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2.3&2.4 Flashcards

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1
Q

Double helix

A

Shape of DNA molecule, due to cooling of two sugar phosphate backbone strands into a right handed spiral configuration

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2
Q

Monomer

A

Molecule that when repeated makes a polymer, nucleotides monomer of nucleic acids

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3
Q

Nucleotides

A

Molecule constituent of five carbon sugar, a phosphate group and a nitrogenous base

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4
Q

Polynucleotide

A

Large molecule containing many nucleotides

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5
Q

DNA polymerase

A

Enzyme that catalysed formation of DNA from activated deoxyribose nucleotides, using single stranded DNA as a template

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6
Q

Helicase

A

Enzyme that catalyses the breaking of hydrogen bonds between the nitrogenous pairs of bases in a DNA molecule

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7
Q

Semi conservative replication

A

How DNA replicates, resulting in two new molecules, each of which contains one old stand and one new strand. One old strand conserved in each new molecule

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8
Q

Gene

A

A length of DNA that codes for a polypeptide or for a length of RNA that is involved in regulating gene expression

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9
Q

Polypeptide

A

A polymer made of many amino acid units joined together by peptide binds

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10
Q

Protein

A

Large polypeptide of 100+ amino acids and terms often used synonymously and insulin described as small molecule

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11
Q

Transcription

A

Prices of making mRNA from DNA template

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12
Q

Translation

A

Formation of a protein at ribosomes by assembling amino acids into a particular sequence according to the coded instructions carried from DNA to the ribosomes by mRNA

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13
Q

Active site

A

Indented area on surface of enzyme molecule with a shape that is complementary to shape of substrate molecule

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14
Q

Catalyst

A

Chemical that speeds up rate of reaction and remains unchanged and reusable at the end of the reaction

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15
Q

Extra cellular

A

Outside of cell

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16
Q

Intracellular

A

Inside of cell

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17
Q

Metabolic/metabolism

A

Chemical reactions that take place inside living cells or organism

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18
Q

Product

A

Molecule produced from substrate molecule by enzyme-catalysed reaction

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19
Q

Substrate

A

Molecule that is altered by an enzyme-catalysed reaction

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20
Q

What’s are nucleotides

A

Biological molecules that participate in almost all biochemical processes

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21
Q

What is composition of a nucleotide and how is it formed

A

Phosphate esters of pentose sugar, where a nitrogenous base is linked to C of sugar residue and phosphate group is linked to C5 or C3 of covalent residue by covalent bond formed in condensation reaction

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22
Q

What is the monomer of DNA and RNA

A

Nucleic acids

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23
Q

What is then pentose sugar in RNA and in DNA

A

Ribose and deoxyribose

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24
Q

When do nucleotides become phosphorlated nucleotides

A

When they contain more than one phosphate group

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25
Q

Give an example of a phosphrated nucleotide

A

ATP adenine triphosphate

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26
Q

What is ATP

A

Energy rich end product of most energy releasing biochemical pathways and used to drive most energy requiring metabolic processes in cells

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27
Q

What do nucleotides do (pathways by ATP, ADP AND AMP)

A

Help regulate many metabolic pathways by ATP ADP AND AMP

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28
Q

What may nucleotides be components of and example

A

Components of many coenzymes like NADP

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29
Q

What is NADP used in

A

Photosynthesis and of NAD which is a coenzyme used in respiration and of FAD and coenzyme A both also involved in respiration

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30
Q

3 components of nucleotide

A

Phosphate group, pentose sugar, nitrogenous base

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31
Q

Where is DNA found

A

In nuclei of all eukaryotic cells and cytoplasm of some prokaryotes cells and in some viruses

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32
Q

What is DNA and what does it carry

A

Hereditary material and carries coded instructions used in development and functioning of all living organisms

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33
Q

Why is DNA one of the most important macro molecules

A

It makes up structure of the lining of organisms and makes proteins, carbohydrates and lipids

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34
Q

Structure of DNA (simple)

A

Polymer made up of many repeating monomeric units called nucleotides

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35
Q

What does a DNA molecule consist of and how is this described

A

Consists of 2 polynucleotide strands running it opposite directions so described as antiparallel

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36
Q

What are the different nitrogenous bases in DNA

A

Adenine, thymine, guanine, cytosine

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37
Q

What is a phosphodiester bond

A

Covalent bond between the sugar residue and phosphate group in the nucleotide

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38
Q

What happens when polynucleotides are synthesised and broken down

A

Bonds are broken when polynucleotide breaks down and formed when it is synthesised

