Chapter Three: Biological Molecules Flashcards
What are the roles of these anions?:
1. nitrate ions
2. phosphate ions
3. hydroxide ions
4. chloride ions
5. hydrogen carbonate ions
- a mineral ion absorbed by plants to give a source of nitrogen to make amino acids
- involved in the formation of phospholipids for cell membranes, nucleic acid and ATP formation
- catalysis of reactions and pH determination
- involved in the transport of carbon dioxide in the blood as they are a part of the chloride shift to balance positive charges
- involved in the transport of carbon dioxide in the blood
What are the roles of these cations?:
1. calcium ions
2. sodium ions
3. hydrogen ions
4. potassium ions
5. ammonium ions
- nerve impulse transmission and muscle contraction
- involved in co-transport, reabsorption of water in the kidney, regulating water potential and nerve impulse contraction
- involved in chemiosmosis, pH regulation, and translocation
- nerve impulse transmission and stomatal opening
- involved in nitrogen cycle, where bacteria convert ammonium ions into nitrate ions
How does hydrogen bonding occur between water molecules?
- oxygen is more electronegative than hydrogen so it attracts the electrons
- forms a slightly negative oxygen, and slightly positive hydrogens, making water a polar
- intermolecular forces of attraction between lone pair on oxygen and one atom of hydrogen on a nearby molecule
What are the six most biologically important properties of water?
- universal solvent
- high specific heat capacity
- high latent heat of vaporisation
- density
- cohesion between molecules
- high surface tension
why is it important that water is a universal solvent?
- things dissolve easily in water because it’s polar
- the slightly positive hydrogens attract negative solutes
- the slightly negative oxygen attracts positive ions in solutes
why is it important for prokaryotes and eukaryotes that water is a universal solvent?
- cytosol in those cells is mainly water so many solvents can dissolve with the cell and be transported
why is water important as a transport medium?
- cohesion (water molecules ‘sticking’ together by hydrogen bonds) allows water to move up xylem as a continuous column of water which is an advantage as it’s easier to move than individual molecules
why does water have a high specific heat capacity and why is it important?
- has a high specific heat capacity because hydrogen bonds between molecules need lots of energy to be broken
- it’s important because it allows internal temps in animals and plants to stay relatively the same so enzymes won’t denature or reduce activity because of temp changes
why does water have a high latent heat of vaporisation and why is it important?
- has a high latent heat of vaporisation because lots and f energy is needed to break hydrogen bonds between water molecules and turn it into a gas
- it’s important because it gives animals a cooling effect
why is water important as a habitat and why is it important that it has a high surface tension?
- it buffers temperature which allows a stable environment
- cohesion gives water a high surface tension which allows small invertebrates to move and live on surface, and give them a habitat away from predators
why is density as a property of water important?
- ice is less dense than water because of hydrogen bonds so it floats on water and gives animals a surface habitat
what is a monomer and what is a polymer? give the examples.
- monomer: smaller units which can create larger molecules. examples are glucose (and other monosaccharides), amino acids, and nucleotides
- polymer: lots of monomers bonded together. examples are starch (and other polysaccharides), cellulose, glycogen, protein, DNA and RNA
what are carbohydrates?
- a group of substances used as both energy sources and structural materials in organisms
what are the chemical elements that make up biological molecules?
- carbohydrates: C, H, and O
- lipids: C, H, and O
- proteins: C, H, O, N, and S
- nucleic acids: C, H, O, N and P
what are the main three groups of carbohydrates? what do they consist of?
- monosaccharides: simple sugars. general formula (CH2O)n, where ‘n’ can be 3-7.
- disaccharides: ‘double’ sugars, formed from two monosaccharides.
- polysaccharides: large molecules formed from many monosaccharides.
what are the four types of monosaccharides?
- glucose
- fructose
- galactose
- ribose
what are the three types of disaccharides? how are they formed?
- sucrose
- maltose
- lactose
- joined together by a glycosidic bond which produces water, making disaccharides formed by a condensation reaction
what are the three types of polysaccharides?
- starch
- cellulose
- glycogen
what are the two monosaccharides that form each of the disaccharides?
