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biology > 1.3 Biological molecules 2 > Flashcards

1.3 Biological molecules 2 Flashcards

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1
Q

what are the 3 components of nucleotides

A

pentose sugar - in RNA the pentose sugar is ribose and in DNA its deoxyribose
nitrogen containing base - adenine, thymine, guanine, cytosine
phosphate group

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2
Q

what are the 2 names of the types of bases that can be present in a nucleotide

A

purine bases and pyrimidine bases

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3
Q

what are purines and some examples

A

purines have 2 nitrogen containing rings
guanine and adenine

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4
Q

what are pyrimidines and some examples

A

pyrimidines have 1 nitrogen containing ring
cytosine, thymine (only found in DNA), uracil (only found in RNA)

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5
Q

what is the formula for a phosphate ion

A

PO4^3-

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6
Q

what are 2 properties of nucleotides

A

-acidic molecules
-carry a negative charge

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7
Q

how is a nucleotide formed

A

-the pentose sugar, base and phosphate group are joined together by condensation reactions
-2 water molecules are lost for every nucleotide made
-the phosphate group and pentose sugar and joined by an ester bond, which turns into a phosphodiester bonds when multiple nucleotides are joined by the phosphate groups
-the pentose sugar and nitrogen containing base are joined by a glycosidic bond

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8
Q

what is the structure of ATP

A

-its a nucleotide
-adenine, ribose, 3 phosphate groups

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9
Q

when energy is required what happens to the structure of ATP

A

-the 3rd phosphate group in ATP is broken down by a hydrolysis reaction which is catalysed by ATPase (an enzyme)
-the products are adenosine diphosphate (ADP) and 1 free inorganic phosphate group and energy is released
-because 1 phosphate is broken, it uses energy
-2 bonds are made to produce the ADP and the inorganic phosphate group, which releases energy

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10
Q

what does ATP stand for

A

adenosine triphosphate

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11
Q

is the breakdown of ATP into ADP a reversible reaction

A

yes

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12
Q

explain how ADP can be synthesised into ATP

A

-ADP and a phosphate group can be synthesised by ATPase in a condensation reaction
-a water molecule is released
-this requires an input of energy
-this energy usually comes from redox reactions

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13
Q

what are nucleic acids

A

polynucleotides, so made up of many monomer nucleotides

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14
Q

what are the differences between RNA and DNA

A

-RNA has a single polynucleotide strand, this can fold into complex shapes held together by hydrogen bonds or remain as long molecules
-DNA has 2 polynucleotide strands held together by hydrogen bonds and twisted into a double helix
-RNA has the bases guanine, cytosine, adenine, uracil
-DNA has the bases guanine, cytosine, adenine, thymine
-the pentose sugar in RNA is ribose
-in DNA its deoxyribose

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15
Q

how many base pairs are present in 1 complete twist of the DNA double helix

A

10

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16
Q

state the 2 main ideas about how DNA replication happens

A

conservative replication
semiconservative replication

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17
Q

describe the conservative model for DNA replication

A

the original double helix remains intact and instructs the formation of a new identical double helix

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18
Q

definition of gene

A

a sequence of bases on a DNA molecule, which codes for a sequence of amino acids in a polypeptide chain that affect a characteristic in a phenotype of the organism

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19
Q

what are 3 features of the genetic code

A

-triplet code
-non-overlapping
-degenerate

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20
Q

triplet code definition

A

3 bases which code for a specific amino acid

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21
Q

codon definition

A

a sequence of 3 bases in DNA or mRNA

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22
Q

what is meant by non-overlapping code

A

each base is read only once so adjacent codons don’t overlap

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23
Q

what is meant by degenerate code

A

multiple codons code for the same amino acid
this limits the effects of mutations

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24
Q

what are polysomes

A

groups of ribosomes joined by a thread of mRNA, which produce large amounts of a particular protein

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25
Q

what is the function of polysomes

A

-involved in mass production of a particular protein
-a polysome attaches to a mRNA strand and these ribosomes move along one after the other to translate many identical polypeptide chains

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26
Q

does all of the genome code for proteins

A

-no there are non-coding DNA sequences which are involved in regulating protein coding sequences
-there are also start and stop codons which code for the beginning and end of a polypeptide chain

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27
Q

describe the structure of tRNA

A

-clover leaf shape, due to hydrogen bonding between different bases
-one end of the tRNA molecule has an anticodon, a sequence of 3 bases which is complementary to a specific codon on the mRNA strand and corresponds to one particular amino acid
-there is a binding site which attaches to one particular amino acid from the many amino acids in the cytoplasm