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39
Q

What do DNA molecules carry

A

A lot of encoded genetic material

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40
Q

Are DNA molecules long or short

A

Long

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41
Q

Which nitrogenous bases are purines and how do we know

A

Adenine and guanine as they have two rings

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42
Q

Which nitrogenous bases are pyrimidine and how do we know

A

Thymine and cytosine as they only have one ring

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43
Q

What are the two categories the nitrogenous bases are split into

A

Purines and pyrimidines

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44
Q

How do the two antiparallel strands join together

A

Hydrogen bonds between two nitrogenous bases

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45
Q

Which groups of nitrogenous bases pair together

A

A and T, G and C

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46
Q

How do adenine and thymine pair together

A

By means if two hydrogen bonds

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47
Q

How do cytosine and guanine pair together

A

By means of three hydrogen bonds

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48
Q

Why do purines always pair with pyrimidines

A

To ensure equal sized ‘rungs’ on DNA ladder

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49
Q

What happens when DNA molecule is bonded together and what does this provide

A

Twists into a double helix which provides molecule with stability

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50
Q

What is the purpose of hydrogen bonds in DNA molecule

A

Allow molecule to be unzipped as they are weak for transcription and replication

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51
Q

What is the upright section of a large DNA molecule resembling a laser formed by

A

Sugar-phosphate backbone of antiparallel nucleotide strands

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52
Q

What happens at the 5th end of DNA molecule

A

Phosphate group attaches to C5 of deoxyribose sugar

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53
Q

What happens at 3’ end of DNA molecule

A

Phosphate group attaches to C3 of deoxyribose sugar

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54
Q

What do the rings on the ladder consist of

A

Complimentary base pairs joined by hydrogen bonds

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55
Q

Why is it good that DNA is very stable

A

Integrity of coded information with base sequence is protected

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56
Q

Where is the majority of DNA content of genome found in eukaryotics

A

Nucleolus

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57
Q

How is DNA kept

A

Each large DNA molecule is tightly wound around special histone proteins into chromosomes making each chromosome one DNA molecule

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58
Q

What is DNA like in mitochondria and chloroplasts

A

A loop of DNA without histone protein

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59
Q

What is DNA like in prokaryotes as what is it described as

A

It is a loop within cytoplasm not enclosed in a nucleus or wound around histone protein so described as naked

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60
Q

What do virus DNA look like

A

They have it in the form of a loop of naked DNA

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61
Q

What do all DNA within a cell and within all cells in organism carry and why

A

Coded instructions to make and maintain that organism

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62
Q

What must happen when a cell divides

A

DNA must be copied so that each daughter cell receives a full set of instructions

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63
Q

When does replication of DNA happen during mitosis

A

Interphase

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64
Q

What happens in interphase

A

Chromosomes first join at centromere forming two sister chromatids so each each chromosome gets an identical copy of itself

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65
Q

Does DNA in mitochondria and chloroplasts also replicate each time organelle divides

A

Yes happens just before cell actively divides

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66
Q

How does DNA make new copies of itself firstly

A

Unwinds and double helix untwisted but by bit by enzyme gyrase

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67
Q

What happens in DNA replication when DNA unzips

A

DNA unzips and hydrogen bonds between nucleotides are broken, catalysed by helicase to make 2 strands of DNA with exposed bases

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68
Q

What happens in DNA replication after it has been unzipped

A

Free phosphorlated nucleotides, present in nucleoplasm, are bonded to expose bases following complementary base pairing

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69
Q

What enzyme catalysed the addition of new bases

A

DNA polymerase

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70
Q

Which direction is leading strand in and then lagging strand

A

3” to 5” and lagging is 5” to 3”

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71
Q

What is each single strand described as

A

Template strand for new bass to be added to

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72
Q

How is leading strand synthesised with addition of new nucleotides

A

Continuously

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73
Q

How is lagging strand synthesised with addition of new nucleotides

A

Added in fragments discontinously

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74
Q

What enzyme joins new nucleotides together and zips up the DNA molecule

A

Ligase

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75
Q

What supply’s energy to make new phosophodiester bonds

A

Hydrolysis of active nucleotides which release extra phosphate groups which supply energy

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76
Q

What is the product of replication

A

2 DNA molecules identical to each other and parent molecule

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77
Q

Why is a DNA replication described as semi-conservative replication

A

Each DNA molecule contains an old strand of DNA and a new strand

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78
Q

Do loops of DNA in mitochondria chloroplast and prokaryotes also replicate semi conservatively

A

Yes

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79
Q

How does DNA in prokaryotes replicate

A

A bubble sprouts from loop and unwinds and unzips it and complementary nucleotides join exposed ones till as whole new loop is copied

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80
Q

What are issues that could occur with replication

A

During replication errors may occur and wrong nucleotides may be inserted which could change genetic code and is a point of mutations

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81
Q

How often does replication errors occur

A

1 in 10*8 base pairs

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82
Q

What reduces the rate of mutations produced

A

During replication process there are enzymes which can proof read and edit incorrect nucleotides

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83
Q

Are all mutations harmful

A

No many genes have changes to their nucleotide sequence called an allele or gene variant

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84
Q

Do all mutations give an advantage or disadvantage and example

A

No all are (roll your tongue or not) but some are such as animals which are white and live in snow

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85
Q

What can some mutations lead to

A

Cancer

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86
Q

Why are can helicase break hydrogen bonds easily

A

As they are weak

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87
Q

What must be added before DNA polymerase can add new bases

A

A primer must be added

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88
Q

Why is the lagging strand slower

A

As a new primer must be added for every fragment

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89
Q

What are the fragments on lagging strand called

A

Okazaki fragments

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90
Q

What is strand that new bases added to called

A

Template strand

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91
Q

How is RNA different from DNA (4 things)

A

Sugar molecule in RNA is ribose not deoxyribose, nitrogenous base uracil (pyrimidine) replaces thymine, poly-nucleotide chain is single stranded and shorter, 3 forms of RNA (mRNA, tRNA and rRNA

