts as a template for the formation of a new strand
2) made from new, free nucleotides in the nucleus that are attracted and hydrogen bond to their complementary, exposed bases on the template strand by base pairing.
what is stage 4 of DNA replication? (2)
1) DNA polymerase synthesises new DNA strands from the two template strands and joins the complementary nucleotides forming new phosphodiester bonds
2) It does this by catalysing condensation reactions between the deoxyribose sugar and phosphate groups of adjacent nucleotides within the new strands, creating the sugar-phosphate backbone of the new DNA strands
what is stage 5 of DNA replication? (2)
1) 2 identical daughter DNA molecules contain 1 original and 1 new strand
2) The original strand and the new strand join together through hydrogen bonding between base pairs to form the new DNA molecule
why is DNA replication referred to as ‘semi conservative’ replication? (4)
1) both parental strands are used as templates
2) in each new DNA molecule produced, one of the polynucleotide DNA strands is from the original DNA molecule being copied
3) The other polynucleotide DNA strand has to be newly created by the cell
4) Therefore, the new DNA molecule has conserved half of the original DNA and then used this to create a new strand
what is stage 1 of the Meselsohn and Stahl experiment? (3)
1) grow bacteria in normal nitrogen, 14N
2) this makes normal density DNA
3) this spins to the top of the tube when centrifuged
what is stage 2 of the Meselsohn and Stahl experiment? (3)
1) grow bacteria in heavy nitrogen, 15N
2) this makes heavy density DNA
3) this spins to the bottom of the tube when centrifuged
what is stage 3 of the Meselsohn and Stahl experiment? (4)
1) transfer bacteria to normal nitrogen, 14N medium
2) new DNA strands made will be ‘light’ but their original DNA will be heavy
3) new DNA molecules are shown to have 1 light and 1 heavy strand
4) overall medium density
what is stage 4 of the Meselsohn and Stahl experiment? (4)
1) bacteria continued to grow in normal nitrogen, 14N
2) new DNA strands formed are light whilst the two original strands are still ‘heavy’
3) light strands will spin to the top of the test tube in the centrifuge
4) medium density DNA will spin to the middle of the centrifuge
what is the purpose of semi conservative replication? (3)
1) Before a cell divides, the number of DNA molecules in the parent cell must be doubled before mitosis takes place
2) so that the two new (daughter) cells produced will both receive the full copies of the parental DNA
3) ensures genetic continuity between generations of cells.
what is the importance of retaining one original DNA strand? (3)
1) ensures there is genetic continuity between generations of cells
2) ensures that the new cells produced during cell division inherit all their genes from their parent cells
3) This is important because cells in our body are replaced regularly and therefore we need the new cells to be able to do the same role as the old ones
what is a single molecule of adenosine triphosphate (ATP)? (2)
1) a nucleotide derivative
2) formed from a molecule of ribose, a molecule of adenine and three phosphate groups.
what enzyme is involved in the hydrolysis of ATP to ADP and an inorganic phosphate group (Pi)?
catalysed by the enzyme ATP hydrolase.
what can the hydrolysis of ATP be coupled to? give an example
1) energy-requiring reactions within cells
e.g The active transport of ions up a concentration gradient, enzyme controlled reactions that require energy or muscle contraction and muscle fibre movement.
what can the inorganic phosphate released during the hydrolysis of ATP be used for?
can be used to phosphorylate other compounds, often making them more reactive, lowering the activation energy of enzyme controlled reactions
what reaction is the enzyme ATP synthase involved in?
ATP is resynthesised by the condensation of ADP and Pi which is catalysed by the enzyme ATP synthase during photosynthesis, or during respiration.
why can DNA polymerase only build the new strand in one direction (5’ to 3’ direction)? (5)
1) DNA has antiparallel strands
2) shapes of nucleotides are different/ aligned differently
3) DNA polymerase active site is specific
4) meaning it’s only complementary with the 3’ end of the strand/ only substrates with the complementary shape can bind with active site
5) the shapes of the 5’ end of the 3’ end are different.
how does ATP store energy? (4)
1) has 3 phosphate groups and the bonds between them are unstable
2) have a low activation energy so are easily broken
3) when these bonds break they release a considerable amount of energy
4) it is usually only the terminal phosphate that is removed
what is the equation for the hydrolysis of ATP?
why is the reaction called ‘hydrolysis’? (2)
1) ATP + H2O –> ADP + Pi + E
2) uses water to split ATP into ADP and a phosphate/ Pi
what is the difference between ATP and a nucleotide found in DNA? (2)
1) DNA nucleotide sugar is deoxyribose, ATP is ribose
2) DNA nucleotide has one phosphate group, ATP has 3
what 3 ways can cells make ATP from ADP and a phosphate? (3)
1) respiration releases energy from glucose for ATP synthesis
2) stage 1 of photosynthesis uses light energy for ATP synthesis
3) creating phosphate + ADP –> creation + ATP (gives its phosphate to ADP)
what are inorganic ions and where can they be found? (4)
1) in solution in the cytoplasm
2) body fluids of organisms
3) some in high concentrations and others in very low concentrations
4) each type of ion has a specific role, depending on its properties
what is the role of hydrogen ions in pH? (3)
1) pH is calculated based on the concentration of hydrogen ions (H+). 2) The more H+ present the lower the pH level and the more acidic the environment is.
3) Enzyme-controlled reactions are affected by pH.
what is the role of iron ions as a component of haemoglobin? (4)
1) Haemoglobin is a large protein that carries oxygen around the body in red blood cells
2) It’s made of four polypeptide chains - each with an iron ion in the centre
3) the iron ion is a key component that binds to the oxygen in haemoglobin
4) When oxygen is bound, the Fe2+ ion temporarily becomes an Fe3+ ion until oxygen is released
what is the role of sodium ions in the co-transport of glucose and amino acids? (3)
1) Helps glucose and amino acids cross cell membranes
2) A molecule of glucose or an amino acid can be transported into a cell across the cell-surface membrane alongside sodium ions (Na+)
3) This is known as co-transport
what is the role of phosphate ions as components of DNA and of ATP? (3)
1) Used in production of nucleic acids (DNA and RNA)
2) and in the production of ATP
3) and phospholipids which are essential in cell membranes
how is the hydrolysis of ATP used in cells? (3)
1) to provide energy for active transport to change the shape of the carrier protein
2) phosphorylate other compounds to make them more reactive, lowering the activation energy in enzyme controlled reactions
3) metabolic processes- provides energy to build up macromolecules from their basic units