28
Q

mutation definition

A

a permanent change in the DNA of an organism

29
Q

what are point / gene mutations

A

-one or a small number of nucleotides are miscopied during transcription
-can include substitutions, deletions, or insertions

30
Q

what is a substitution mutation

A

a type of point / gene mutation where one base is substituted for another in a gene

31
Q

what is a deletion

A

a type of point / gene mutation where a base is completely lost from the sequence in a gene

32
Q

what is an insertion

A

a type of point / gene mutation where an extra base is added into a gene, this may be a repetition of a previous base or a new base completely

33
Q

what are chromosomal mutations

A

changes in the positions of genes within chromosomes

34
Q

what are whole-chromosome mutations

A

where an entire chromosome is lost or duplicated during meiosis

35
Q

describe sickle cell disease and it’s cause

A

-a genetic disease that affects the polypeptide chains which make haemoglobin in red blood cells
-caused by a substitution point mutation in one codon, which changes the amino acid, which changes the properties of the haemoglobin
-haemoglobin stick together to form rigid rods causing the red blood cell to have a sickle shape
-these red blood cells don’t carry oxygen efficiently and block small blood vessels

36
Q

what are mutagens

A

anything that increases the rate of mutation, such as x-rays, ionising radiation and certain chemicals

37
Q

what are enzymes

A

-biological catalysts
-change the rate of reaction (can speed up or slow down)
-but don’t change the products or conditions in the cytoplasm
-globular proteins
-show great specificity

38
Q

what are anabolic reactions

A

reactions that build up new chemiclas
(ana means build up)

39
Q

what are catabolic reactions

A

reactions that break down substances
(cata means break down)

40
Q

definition of metabolism

A

the combination of catabolic and anabolic processes that take place in a cell

41
Q

what is a metabolic chain / metabolic pathway

A

a series of linked reactions in the metabolism of a cell
the product of one enzyme-controlled reaction is used as the product of the next reaction

42
Q

what are intracellular enzymes

A

enzymes that catalyse reactions inside the cell

43
Q

what are extracellular enzymes

A

enzymes that catalyse reactions outside of the cell in which they were made

44
Q

what is required for a chemical reaction to take place

A

-activation energy
-which is the minimum energy required to break the bonds that hold a molecule together

45
Q

how do enzymes catalyse reactions

A

-they lower the activation energy needed for a reaction to occur
-they do this by forming a enzyme-substrate complex with the substrate
-when the substrate is in the active site, the active site effects the bonds in the substrate, making it easier to break them for catabolic reactions
-for anabolic reactions during the enzyme substrate complex the reacting substances are brought closer together, making it easier for bonds to form

46
Q

describe the lock and key hypothesis

A

-within each enzyme there is an active site
-only one substrate or type of substrate has a complementary shape to the active site
-this gives the enzyme its specificity
-an enzyme-substrate complex is formed
not included in lock and key hypothesis but extra info:
-once the reaction is complete and the enzyme-product complex has formed the products no longer have a complementary fit to the active site, so products are released
-the active site is free to catalyse another reaction

47
Q

describe the induced-fit hypothesis

A

-the active site has a highly specific shape complementary to its specific substrate, but its flexible
-when the substrate enters the active site, the shape of the active site is modified around the substrate to form the enzyme-substrate complex
-after the reaction has completed an enzyme-product complex if formed, the product are released
-the enzyme goes back to its inactive relaxed form until another substrate binds to it

48
Q

at what point in a reaction is the rate the quickest

A

the initial rate of the reaction is the quickest, so it tells us the maximum reaction rate
Initial rate of reaction is used because products are at a concentration of 0 so will not affect results or the reaction
And we know the concentration of the products so plotting graphs and comparing results is more reliable

49
Q

what are the 3 factors which affect the rate of enzyme-catalysed reactions

A

temperature, PH, substrate concentration

50
Q

what is the molecular activity / turnover number of an enzyme

A

the number of substrate molecules transformed per minute by a single enzyme molecule

51
Q

what is the temperature coefficient (Q10) equation and what does it show

A

Q10 = rate of reaction at (x+10)°C / rate of reaction at x°C

the temperature coefficient is the measure of the effect of temperature on the rate of reaction
between 0°C-40°C in the human body usually, as the temperature increases by 10°C the rate of an enzyme-controlled reaction doubles, so Q10 has a value of 2
this doesn’t apply to temperatures above the optimum temperature

52
Q

explain the effect of substrate concentration on the rate of enzyme-catalysed reactions

A

-at lower substrate concentrations the rate of reactions is lower because some enzyme molecules have their active sites free
-as substrate concentration increases the rate of reaction increases too because there will be more frequent collisions between the enzyme and substrate, so a higher frequency of substrate-complexes formed
-beyond the optimum, rate of reaction doesn’t increase as substrate concentration increases because all active sites are saturated
-enzyme concentration is now the limiting factor