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92
Q

What is a gene and what does it contain in eukaryotic cells

A

Each chromosome in nucleus has DNA molecule and on each chromosome their are specific lengths of DNA called genes, each gene contains code that determines sequence of amino acids in particular polypeptide/ protein

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93
Q

What are proteins and how many of them are there in an organism

A

Account for 75% of organisms dry mass, some proteins are structural like cytoskeleton, others make up cells tool kit like enzymes which many catalyse formation of non protein molecules like lipids and carbs

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94
Q

What determines the amino acid/ primary structure of a protein

A

A sequence of base triplets found in each DNA molecule

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95
Q

What happens is primary structure of polypeptide is incorrect

A

It will fold incorrectly and won’t be held in its tertiary structure so it won’t be able to carry out its function

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96
Q

Why is proteins structure important for enzymes

A

Shape of enzymes active site must be complementary to shape of substrate molecule

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97
Q

Why is proteins shape important for antibodies

A

Part of antibodies have to be complementary to shape of antigen of invading pathogens surface

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98
Q

Why is shape of protein important for receptors on cell membrane

A

They must have complementary shape to cell signalling molecule which it much detect (drug/hormone)

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99
Q

Why is shape of protein important for ion channel proteins

A

Needs hydrophilic amino acids lining protein and lipophilic on outside layer next to the lipid by layer of plasma membrane

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100
Q

Where are genes found and where are proteins made

A

Gene found in cells nucleus but proteins made in cytoplasm at ribosomes

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101
Q

What happens to gene instructions as they are too big to leave the nucleus

A

Copy of each gene must be transcribed into a length of mRNA

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102
Q

When gene code is in form of mRNA what are the sequence of base triplets called and what does this now mean

A

Codons, which can pass out of nucleus

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103
Q

What happens once coded instructions are translated

A

Protein is assembled correctly from amino acids

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104
Q

Why is genetic code universals

A

As almost all living organisms have the same triplet if DNA bases code for the same amino acids

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105
Q

Why is genetic code degenerate

A

For all amino acids except methionine and tryptophan there is more than one base triplet which may reduce effect of the point of mutation as a change in one base of the triplet code could produce another base triplets that still codes for same amino acid

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106
Q

Why is genetic code none overlapping

A

As it is read starting from fixed points in groups of 3 bases

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107
Q

What happens is a base is added or deleted

A

Causes frame shift as every base triplet after that and every amino acid coded for is changed

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108
Q

What is the first step in transcript

A

Gene unwinds and unzips and hydrogen bonds break between complementary nucleotide bases

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109
Q

What happens in transcription once gene is unzipped

A

Enzyme RNA polymerase catalyses temporary formation of hydrogen bonds between RNA nucleotides and their complementary unpaired DNA bases on the unwound DNA strand (template strand)

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110
Q

What bases go together in RNA pairing

A

A-T. A-U. G-C.

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111
Q

What is produced after RNA polymerase has finished adding bases

A

Length of RNA which is complementary to the template strand of the gene is produced and identical to coding strand

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112
Q

What happens once mRNA strand is formed

A

mRNA passes out of nucleolus through nuclear envelope and attaches to ribosome

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113
Q

Where and how are ribosomes made

A

Made in nucleolus in two smaller subunits which pass separately out of nucleus via pores and then come together to form ribosomes (magnesium ion helps bind the two subunits together)

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114
Q

What are ribosomes made of

A

ribosomalRNA and protein in roughly equal parts

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115
Q

Where is tRNA made and where does it go

A

Made in nucleolus and passes out of nucleus to cytoplasm

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116
Q

What are tRNA

A

Single stranded polynucleotides which can twist into a hairpin shape

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117
Q

What are at the two different ends of a tRNA molecule

A

One end is a trio of nucleotide bases that recognise and attach to specific amino acids and at other end is another triplet base called anticodon that is complementary to specific codon it bases on mRNA

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118
Q

What catalyse synthesis of polypeptides

A

Ribosomes

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119
Q

What does the tRNA do in translation

A

Brings amino acids and find their place when anti codon binds by temporary hydrogen bonds to complementary codon on mRNA molecule

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120
Q

What happens as ribosomes move along the length of mRNA

A

It reads the code and when 2 amino acids are adjacent to each other a peptide bond forms between them

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121
Q

What is needed for polypeptide synthesis

A

Energy in form of ATP

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122
Q

What is the amino acid sequence for a polypeptide determined by

A

Sequence of triplet nucleotide bases on length of DNA (the gene)

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123
Q

What happens after polypeptide is assembled

A

mRNA breaks down and it’s component molecules are recycled into new lengths of mRNA with a different codon sequence

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124
Q

What helps newly synthesised polypeptide fold into its 3D or tertiary structure so it can carry out its function

A

Chaperone proteins

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125
Q

What does mRNA attaching to ribosomes cause

A

Amino acids to assemble in correct order with the help of tRNA

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126
Q

Why does tRNA fold in on itself into a 3D shape

A

So they can bind to amino acids at one end and mRNA at the other end

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127
Q

What happens before tRNA arrives at ribosomes

A

Amino acids attaches by specific enzyme for each different amino acid

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128
Q

What happens once the amino acids are aligned

A

Peptide bonds formed between amino acids and polypeptide chain is eventually formed