- maltose= glucose + glucose
- lactose= glucose + galactose
- sucrose= glucose + fructose
what are the properties of alpha glucose? what is the ring structure for alpha glucose?
- small and soluble so is easily transported in the bloodstream
- major energy store for most cells
(find a picture of alpha glucose structure to find out if correct)
what is a condensation reaction?
joining two molecules together by removing a water molecule, a chemical bond is formed
what is a hydrolysis reaction?
splitting apart molecules through the addition of a water molecule, a chemical bond is broken
what are the properties of starch? (give the monomers, bonds between monomers, function, location, structure, and how structure leads to function)
monomers: alpha glucose
bonds between monomers: 1-4 glycosidic bonds in amylose. 1-4 and 1-6 in amylopectin
function: store of glucose
location: plant cells
structure: made of two polymers- amylose (unbranded helix) and amylopectin (branched molecule)
how does structure lead to function: insoluble- needed for storage, branches- easily hydrolysed to release glucose monomers for respiration, helix formed- compact
what are the properties of cellulose? (give the monomers, bonds between monomers, function, location, structure, and how structure leads to function)
monomers: beta glucose
bonds between monomers: 1-4 glycosidic bonds
function: structure strength for cell wall
location: plants (cell wall)
structure: polymers form long, straight chains which are held in parallel by many hydrogen bonds that form fibrils. microfibrils join to form a cellulose fibre
how does structure lead to function: insoluble- so can hold in water. strong- hydrogen bonds provide strength which supports plant and prevents cell from bursting. microfibrils- water can move through and along cell wall and determines how cell changes shape
what are the properties of glycogen? (give the monomers, bonds between monomers, function, location, structure, and how structure leads to function)
monomers: alpha glucose
bond between monomers: 1-4 in short chains and 1-6 in branching
function: storage for glucose
location: animals- mainly in muscle and liver cells
structure: a highly branched molecule
how does structure lead to function: branched structure- increases surface area for quicker hydrolysis. insoluble
what are the four features of lipids?
- they are macromolecules
- they are non-polar molecules (so insoluble in water)
- they dissolve in organic solvents
- they are hydrophobic
what are lipids made up of?
- made up of two molecules, fatty acids and glycerol
do lipids form polymers?
no
what are the uses of lipids?
- energy store
- energy source
- hormones
- insulation
what does the structure of a triglyceride consist of? what is the structure?
- consists of a glycerol molecule and three fatty acids (find a picture of structure to check if answer is correct)
how are triglycerides formed? what does this reaction form?
- glycerol molecule binds to the three fatty acids through a condensation reaction
- forms an ester bond
what are the properties of triglycerides?
- can transfer energy because of its large ratio of energy storing carbon-hydrogen bonds compared the the number of carbon atoms. a lot of energy can be transferred when broken down
- can act as a metabolic water source due to the high ratio of hydrogen to oxygen atoms because triglycerides can release water if oxidised. (essential for desert animals)
- lipids relatively low in mass so a lot can be stored in an animal without increasing mass and preventing movement.
what are phospholipids made up of?
- a glycerol molecule
, two fatty acid chains and a phosphate group (attached to the glycerol) - the fatty acids also bond to the glycerol via two condensation reactions, resulting in two ester bonds
what are the properties of phospholipids?
- hydrophilic ‘head’ of phospholipid can attract with water as it’s charged. due to it being charged it repels other fats
- fatty acid chains isn’t charged. hydrophobic ‘tail’ repels water but mixes with fats
- has two charged regions making it polar
- heads are exposed to water and the tails are not, forming a phospholipid bilayer membrane structure which makes up the plasma membrane around cells
what is the structure and function of cholesterol?
- a sterol
- sterols have 4 carbon rings and a hydroxyl group at one end and they both have hydrophobic and hydrophilic areas
- cholesterol is embedded within cell membranes to impact fluidity. they help reduce the fluidity of membranes at high temps and increase fluidity at low temps
what are proteins made up of?
- made up of one or more large polymers, creating a macromolecule
What is the general structure of an amino acid?
-COOH carboxyl / carboxylic acid group.
