biological molecules Flashcards
1
Q
define the term “monomer.”
A
simple, basic, molecular unit from which larger molecules are made from.
- monosaccharides, amino acids, nucleotides
2
Q
define the term, “polymer.”
A
large, complex molecule made up of repeating monomers joined together.
- starch, glycogen, cellulose, DNA/RNA
3
Q
what occurs during a condensation reaction?
A
- joins two monomers together
- forms chemical bond
- eliminating a water molecule
4
Q
what occurs during a hydrolysis reaction?
A
- separates two monomers
- breaks chemical bond
- requires addition of a water molecule
5
Q
what elements do carbohydrates contain?
A
- carbon, hydrogen and oxygen
6
Q
what are monosaccharides? give 3 examples that all have formula C6H12O6.
A
simplest sugars, monomers from which larger carbohydrates are made.
- glucose
- fructose
- galactose
7
Q
how does formation of disaccharides occur?
A
- forms when 2 monosaccharides join together by a condensation reaction forming glycosidic bond.
- hydroxyl group on one joins with hydrogen from another - release water molecule for each bond. one oxygen joins 2 sugars
8
Q
how is maltose formed from?
A
glucose + glucose
9
Q
how is sucrose formed from?
A
glucose + fructose
10
Q
how is lactose formed from?
A
glucose + galactose
11
Q
how is lactulose formed from?
A
galactose + fructose
12
Q
define what is meant by the term “polysaccharide”
A
formed when more than 2 monosaccharides join together via condensation reaction, releasing a water molecule for each glycosidic bond
- starch, glycogen, and cellulose are polysaccharides
13
Q
what is the function and structure of starch?
A
function
- found in parts of plant in form of small grains. large amounts occur in seeds/storage organs like potato tubers - energy source
structure
- made of 2 polysaccharides of a-glucose: amylose (unbranched helical case, C1-4) and amylopectin (branched every 20 monomers.)
- contain C1-4 + C1-6 glycosidic bonds
14
Q
how does is the structure of starch relate to its function?
A
- helical as angles on glycosidic bonds - compact, fit more in, good for storage
- insoluble: not affect water potential
- branched chains: more efficient hydrolysis for respiration
- large: can’t leave cell
15
Q
what is the main function and structure of glycogen?
A
function
- main storage of energy in animals, stores in muscle and liver cells
structure
- polysaccharide of alpha glucose with branded chains every 10 monomers. C1-4 and C1-6 glycosidic bonds
16
Q
how does glycogen’s structure relate to its function?
A
- branched: rapid hydrolysis into glucose to meet demands of cell
- insoluble: doesn’t affect water potential
- compact: good for storage
17
Q
describe the function of cellulose
A
- provides structural strength in cell walls of plants - results many hydrogen bonds between parallel chains of microfibrils
- high tensile strength of cellulose - stretched without breaking which makes possible for cell walls to withstand turgor pressure
- cellulose fibres freely permeable allows water to leave and reach cell surface membrane
18
Q
describe the structure of cellulose
A
- polysaccharide of beta glucose monosaccharides joined by C1-4 glycosidic bonds
- form straight chains = due to inversion of b-glucose many hydrogen bonds form between long chains giving cellulose its strength —> forms microfibrils
19
Q
how is cellulose’s structure relates to its function?
A
hydrogen bonds form between chains - collective strength to the cell wall
20
Q
what’s the test for reducing sugars? (benedict’s)
A
- can donate e-
- glucose, fructose, galactose, maltose, lactose
- add benedict’s reagents (contains copper II sulfate) to the sample.
- place in a gently boiling water bath for 5 mins
21
Q
what’s a positive result of reducing sugars?
A
blue —> green, yellow, orange, brick-red
semi-quantitive = depend on conc. reduces blue copper sulfate into red copper oxide
22
Q
what is the method testing for non-reducing sugars?
A
- can’t donate e-
- sucrose
- if negative from first test, needs hydrolysis into monosaccharides.
- add HCl then neutralise with sodium hydrogen carbonate
- then add benedict’s solution + in gently boiling water bath 5 mins
23
Q
what is the positive result for non-reducing sugars?