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129
Q

Example of why genetic code is non overlapping

A

If the code was ACU GCA it would only read it as 2 groups (ACU AND GCA) not ACU then CUG then UGC

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130
Q

What is an advantage of the genetic code being non overlapping

A

It is more flexible

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131
Q

Cofactor

A

A substance that has to be present to ensure an enzyme catalysed reaction takes place at the appropriate rate

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132
Q

Enzyme substrate complex

A

Complex formed by temporary binding of enzyme and substrate molecules during an enzyme catalysed reaction

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133
Q

Enzyme product complex

A

Enzyme molecule with product molecules in its active site joined temporarily by non-covalent forces

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134
Q

Q10

A

Temperature coefficient, calculated by diving rate of reaction at (T+10)degreesC by rate of reaction at T degrees C

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135
Q

Concentration

A

Number of molecules per unit volume

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136
Q

Competitive inhibition

A

Inhibition of an enzyme where the inhibitor molecule has similar shape to substrate molecule for enzymes active site. Blocks active site and prevents formation of ES complexes

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137
Q

Inhibitor

A

A substance that reduces or stops a reaction

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138
Q

Non-competitive inhibition

A

Inhibition of an enzyme where competitor molecule attaches to part of the enzyme molecule but not the active site. This changes the shape of active site which prevents ES complexes forming, as the enzyme active site is no longer complementary in shape to the substrate molecule

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139
Q

What are enzymes

A

Biological catalysts because the sped up metabolic reactions in living organisms

140
Q

What do enzymes actions effect

A

Both structure and function within cells, tissues and organs

141
Q

What are catalysts

A

Speed up reactions and remain unchanged at the end of the reaction, so they can be re-used

142
Q

What can small amounts of catalyst do

A

Catalyse conversion of large numbers of substrate molecules into product molecules

143
Q

What is Turnover number

A

Number of reactions enzymes can catalyse per second

144
Q

What do chemical catalysts usually need

A

High temperatures and extremes in pH

145
Q

How are enzymes different to chemical catalysts

A

Speed reactions up at much lower temperature and natural pH and normal pressures

146
Q

Due to enzymes working at neutral pH, low temp and normal pressure what does this mean

A

They can function in conditions which sustain life

147
Q

Mare enzymes or chemical catalysts more specific and why

A

Enzymes as they don’t produce unwanted bi-products and very rarely make mistakes

148
Q

What do cells do where enzymes are made and/or act in

A

They regulate their production and activity and o fit the needs of a cell or organism at that time

149
Q

What does enzymes structure all them to do

A

Carry out their function like all biological molecules

150
Q

What my enzymes need when catalysing a reaction

A

Help from cofactors

151
Q

Where are instructions for making enzymes found

A

They are encoded in genes

152
Q

What happens to making of enzymes if a gene mutates

A

It alters the order of amino acids in a protein which alters enzymes tertiary structure so it won’t work

153
Q

What happens when an enzyme which catalyses a metabolic reaction is deficient

A

Metabolic disorders can occur

154
Q

What do enzymes catalyse as well as reactions

A

The formation of organisms structural components like collagen in bone, cartilage and vessel walls

155
Q

What do some genetic disorders cause, give an example

A

Cause malfunction of connective tissue and can be harmful and lead to ‘stone man syndrome’

156
Q

What is enzymes basic structure

A

Large molecules with a specific area/indentation on molecules surface called active site

157
Q

How many amino acids does the active site consist of

A

Only 6-10

158
Q

What is so special about the tertiary structure of enzymes active site

A

It is complementary to the shape of the substrate molecule

159
Q

What does enzymes active site and substrate being complementary mean

A

Each type of enzyme is highly specific in function as it can only catalyse reactions involving a particular type of substrate that fits into its active site

160
Q

How can the shape of enzymes active site and its ability to catalyse a reaction be altered

A

By change in temperature and pH as it affects bonds which hold the protein in its tertiary structure

161
Q

Do enzymes catalyse intercellular or extra cellular reactions

A

Both

162
Q

How many metabolic reactions happen at the same time within organelles in cells and how does this relate to enzymes

A

1000, each catalysed by a different enzyme but some are part of the same metabolic pathway

163
Q

What is each metabolic pathway in living cells

A

Is one of a series of consecutive reactions, every step catalysed by a specific enzyme that produces a specific product

164
Q

What acts as substrate for specific enzymes

A

Various reactants and intermediates

165
Q

What are known as metabolites

A

Reactants, intermediates, products

166
Q

What happens in catabolic metabolic pathways

A

Metabolites are broken down into smaller molecules and release energy

167
Q

What happens with anabolic metabolic pathways

A

Energy is used to synthesise larger molecules from smaller ones

168
Q

What are two examples of complex metabolic pathways and why

A

Respiration and photosynthesis as many enzymes are involved

169
Q

Where is catalase found

A

In almost all living organisms that are exposed to oxygen

170
Q

Why is catalase so important

A

Protects cells from damage by reactive oxygen quickly breaking down hydrogen peroxide which is a potentially harmful bi-product if many metabolic reactions of water and oxygen