-R variable side group consists of carbor chain & may include other functional groups e.g. benzene ring or -OH (alcohol).
-NH, amine/ amino group.
How do polypeptides form?
- Condensation reactions between amino acids form peptide bonds
(-CONH-). - There are 4 levels of
protein structure.
define ‘primary and secondary structure’ of a protein?
primary: the sequence/order, number, and type of amino acids in the polypeptide chain- this is a polymer
secondary: the sequence of amino acids causes parts of a protein molecule to bend into a alpha helix shaped or beta pleated sheets
- the shapes are held together by hydrogen bonds that form between the C=O groups of the carboxylate group of one amino acid, and the H in the amino group of another amino acid
Describe the 2 types of secondary protein structure.
alpha helix:
- All N-H bonds on same side of protein chain.
- Spiral shape.
- H-bonds parallel to helical axis.
beta-pleated sheet:
- N-H & C=0 groups alternate from one side to the other.p
Define ‘tertiary structure’ of a protein. Describe the bonds present.
- 3D structure is formed from the secondary structure bending and folding. the shape is held in place by:
- weak hydrophobic and hydrophilic interactions
- many hydrogen bonds (weak, easily broken)
3.ionic bonds, relatively strong bonds between charged
R groups (pH changes cause these bonds to break) - disulfide bonds, strong covalent bonds which form between the R-groups of two amino acids that contain sulphur
Define ‘quaternary structure’ of a protein.
- a functional protein made of more than one polypeptide chain, for example, haemoglobin
-Precise 3D structure held together by the same types of bond as tertiary structure.
what is the structure and function of globular proteins? give examples
- polypeptide chains ‘roll up’ into a spherical shape
- relatively unstable structure
- hydrophobic R groups on inside, hydrophilic R groups on the outside, making it soluble
- involved metabolic functions
- examples: enzymes, antibodies, some hormones like insulin, haemoglobin
Describe the structure of haemoglobin.
- globular protein with a prosthetic group attached to each polypeptide chain.
- not made of amino acids, instead contain iron
- has a prosthetic group attached so can be described as a conjugated protein, meaning a non- protein group is added to it
Describe the structure and function of fibrous proteins. give examples
- polypeptide chains form long twisted strands linked together (rope-like shape)
- stable (unreactive) structure
- form hydrogen bonds with adjacent chains
- insoluble in water
- useful for structure and support
- examples: collagen in bone and keratin in hair
list the components of collagen, keratin, and elastin (fibrous proteins)
- collagen: quaternary structure with three polypeptide chains held together by hydrogen and covalent crosslinks between the molecules. forms part of bones, tendons, cartilage, ligaments, and connective tissue
- keratin: used to form skin and hair which protects the body. important that its insoluble so the structures aren’t broken down by water in the environment
-elastin: makes up elastic fibres around alveoli and blood vessels, allows these structures to stretch and recoil to their original shape and size
list the components of pepsin and insulin (globular proteins)
pepsin: enzyme found in the stomach, a protease enzyme able to digest other proteins using its specifically shaped active site complementary to the substrate. (enzymes are globular proteins)
insulin: hormone produced by the beta cells in the pancreas to lower blood glucose concentration. the specific 3D shape is complementary to the receptors on the cell surface membranes of its target cells (liver and muscle)
describe how to test for starch
- add iodine solution
- positive test observation = solution turns from orange to blue-black
describe how to test for reducing sugars
- add Benedict’s solution and heat for 5 mins at 80°C
- positive test observation = solution turns from blue to green, yellow, orange, or brick red (more red = higher conc. of reducing sugar)
OR, use a reagent test strip to test for the presence and conc. of reducing sugars
describe the benedict’s test for non reducing sugars
- negative benedict’s test, solution remains blue
- hydrolyse non reducing sugars using hydrochloric acid and boil for 5 mins
- cool solution then add an alkali (like sodium hydroxide) to neutralise
- add benedict’s solution and hear for 5 mins at 80°C
- positive test observation = solution turns from blue to green, yellow, orange, or brick red (more red = higher conc. of reducing sugar)
describe how to test for proteins in a sample
- add biruet solution (confirms presence of a peptide bond)
- positive test observation = solution turns from blue to purple
describe how to test for lipids in a sample
- dissolve sample in ethanol
- pour sample on top of distilled water
- positive test observation = milky white emulsion forms
how can the concentration of a solution be measured quantitatively?