A
blue —> brick red
(high conc sugars now as 2 monosaccharides)
24
Q
what is the test for starch? and what is the positive result?
A
method
- add iodine in potassium-iodide solution to the sample.
positive result
- orange —> blue/black
25
what elements do lipids contain?
C, H and O
26
what is the structure and function of triglycerides ?
structure:
- 1 molecule of glycerol attached to 3 fatty acids. non-polar, hydrophobic.
formation:
- condensation reaction where a H from OH on glycerol joins with OH group on COOH to release water molecule —> forms ester bond.
function:
- storage molecules
properties:
- insoluble in water - hydrophobic fatty tails face inwards, glycerol outwards = water potential unaffected
- long hydrocarbon tails, lots of C-H little O - oxidised releases energy
27
describe the structure of phospholipids
- 1 glycerol, 1 phosphatase group 2 fatty acid tails
- glycerol + phosphate group are head = PO4^2- charged, polar, hydrophilic, soluble 2 fatty acids tails = non polar, insoluble in water, hydrophobic
- amphipathic = both hydrophobic and hydrophilic regions
28
describe the formation of phospholipids
condensation reactions between glycerol and phosphate group forming phosphate ester bond + reaction between glycerol and fatty acids form ester bond
releases water molecule per bond
29
what is the main function and properties of phospholipids ?
function = mainly phospholipid bilayer and micelles
properties =
- bilayer —> hydrophilic heads attract water, tails repel, tails inwards shielded, heads outward
- barrier —> cell membrane to water soluble molecules
- electrical insulator —> ions can’t enter as they charges and repel fatty acid hydrophobic tails
- stability —> saturated fatty acids less fluid - move past each other to keep membrane fluid change shape and move
30
what do fatty acids compose of?
a carboxyl group (COOH) and a hydrocarbon rail which can vary (R)
- saturated (no double bonds), saturated with hydrogen or unsaturated (C=C double bond) —> chain to kink
31
describe the test for lipids
method
- add ethanol to the sample
- then add water
- shake
positive result
- white/milky emulsion
hazards
- ethanol is flammable - don’t test near open flames
32
33
what is proteins composed of?
monomers are amino acids
contain carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur
34
amino acid structure
NH2 = anime group
COOH = carboxyl group
R = variable group
20 amino acids
only vary in R group
glycine - H in R group
35
dipeptide and polypeptide formation
condensation reaction between OH on carboxyl group and H on amine group - releasing water molecule + form peptide bond
2 amino acids only vary- dipeptide
2+ amino acids - polypeptide
36
describe the primary structure of proteins
- sequence of amino acids in polypeptide chain
- DNA of cell determines primary structure of protein by instructing cell to add certain amino acids in specific quantities in sequence
- affects shape = this function of protein - primary structure specific for each protein
37
describe the secondary structure of proteins
- hydrogen bonds form between amino acids close together
- causes polypeptide chain to be coiled into an alpha helix folded into a beta pleated sheet
38
describe the tertiary structure of proteins
- further conformational change of the secondary structure, coiled or folded further, leaded to addition bonds forming between the R groups.
addition bonds:
- hydrogen bonds = between R groups
- disulphide bridges = occurs between cysteine amino acids
- ionic bonds = between charged R groups
39
describe the quaternary structure of proteins
- the way polypeptide chains assembled. stabilised with hydrogen bonds, ionic bonds and disulfide bridges
- same polypeptide chains = homodimer
- different = heterodimer
- more than one polypeptide chains
40
explain the relationship between protein structures and function
- the sequence of amino acids determined by genetic code
- effects primary structure. primary structure determines how the polypeptide is coiled or folded in secondary structure
- determines where bonds form, affects whole protein shape. shape of proteins determines its function
41
explain how a change in DNA base sequence can affect an enzyme reaction
1) base sequence determines sequence of amino acids in polypeptide chain
2) 3 bases code for one amino acids
3) primary structure determines position of bonds between R groups in tertiary structure
4) hydrogen, ionic bonds and disulphide bonds
5) change in tertiary structure changes shape of active site of enzyme
6) substrate can no longer bind to form enzyme substrate complex
42
how to test for proteins
biuret test
positive result: blue —> purple
43
what are enzymes?