171
Q

What is catalase structure

A

4 polypeptide chains and each contain a haem group with iron

172
Q

How fast does catalase act

A

Fastest acting enzyme with a turnover of 6million per second

173
Q

Where is catalase found in eukaryotes

A

Inside small vesicles called peroxisomes

174
Q

When do white blood cells use catalase

A

When ingesting pathogens, as it helps invade the invading microbes

175
Q

What is catalase optimum pH

A

7

176
Q

What is optimum pH and temp for enzyme catalase

A

Between pH 4-11 and temp for humans is 45degreesC but for some thermophilic archea it is 90

177
Q

What happens to enzymes which act extracellularly

A

Enzymes are secreted from cells where they are made and act on their substrate outside the cell

178
Q

Give an example of an extracellular and how it works

A

Fungi(bread mould), releases hydrolytic enzymes from their thread like hyphae, the enzyme digests carbs, proteins and lipids in the bread and the products of digestion-glucose, amino acids, fatty acids, are absorbed into fungal hyphae for use in respiration and growth

179
Q

What happens to many enzymes in our digestive system

A

They are secreted from cells lining alimentary canal into the guts lumen where they extracellularly digest large molecules (carb,protein,lipids) and nucleic acids found in food. Products of digestion are then absorbed by epithelial cells of gut wall, into bloodstream to be used from respiration, growth and repair of tissue

180
Q

Where is amylase produced and where does it act and how does it work

A

Produced in salivary glands and acts in mouth to digest polysaccharide starch to the disaccharide maltose, amylase also made in pancreas and acts to catalyse starch into maltose in small intestine

181
Q

Where is trypsin made, act and how does it work

A

Made in pancreas, acts in small intestine lumen to digest proteins into smaller peptides by hydrolysing peptide bonds

182
Q

What is trypsin optimum pH

A

pH7.5-8.5

183
Q

What is lock and key hypothesis

A

Substrate fits into enzymes active site as the tertiary structure of an enzymes active site give it a complementary shape to substrate molecule (like a key fits into a lock)

184
Q

What does the lock and key represent

A

Lock is enzymes active site and key is substrate molecule

185
Q

What happens when substrate fits into enzymes active site according to lock and key

A

Substrate fits into active site and temporary hydrogen bonds hold the two together forming and enzyme-substrate complex

186
Q

What happens once ES complex formed

A

Substrate molecule broken into smaller product molecules that leave the active site

187
Q

What happen when a larger molecule is being formed according to lock and key

A

Substrates fit in ES complex forming bonds between the two substrates making and enzyme-product complex then the larger molecule leave the active site

188
Q

What energy do both substrate and enzyme molecule have

A

Kinetic energy and are constantly moving randomly

189
Q

What happens when substrate successfully collided with enzyme according to lock and key

A

ES complex is formed and substrate fits into complementary active site on enzyme

190
Q

What happens to substrate molecule in active site

A

Either broken down, or built up into product molecules-forming an enzyme-product complex whilst still in active site

191
Q

What happens once product molecules leave the active site according to lock and key

A

Enzyme can form another ES complex

192
Q

What can a small number of enzymes do

A

They can convert a large number of substrate molecules into product molecules

193
Q

Who c up with induced fit hypothesis and how

A

Koshland modified lock and key hypothesis by suggesting active site is not a rigid structure but the presence of a substrate molecule induces a shape change giving it a good fit

194
Q

What did Koshland say about induced fit model

A

When the substrate molecule fits into active site, the active site changes shape to mould itself around the substrate molecule

195
Q

How is the induced fit model often described

A

Putting a glove onto a hand

196
Q

What is similarity and difference between induced fit model and lock and key

A

Substrate still have a complementary shape but on binding there is a subtle change in the shape of the side chains(r-groups) of the amino acids that make up the active site to give a more precise confirmation that exactly fits substrate molecule

197
Q

What does induced fit moulding around substrate mean

A

Enables substrate to bind more effectively to active site, an ES complex is formed and

198
Q

What forces bind substrate to active site

A

Non-covalent forces like hydrogen bonds, ionic attractions, Van Der Waals forces and hydrophobic interactions

199
Q

What is the name for a product molecule that hasn’t left the active site yet

A

Enzyme-product complex

200
Q

Why do product molecules detach from enzymes active sites

A

As they have a slightly different shape from the substrate so they no longer fit

201
Q

What happens when product leave active site

A

Enzyme molecule is free to catalyse another reaction with another substrate molecule of the same type

202
Q

What is the sequence of substrate becoming a product molecule

A

Enzyme+substrate->ES complex ->enzyme-product complex ->enzyme+product

203
Q

What do chemical reactions need to begin

A

Energy

204
Q

How are chemical reactions often provided with energy to begin them

A

Heated to provide energy so reactants react together

205
Q

What happens when chemical reactions are heated

A

Increases kinetic energy of molecules so that they move faster and more randomly and are more likely to successfully collide together and react together

206
Q

Why can’t biological reactions active by adding heat

A

Temp can’t be increased as it would denature proteins and lipids would melt

207
Q

How do enzymes work to start a reaction without need of excess heat

A

Enzymes have a specific active site if a substrate, they bring substrate molecules close enough together to react with the need for excess heat so they lower the activation energy and speed up metabolic reactions

208
Q

What do enzymes involved in catalysing oxidation-reduction and others like it need to work and what is it called