53
Q

explain the effect of temperature on the rate of enzyme-controlled reactions

A

-in the human body between 0°C-40°C as temperature increases the rate of reaction increases because the substrate and enzyme have more kinetic energy, so there are more frequent collision between them
-as the enzyme and substrate have greater kinetic energy, the frequency of collision between the enzyme and substrate with the minimum activation energy needed will increase
-at the optimum the rate of reaction is at its maximum (usually 37°C in the human body)
-beyond the optimum, enzymes start to denature, because enzyme molecules are vibrating more rapidly, hydrogen bonds within the enzymes break. tertiary structure of the globular protein changes causing the active site to change too, so the active site and substrate no longer are complementary
-at very low temperatures the rate of reaction can be low/0 but the enzyme is not denatured

54
Q

explain the effect of PH on the rate of reaction on enzyme-catalysed reactions

A

-PH depends on the concentration of H+ ions present
-when PH decreases the concentration of H+ ions increases
-these H+ ions can bond to the R groups on the amino acids in the active site
-usually the active site forms temporary bonds with the substrate, but when H+ ions bond to the R groups on the active site, they prevent the bonding between the active site and substrate, which reduces how effectively the substrate binds into the active site, reducing the rate of reaction
-when PH decreases, H+ can bond to R groups on amino acids in the rest of the protein, this breaks the ionic bonds within the amino acids
-when PH increases the concentration of H+ ions decrease, hydrogen bonds within the R groups of amino acids break
-therefore changing the PH can break the bonds which hold the tertiary structure of the enzyme together, so the active site changes shape, meaning the enzyme is denatured

55
Q

what are enzyme inhibitors, what are the 2 types

A

enzyme inhibitors are substances that slow down the rate of enzymes or stop them from working
there can be reversible and irreversible inhibition of enzymes

56
Q

what are the 2 types of reversible inhibition of enzymes

A

competitive inhibition
non-competitive inhibition

57
Q

describe overall the key features of reversible inhibition of how enzyme inhibitors work

A

-reversible inhibition is when an inhibitor affects an enzyme in a way that doesn’t permanently change it
-when a reversible inhibitor is removed the enzyme can function normally
-this is a way of controlling metabolic reactions within a cell

58
Q

describe competitive reversible inhibition

A

-the inhibitor molecules has a similar shape to the substrate molecule
-the inhibitor molecule can bind to the active site, forming an enzyme-inhibitor complex
-this prevents the substrate from colliding with the active site, which reduces the rate of reaction
-the substrate and inhibitor are competing for the active site-
-if the concentration of competitive inhibitor is kept constant, and we increase the substrate concentration, we can reduce the effect of the competitive inhibitor

59
Q

describe non-competitive inhibitors

A

-non-competitive inhibitors bind to a different site on the enzyme molecule-not the active site
-this is the allosteric site
-when a non-competitive inhibitor binds to the allosteric site, the tertiary structure of the enzyme changes, the shape of the active site changes so its no longer complementary to the substrate, so enzyme-substrate complex can’t form
-the effect of a non-competitive inhibitor isn’t affected by the substrate concentration because as long as it is bonded to the allosteric site a substrate molecule cannot bond to the active site

60
Q

how can the effect of a competitive inhibitor be overcome

A

by increasing substrate concentration

61
Q

how can the effect of a non-competitive inhibitor be overcome

A

it cannot be overcome
increasing the substrate concentration won’t increase the rate of reaction

62
Q

describe irreversible inhibition of enzymes

A

-the inhibitor molecule binds with the enzyme by forming a permanent covalent bond to one of the groups vital for catalysis to occur
-this changes the shape and structure of the enzyme permanently, so a substrate molecule can never bind to the active site of that enzyme
-irreversible inhibition occurs more slowly than reversible inhibition
-irreversible inhibition is never used tithin the cell to control metabolism

63
Q

what is the function of regulatory enzymes

A

-regulatory enzymes have a site separate from the active site where another molecule can bind and bring about non-competitive inhibition
-regulatory enzymes are found in complex metabolic pathways
-they are used in end-product inhibition

64
Q

explain what happens in end-product inhibition

A

-the final product in a metabolic pathway inhibits a regulatory enzyme found towards the beginning of the metabolic pathway
-by binding to the allosteric site of the regulatory enzyme, it brings about non-competitive inhibition which slows the rate of the metabolic pathway

65
Q

what is the main function of end-product inhibition

A

to reduce the rate of a metabolic pathway so that valuable resources in the cell like energy is not wasted by catalysing reactions that are not required

biology (4 decks)

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