biological catalysts that speed up the rate of a chemical reaction
44
how do enzymes speed up a reaction?
lowers the activation energy by:
- providing an alternate pathway for the reaction with lower energy
- binding reactants at active site and positioning them correctly
- bring reactants together so less kinetic energy used by moving round and trying to collide
45
describe the lock and key model
1) active site fixed shape
2) substrate is complementary to active site
3) binds to it
4) forms enzyme substrate complex
5) enzyme catalyses reaction to form products
6) enzyme is unchanged
46
describe the induced fit model
1) active site of enzyme not completely complementary to substrate
2) substrate bunds and distorts hydrogen bonds holding enzyme in shape
3) active site changes shape to complete fit
4) enzyme substrate complex formed. enzyme catalyses reaction and releases products
5) conformational change of active site
47
what are the factors affecting enzyme activity?
- temperature
- pH
- enzyme conc
- substrate conc
- competitive inhibitors
- non-competitive inhibitors
48
explain how temperature affects enzyme activity
- as temp increases, particles vibrate more as they have more KE/ move faster
- collisions to form enzyme-substrate complexes more likely. energy of collisions also increases
- rate increases up to optimum temp
- if temp continues to increase past optimum, vibrations cause hydrogen bonds to break - holding enzyme its tertiary structure
- enzyme denatures at the active site changes shape
49
how does pH affect enzyme activity?
- enzymes have optimum pH (pH7 but pH2 got pepsin)
- above and below the optimum the enzyme denatures due to H+ and OH- ions altering hydrogen and ionic bonds holding enzyme in tertiary structure
50
how does enzyme concentration affect enzyme activity ?
- increasing enzyme concentration increases rate of reaction.
- more enzymes available so collisions with substrates to form enzyme-substrate complexes likely.
- if substrate conc limiting increasing conc of enzymes has no further effect.
51
how does substrate concentration affect enzyme activity?
- increasing substrate conc increases rate of reaction.
- as collisions form enzyme-substrate complexes more likely to—> increases up to saturation point where all enzyme active sites in use
- increasing this after this has no further effect. over reaction substrate conc reduces as product formed
- rate reaction decrease over time, initial rate highest. when it plateaus, reaction hasn’t stopped —> constant rate
52
what are competition inhibitors? how does this affect enzyme activity?
- have similar shape to the substrate so it competes with the substrates to bind to the enzyme
- they block active site —> reduces the amount of enzyme-subtrate complexes that can form
- increasing competitive inhibitors reduces rate as they take up active sites.
- increasing substrate conc reduced effect of competitive as collisions more likely to a point
53
what are non-competitive inhibitors? how do they affect enzyme activity?
- they don’t compete for the active sites as they have a diff shape.
- they bind away from active site in allosteric site —> cause permanent conformational change in active site
- substrates cannot bind + form enzyme-substrate complexes as no longer complementary
- increasing substrate conc has no effect as non-competitive inhibitor doesn’t compete and alters active site shapes
54
describe the function of DNA (deoxyribonucleic acid)
- stores genetic info
- hereditary material responsible for passing genetic material from cell to cell from generation to generation
- provides generic diversity in organisms
55
describe the function of RNA.
- transfer genetic info
- from DNA to ribosomes to make proteins (translation)
56
what does the structure of a nucleotide structure contain?
- phosphate group
- pentose sugar - deoxyribose or ribose
- nitrogenous base - A,T,C,G,U
57
how is a polynucleotide formed?
- condensation reaction between phosphate group + pentose sugar - form phosphodiester bond
- forms sugar-phosphate backbone where pentose sugars and phosphate groups joined in a chain.
58
describe the DNA structure
- double helix structure
- 2 seperate polynucleotide strands wound round each other
- very long
- coiled tightly
- held by hydrogen bonds between bases
- pentose sugar in nucleotides - deoxyribose
- nitrogenous bases - adenine, thymine, cytosine, guanine.
59
how is DNA adapted for its function?