A

Only work if another small non-protein molecule is attached to them-called cofactors

209
Q

What is a cofactor which is permanently bound to enzyme called

A

Molecule permanently bound by covalent bonds to an enzyme molecule is called a prosthetic group

210
Q

What is an example of an enzyme with a prosthetic group

A

Carbonic anhydrase contains a zinc ion permanently bound to its active site

211
Q

Where is carbonic anhydrase found and what does it catalyse

A

Found in erythrocytes and catalyses interconversion of carbon dioxide and water to carbonic acid which then breaks down to protons and hydrogencarbonate ions

212
Q

What is true about most enzyme-catalysed reactions

A

They can happen either way depending on the concentration of product or substrate molecule

213
Q

Can only enzymes have prosthetic groups

A

No other proteins can such as haemoglobin has a haem group

214
Q

How do some enzymes work better not permanently bound to a cofactor but work in the presence of ions

A

Ions act as cofactors, during enzyme-catalysed reactions, enzyme and substrate temporarily bind forming an ES Complex, presence of certain ions that may temporarily bind to either substrate or enzyme may ease formation of ES complex and increase rate of reaction

215
Q

What do some cofactors act as

A

Co-substrates as they and the substrate form the correct shape to bind to the active site of the enzyme

216
Q

What do some other cofactors do

A

Some cofactors change the charge distribution on the surface of the substrate molecule or on the surface of the enzymes active site and make temporary bonds in ES complex easier to form

217
Q

What does the enzyme amylase digest and when will it function

A

Digests starch to maltose and only functions if chloride ions are present

218
Q

What is the main difference between cofactors and coenzymes

A

Cofactors are inorganic and coenzymes are organic

219
Q

What are coenzymes

A

Small organic non-protein molecules that temporarily bind to the active site of the enzyme, either just before or at the same time as the substrate

220
Q

What happens to coenzymes during a reaction and after

A

They are chemically changed during a reaction and need to be recycled to their original state sometimes by a different enzyme

221
Q

What do many coenzymes derive from and what happens if these are deficient in human diet

A

Water soluble vitamins, if these vitamins are deficient in human diet then certain diseases may occur

222
Q

What is the coenzyme derived from vitamin B12 and what disease is caused it there’s a deficiency

A

Cobalamin coenzymes and causes pernicious anaemia (progressive and fatal)

223
Q

What is the coenzyme derived from folic acid and what disease occurs if it is deficient

A

Tetrahydrofolate and causes megablastic anaemia (large, irregular RBC)

224
Q

What is coenzyme is derived from vitamin B3, nicotinamide and what disease happens if it is deficient

A

NAD OR NADP and causes pellagra (diarrhoea, dermatis, dementia)

225
Q

What is coenzyme derived from vitamins B6, pantothenate and what happens if it’s deficient

A

Coenzyme A and causes elevated blood-plasma triglyceride levels

226
Q

What coenzyme derived from vitamin B1, thiamine and what happens if it’s deficient

A

Thiamine pyprophosphate and causes beriberi (mental confusion and irregular heartbeat)

227
Q

What are NAD AND NADP and what do they derive form

A

They are hydrogen acceptors and derived form nucleotides

228
Q

What does organic mean

A

Carbon based, associated with molecules in living organisms such as lipids, carbs and proteins

229
Q

What is inorganic mean

A

Salts and metals

230
Q

What do organic cofactors/coenzymes derive from

A

Vitamins in our diet

231
Q

What do inorganic cofactors derive from

A

Minerals in human diet

232
Q

What is an apoenzyme

A

Inactive enzyme which is incomplete as no cofactor or co enzyme has been added

233
Q

What is a holoenzyme

A

Active whole enzyme as a cofactor or coenzyme has been added

234
Q

Precursor activation

A

Many enzymes only activate under certain conditions and when they do they are precursor enzymes, when cofactor added to apoenzyme becomes holoenzyme and that is precursor activation

235
Q

What energy do all molecules have and what does this cause

A

Kinetic energy and can continuously more around randomly

236
Q

What does molecules randomly moving around cause

A

Molecules collide with each other

237
Q

What happens to molecules when a substance is heated

A

The extra energy causes molecules to move faster which increases rate of collisions between molecules and also increases the force with which they collide with as they are moving faster

238
Q

What happens when the reaction mixture containing enzymes and substrate is heated

A

Both types of energy will gain energy and move faster, this increases the rate of collision per second, so rate of formation of ES complexes increases and rate of reaction increases and this increases number of enzyme product complexes up to a certain temp, after 37.5degreeC in humans enzymes are at their optimum temp and rate of reaction is at its max

239
Q

As well as moving faster what does increasing temp do to the molecules

A

Makes them vibrate

240
Q

What does temp making the molecules vibrate cause

A

May break the weak bonds, such as hydrogen and ionic bonds that hold tertiary structure of enzymes active site

241
Q

What happens as bonds of enzymes active site begin to break

A

Active site shape will change and substrate won’t fit in so well so rate of reaction will begin to decrease

242
Q

What happens as more and more heat is applied to enzyme substrate mixture

A

Active site completely and irreversibly changes so no longer complementary to substrate molecule, so, enzyme has denatured and reaction can’t continue