using a colourimeter: to measure absorbance/% transmission
1. set filter in colorimeter
2. calibrate to zero using distilled water
3. insert samples from your biochemical test
4. measure the % transmission of light
5. draw a calibration cure using results from know concs. of glucose
using a biosensor: detects the presence of a chemical
1. single strand of DNA or protein that are complementary to the test sample is immobilised. the added sample binds to the immobilised DNA/protein
2. binding causes a change in a transducer and as a result, an electronic current is released
3. this current is processed to determine the conc. of the sample present
Outline the principles and process of paper/ thin-layer chromatography.
- Use capillary tube to spot solution onto pencil ‘start line’ (origin) 1 cm above bottom of paper.
- Place chromatography paper in solvent. (origin should be above solvent level).
- Allow solvent to run until it almost touches other end of the paper. Molecules in mixture move different distances based on relative solubility in solvent/attraction to paper.
What are Rf values? How can they be calculated?
- Ratios that allow comparison of how far molecules have moved in chromatograms.
- Rf value = distance between origin and
centre of pigment spot ➗ distance between origin and solvent front.
what are nucleotides? what do they contain? what is its structure?
- the monomers from which nucleic acids (like DNA and RNA) are formed
- contains nitrogenous bases that can be categorised by their ring structure, purines and pyrimidines
- look at a picture of their structure
how many carbon rings do purines and pyrimidines have? describe their structure
- purines have 2 carbon rings structures (adenine and guanine)
- pyrimidines have 1 carbon ring structure (cytosine, thymine, and uracil)
- look at pictures of their structures
what are the penrose sugars in DNA and RNA?
DNA = deoxyribose
RNA = ribose
name the complementary bas pairs in DNA and RNA
DNA:
- 2 hydrogen bonds between adenine and thymine
RNA:
- 2 hydrogen bonds between adenine and uracil
BOTH have 3 hydrogen bonds between guanine and cytosine
how are polynucleotide strands are formed and broken down?
- nucleotides undergo condensation reactions which forms strong phosphodiester bonds (sugar-phosphate backbone) between the nucleotide monomers, creating the polymer (the polynucleotide)
- hydrolysis reactions use a molecule of water to break these bonds
what is a phosphodiester bond?
- a strong covalent bond that forms between the pentose sugar and phosphate of different nucleotides
what is the structure of ATP and ADP?
- nucleotide derived from adenine
- contains 3 inorganic phosphate groups and ribose (a pentose sugar)
- ADP has 2 phosphate groups
- look at a picture
what are the roles of ATP? how is it made? how can it be reversed
- essential for metabolism
- an immediate source of energy for biological processes
- made during respiration via a condensation reaction and using the enzyme ATP synthase
- the reaction is reversible because ATP can be hydrolysed using the enzyme ATP hydrolase
true or false? 1. the inorganic phosphate formed from hydrolysing ATP can bond onto completely different compounds to make them more reactive. 2. breaking one of the bonds between the phosphate groups does not release a small amount of energy
- true (phosphorylation)
- false (it does release a small amount of energy)
describe the structure of DNA
- codes for the sequence of amino acids in the primary structure of a protein which determines the final 3D structure and function for a protein
- polymer forms a double helix made of two anti parallel strands joined together by hydrogen bonds between the bases on the two different strands
how does the structure of DNA relate to its function?
- stable structure due to the sugar-phosphate backbone (covalent bonds) and the double helix
- double stranded so replication can occur using both strands as a template
- weak hydrogen bonds between the bases for easy separation of the two strands in a double helix during replication
- large molecule that carries lots of information
- complementary base pairing allows identical copies to be made
explain DNA precipitation.