- double stranded —> both strands act as templates for semi-conservative replication
- weak hydrogen bonds between bases —> unzipped for replication
- complementary base pairing —> accurate replication as free nucleotides complementary exposed bases: reduced mutation
- many hydrogen bonds —> stable/strong molecule
- long molecule —> stores lots genetic info
- double helix —> compact, store lots in small space
60
what is the purpose of complementary base pairings ?
helps when DNA relocate as enables identical copies to be created as free nucleotides bind to complementary base + reduce copying errors that causes mutations
- A to T/U
- C to G
hydrogen bonds :
- 2 bonds between A + T/U
- 3 bonds between C + G
61
describe the RNA structure
- single polynucleotide strand
- shorter chain
- penrose sugar in nucleotides- ribose sugar
- nitrogenous bases - adenine, uracil, cytosine, guanine
62
why does DNA replicate by semi-conservative replication?
- DNA copies itself before cell division so new cell has full amount of DNA —> in interphase of cell cycle, synthesis phase
- half of the strands in new DNA molecule from original DNA molecule + half newly synthesised
- ensures genetic continuity between generations of cells
63
what’s the purpose of DNA helicase?
- unzipping, breaks hydrogen bonds to separate the polynucleotide strands
64
what’s the purpose of DNA polymerase?
- join together adjacent nucleotide
65
what’s the purpose of DNA primase?
catalyse the synthesis of short RNA molecule used as primers for DNA polymerases
66
what’s the purpose of DNA ligase?
- joins DNA fragments together
67
describe the stages of semi-conservative replication
1) DNA helicase attaches to molecule, breaks hydrogen bonds between DNA bases. 2 strands unwinds/seperates. —> each strand is a template for new strand
2) free DNA nucleotides attach to complementary exposed base pairs from original strand
3) DNA polymerase catalyses condensation reactions so a phosphodiester bond can form between activated adjacent nucleotides to form new polynucleotides
4) 2 sets of daughter DNA each with one strand of original DNA and one newly synthesised strand
68
what’s the role of DNA ligase?
- DNA polymerase work in one direction (5’ to 3’) as active site of enzyme complementary to 3’ end
- 5’ to 3’ strand is leading strand AS DNA polymerase follows the DNA helicase
- strands are antiparallel —> other strands runs 3’ to 5’
- section of strand jumps to next bit leaving Okzaki fragments —> lagging strand.
- DNA ligase joins together the shorter polynucleotides fragments together
69
explain what is meant by the ‘conservative model.’
- original DNA molecule remain intact and that separate daughter DNA copy built up from new molecules of deoxyribose, phosphate and organic bases.
- one would be made entirely of new material while other: original material.
70
explain what is meant by the ‘semi-conservative model.’
the original DNA molecule split into 2 separate strands, each which replicated its mirror image.
each of 2 new molecules have one strand of new material and one strand of original material
71
what are the evidence for semi-conservative replication?
- meselson and stahl proved DNA replication by semi-conservative replication + not by conservative.
3 facts based on experiment:
- all bases in DNA contain nitrogen
- nitrogen has 2 forms: lighter N: N-14 and heavier isotope: N-15
- bacteria they incorporate nitrogen from their growing medium into new DNA they make
72
why is energy important?
- active transport
- DNA replication
- cell division
- protein synthesis
- building larger molecules into smaller
73
ATP description `
- adenosine triphosphate is a nucleotide derivative. Modified form of nucleotide
- not energy!! It’s a store of energy
- energy used to make ATP. Energy released when ATP hydrolysed
- made from adenine nucleotide base, ribose pentose sugar + 3 phosphate groups
74
RESPIRATION description
- release of energy from glucose
- the energy released from glucose used to make ATP
- once ATP made, diffuses to part of the cell that requires energy
75
what are the properties of atp?
1) stores/released only a small, manageable amount energy at a time - no energy wasted as heat
2) small, soluble molecule so easily transported around cell
3) broken down easily to release energy instantly
4) ATP can be remade quickly
5) can make other molecules more reactive by transferring one of their phosphate groups to them - phosphorylation
6) can’t pass out of cell so cell always have immediate supply energy
76
why do we need ATP if we have glucose?
cell can’t get its energy directly from glucose so its broken down in respiration in order energy be released
- glucose bigger molecules so not easy to transfer
- not easily broken down - multistage process
77
explain how ATP is broken down
- when cell needed energy ATP broken down during hydrolysis reaction - requires water molecule into ADP (adenosine diphosphate) and Pi (inorganic phosphate).