243
Q

Does heat break peptide bonds and what does this mean

A

No, so although tertiary structure of enzyme is altered the primary structure remain the same

244
Q

What is optimum temp

A

The temperature at which enzymes work there best and have their max rate of reaction

245
Q

What enzymes work best in cool temps

A

Psychrophilic bacteria, live in cold conditions and their enzymes work best in cool temps

246
Q

What enzymes work best in hot temps

A

Thermophilic bacteria live in hot springs and there enzymes are heat stable and have more disulphides bonds that don’t break with heat and keep shape of enzyme stable

247
Q

What does a graph for optimum temp of enzymes look like

A

Temp will slowly rise and rate of reaction will speed up and up till optimum temp and after that reaction rate will decrease more rapidly until enzymes have denatured

248
Q

How is reaction rate of graph showing optimum temp measured

A

Rate of reaction= 1/time taken to reach end point

249
Q

What does temperature coefficient refer to

A

Increase in rate of a process when a temp increases by 10degreesC

250
Q

What is the equation of temp coefficient (Q10)

A

Q10=rate of reaction at (T+10)degreeC / rate of reaction at T degreeC

251
Q

For a chemical reaction in test tube where Q10 is 2 for every 10degreeC rise in temp what does this do to reaction rate

A

Doubles it

252
Q

For a metabolic reaction catalysed by enzymes, temp between 0-40degreeC what happens to rate of reaction for each 10degreeC increase

A

Roughly doubled as there is more kinetic energy

253
Q

For temp above there optimum what happens to value of temp coefficient

A

It drops as higher temp alters the active site structure so they are no longer complementary to shape of substrate molecules

254
Q

What does pH indicate

A

Whether pH is acidic, alkaline or neutral

255
Q

What is pH 0-6

A

Acidic

256
Q

What does pH 7 indicate

A

Neutral

257
Q

What pH is alkaline

A

8-14

258
Q

What do acids such as hydrochloric acid and sulfuric acid dissociate into

A

Protons and a negatively changed ion (HCL->H+ + Cl-)(H2SO4-> H+ + HSO4-

259
Q

What other type of acids are also proton donors, give example

A

Organic acids, lactic acid dissociates to lactate and H+ and pyruvic acid dissociates to pyruvate and H+

260
Q

What is a buffer

A

Something that resists the change in pH

261
Q

Why is it essential human blood have certain chemicals which help resist change in pH

A

So blood remains within fairly narrow limits close to pH 7.4, the chemical can accept or donate hydrogen ions

262
Q

What can some proteins like haemoglobin do in terms of buffers

A

They can donate or accept protons, so act as buffers

263
Q

What do you use buffers for in lab experiments

A

To maintain desired pH for investigating enzyme action at different pH values it to keep pH constant whilst you investigate another factor

264
Q

What does it mean due to hydrogen ions having a positive charge (proton)

A

Has a positive charge so it is attracted to negatively charged ions/molecules or parts of molecules

265
Q

What does excess hydrogen ions interfere with in enzymes

A

Interferes with hydrogen bonds and ionic forces and so active site of the enzyme molecule will change shape

266
Q

What happens once the excess hydrogen ions has changed the shape of the enzymes active site

A

Substrate molecule does not fit well into the active site, then rate of reaction that the enzyme catalyses will be lowered

267
Q

Why does increasing H+ alter charges on active site and what does this cause

A

Increasing concentration of H+ ions alters charge on enzymes active site as more protons will cluster round negatively charged groups in the active site which interferes with binding of substrate molecule to active site

268
Q

Do enzymes work in a narrow pH range

A

Yes

269
Q

What can small changes in pH on either side of an enzymes optimum pH do

A

Slow rate of reaction as shape of active site is disrupted but is normal pH is restored hydrogen bonds can reform and active site shape is restored

270
Q

What happens to enzymes at extreme pH

A

Enzymes active site may be permanently changed, when enzyme denature it cannot catalyse the reaction

271
Q

Is the optimum pH the same for all enzymes

A

No, they differ for each enzyme

272
Q

What pH do intercellular enzymes have

A

pH close to 7

273
Q

What do extracellular enzymes pH work best at

A

They differ

274
Q

During digestion what happens and what pH does it happen at of starch

A

Food in mouth digested by amylase which digests starch to maltose works best at pH 6.8, as food passes into stomach hydrochloric acid is secreted at low pH, to kill bacteria or pathogens in food

275
Q

What is the enzyme for digesting protein in the stomach and what pH is it’s optimum and how does it work

A

Pepsin, pH 1-2, it digests large protein molecules into smaller peptide molecules

276
Q

What happens as partly digested food moves into small intestines, mention pH

A

Salt in bile made in liver neutralises the food and raises its pH to 7.8 which is optimal for protein-digesting enzymes, trypsin and enterokinase, that catalyses further digestion of peptides to amino acids in small intestines

277
Q

What happens to enzyme catalysed reactions if no substrate is present

A

No reaction happens as no ES complexes can form

278
Q

What happens as substrate is added to an enzyme mixture

A

As substrate concentration increases rate of reaction increases

279
Q

Why does rate of reaction increase as substrate added to enzyme mixture

A

More ES complexes can form resulting in more product molecules forming

280
Q

Why is substrate concentration the limiting factor when the concentration of enzymes is fixed