- DNA can be extracted from plant material
- homogenise the cell with a detergent, this will break open the cell and its membranes to release its contents. filter to remove large debris
- add salt to break hydrogen bonds between the DNA and water molecules
- add protease to digest the proteins associated with the DNA
- add ice cold ethanol to precipitate out the DNA from the solution. the DNA appears as white strands
what are the three types of RNA?
- rRNA (ribosomal RNA) makes up the bulk of ribosomes
- tRNA (transfer RNA)
- mRNA (messenger RNA)
describe mRNA.
- mRNA (messenger RNA) copy of one gene from DNA, much shorter than DNA, created in the nucleus to then leave via the nuclear pore to carry the copy of genetic code of one gene to a ribosome in the cytoplasm.
- short lived as it only needs to survive long enough for protein synthesis
- single stranded and every three. axes in the sequence code for one specific amino acid, the three bases are therefore called codons
describe tRNA.
- found in the cytoplasm
- single stranded but folded to create a cloverleaf shape held in place by hydrogen bonds
- brings a specific amino acid to the ribosome which is determined by the three bases found of the tRNA called the anticodon
- the anticodon is complementary to the three bases on the mRNA (codon)
why is DNA described as semi-conservative?
- in replication one strand from the original DNA is kept as a template and a new strand is made
what is a mutation?
- a change in the DNA base sequence
- often happens spontaneously during DNA replication which happens in S-phase in interphase of the cell cycle
describe the DNA double helix.
- the top and bottom of each strand are described as either 3’ (prime) end or the 5’ (prime) end
- the numbers refer to which carbon within the deoxyribose sugar of the nucleotide is closest to the top or bottom
true or false? the enzyme that catalyses DNA replication is complementary in shape to the 3’ end and can therefore only attach to the DNA at this location
true
describe the stages of DNA replication
- DNA helicase breaks the hydrogen bonds between the complementary bases of the two DNA polymers to allow each strand to act as a template
- free floating DNA nucleotides attach to their complementary bases on the template strand of DNA. hydrogen bonds form between the base pairs
- DNA polymerase joins adjacent DNA nucleotides together in a 5’ to 3’ direction via condensation reactions to form phosphodiester bonds between the nucleotides, creating a new polymer chain for DNA
what are the three special features of the genetic code? describe them.
- degenerate: more than one triple of bases codes for the same amino acid (64 possible triplets for 20 amino acids)
- universal: same triplet of bases codes for the same amino acid in all organisms
- non overlapping: each base in a gene is only part of one triplet of bases that codes for one amino acid. each triplet is only read once
what are the two stages of protein synthesis? describe them.
- transcription - where the DNA sequence for one gene is copied into mRNA
- translation - where the mRNA joins with a ribosome made of protein and rRNA, and a corresponding tRNA molecule brings the specific amino acid the codon codes for
what are introns and exons?
- introns: sequences of bases in a gene that don’t code for amino acids and therefore polypeptide chains. they are removed, spliced, out of mRNA molecules after transcription
- exons: sequences of bases in a gene that code for sequence of amino acids
what are start and stop codons?
- start codons are at the beginning of every gene and allow the ribosome to attach
- stop codons are at the end of every gene, there are three bases that do not code for an amino acid. this stop codon causes the ribosome to detach and ends translation
outline the process of transcription
- DNA helicase breaks the hydrogen bonds between the two strands of DNA, causing the DNA helix to unwind and one strand is used as a template
- free mRNA nucleotides align opposite to the exposed complementary DNA bases
- the enzyme RNA polymerase joins together the adjacent RNA nucleotides, forming phosphodiester bonds to create a new mRNA polymer chain
- once the gene is copied the mRNA is modified (splicing the introns) then leaves the nucleus through the nuclear envelope pores
outline the process of translation
- the tRNA molecule with the complementary anticodon to the start codon aligns opposite the mRNA, held in place by the ribosome (two can be held at a time)
- two amino acids delivered by the tRNA molecule are joined together via a peptide bond which is catalysed by an enzyme using ATP
- ribosome moves along the mRNA molecule to the next codon and another complementary tRNA attaches. this continues until the ribosome reaches the stop codon
- polypeptide chain is now formed and will either the golgi body for folding and modification