- when phosphate bond broken, energy released —> reaction catalysed by ATP hydrolase
78
describe how ATP can be resynthesised
- ATP can be re-synthesised in condensation reaction between ADP and Pi.
- a water molecule lost when a new phosphate bond formed. During both respiration + photosynthesis + catalysed by enzyme ATP synthase.
79
what is the importance of water?
water makes up 80% of cell’s contents and has loads important functions:
Main properties:
- important metabolite
- good solvent
- high latent heat of vaporisation
- high specific heat capacity
- very cohesive
80
describe the structure of water in terms of its polarity.
- shared negative electrons pulled towards oxygen atoms as its more electronegative, other side of each hydrogen atom left with slight positive charge (delta +).
- unshared negative e- on oxygen atoms give it a slight negative charge (delta -). Makes water polar molecule.
81
describe the structure of water in terms of hydrogen bonding
- hydrogen bonds are weak bonds that form between slightly positively charged hydrogen atom in one molecule + slightly negatively charged oxygen atoms give in other as they attracted
82
explain how water is an important metabolite
- metabolic reactions involve condensation/hydrolysis reaction.
- energy from ATP released through a hydrolysis reaction
- metabolic reactions is a chemical reaction in living organism to keep organism alive —> metabolite is a substance involved in metabolic reaction
83
explain how water is a good solvent?
- a solvent is a substance capable of dissolving another substance. —> polar water, delta positive hydrogen atoms attracted to negative ion + delta negative oxygen attracted positive ion
—> ions surrounded by water molecules so it’ll dissolve.
84
explain why water has a high latent heat of vaporisation
- latent heat is the heat energy that’s needed to change a substance from one state to another (e.g liquid to gas)
- water evaporates when hydrogen bonds holding water molecules together broken. - allows water molecules on surface to escape into air as gas —> takes lots of energy to break hydrogen bonds between water
- use water loss through evaporation to cool down without losing too much water.
- when water evaporates it carries away heat energy from a surface, which cools the surface and helps lower temp.
85
explain how water has a high specific heat capacity
- buffers changes in temperature —> energy needed to raise the temp of 1kg of a substance by 1 degree Celsius
- H bonds give water high shc. - when water heated lots heat energy used to break H bonds between water molecules —> less heat energy available to increase temp of water - HIGH SHC.
- organisms doesn’t experience rapid temp - water good habitat as temp under water more stable than on land. - help maintain constant internal body temp
86
explain how water is very cohesive
- cohesion is attraction between molecules of same type.
- water molecules very cohesive (stick together) as they are polar. Strong cohesion helps water to flow, good for transporting substances.
- e.g: water travels in columns up xylem.
- water has high surface tension when it comes into contact with air. —> pond skaters, and other insects can ‘walk’ on surface of ponds
87
what are inorganic ions?
- doesn’t contain carbon
- inorganic ions perform range of functions
- specific function of an ion performs relates to its properties
- ions role determines whether its found in high or low concentrations
88
the inorganic ion of iron, what is its main functions?
- haemoglobin in RBCs.
- Fe2+ that binds to oxygen in haem. When oxygen bound, Fe2+ temporarily becomes an Fe3+ ion, until oxygen released
89
the inorganic ion of phosphate, what is its main functions?
- phosphorylation - phosphate ion attached to another molecule, its known as phosphate group.
- bonds between phosphate group that stores energy in ATP.
90
Hydrogen - inorganic ions
- pH calculated based on conc of hydrogen ions in environment —> more H+ present, lower pH.
- enzyme-controlled reactions are all affected by pH
91
Sodium - inorganic ions
- glucose + amino acids need a bit of help crossing cell membranes.
- a molecule of glucose/amino acid transported into a cell alongside sodium ions —> co-transport
92
explain how a change in DNA base sequence can affect an enzyme reaction
1) base sequence determines sequence of amino acids in polypeptide chain
2) 3 bases code for one amino acids
3) primary structure determines position of bonds between R groups in tertiary structure
4) hydrogen, ionic bonds and disulphide bonds
5) a change in tertiary structure changes shape of active site of enzyme
6) substrate no longer bind to form enzyme substrate complex.