A

As it is limiting the reaction, as substrate concentration increases, rate of reaction increases

281
Q

What happens as substrate concentration is the same as the enzyme concentration

A

Reaction will meet its maximum rate and increasing the substrate even more will not increase the rate of reaction

282
Q

Why does enzyme catalysed reactions eventually meet a Vmax

A

As all enzymes active sites are occupied with substrate molecules, if more substrate added they can’t successfully collide with and fit into enzymes active site

283
Q

What may you be able to change in a lab to do with enzyme concentration

A

You may be able to change the concentration of a solution of a particular enzyme

284
Q

In living cells what does enzymes concentration/availability depend on

A

Rate of synthesis of enzymes and its rate of degradation, each of these rates is directly controlled by the cell

285
Q

What is enzyme synthesis

A

Depending on cells needs genes for synthesising particular enzymes can be switched on or off

286
Q

What is enzyme degradation

A

Protein components of living cells are constantly being turned over, cells are continuously degrading old enzyme molecules to their component amino acid and synthesising new enzyme molecules from amino acids

287
Q

What are the advantages of enzyme degradation

A

Eliminates abnormally shaped proteins that may accumulate and harm cell, regulation of metabolism in the cell by eliminating any superfluous(surplus to requirements) enzymes

288
Q

What must happen for a cell to regulate its metabolism properly

A

The control of enzyme degradation is equally important as the control of enzyme synthesis

289
Q

What happens as enzyme concentration increases

A

More active site in enzyme become available and more successful collisions between enzyme and substrate occur, more ES complexes can form per unit, so rate of reaction increases

290
Q

Why is enzyme concentration a limiting factor when substrate concentration is fixed

A

As enzyme concentration increases so does rate of reaction

291
Q

When is enzyme catalysed reaction at its max reaction rate with fixed substrate concentration

A

When all the substrate molecules are occupied in an active site or being released as product molecules

292
Q

What happens once enzyme catalysed reaction is at its max reaction rate

A

If enzyme concentration increases further, reaction rate won’t increase as active site of extra enzymes aren’t occupied, enzyme concentration is no longer a limiting factor as enzyme concentration increases rate of reaction doesn’t, substrate concentration become limiting factor as rate of reaction will increase if it increases

293
Q

Is initial reaction rate for any reaction faster or slower and why

A

Faster as enzymes and substrate moving randomly at the start have a greater chance of successfully colliding as there aren’t any ES complexes formed yet

294
Q

What happens to rate of reaction as in continues after initial stage

A

Substrate molecules used up as they are converted to product molecules so concentration of substrate drops as a result frequency of successful collisions decreases so initial rate of reaction gives max reaction rate for enzymes under a particular experimental situation

295
Q

What are inhibitors

A

Substances that reduce the activity of an enzyme by combining with the enzyme in a way that influences how the substrate binds to active site or by affecting enzymes turnover number

296
Q

What my some enzyme inhibitors do and what may others do

A

Some may block the active site and some change actives site shape

297
Q

What do both ways of inhibition do

A

Inhibit the formation of ES complexes and therefore formation of product molecules

298
Q

What is a competitive inhibitor

A

A substance with a similar shape to enzymes substrate molecule, so it fits into active site so substrate molecule can’t enter

299
Q

What does the amount of inhibition depend on

A

Relative concentration of substrate and inhibitor molecules

300
Q

What does the more inhibitor molecules mean

A

More inhibitors collide with active site and so effects of inhibition is greater

301
Q

What does effectively increasing substrate concentration do to rate of inhibition

A

Dilutes the effect of the inhibitors as if enough substrate added, the inhibitor is more unlikely to collide with the enzyme

302
Q

What happens to rate of reaction with a competitive inhibitors

A

Rate of reaction is lower but it does eventually reach the original Vmax

303
Q

What do competitive inhibitors form when they directly compete with substrate

A

Enzyme-inhibitor complex formed if collision is successful and it is catalytically inactive

304
Q

Once attached to enzyme what happens to competitive inhibitor

A

Inhibitor isn’t changed by enzyme as normal substrate molecule would be

305
Q

What happens due to presence of inhibitors preventing the substrate molecules joining to active site

A

Reduces the rate of formation of ES complexes and product molecule formation

306
Q

What do competitive inhibitor do

A

Reduce the number of free enzyme active sites available for substrate molecules to bind and form ES complexes

307
Q

What is good about most competitive inhibitors

A

It is reversible as collisions between enzyme and substrate or inhibitor molecules are random and increasing substrate concentration would reduce effects if reversible competitive inhibition as there would be more chance if an enzyme molecule colliding molecules with a substrate molecule than with an inhibitor molecule

308
Q

What is it called when a competitive inhibitor binds irreversibly to enzymes active site

A

Inactivator

309
Q

How do you know a non-competitive inhibitor is present

A

If inhibitor molecule binds to enzyme somewhere other than active site

310
Q

How are non-competitive inhibitors different to competitive

A

They don’t compete with substrate molecules for a place on enzymes active site

311
Q

Where do non-compatible inhibitors attach to enzyme

A

Region known as allosteric site away from active site

312
Q

What happens when non-competitive inhibitor binds to allosteric site

A

They disrupt enzymes tertiary structure and change active sites shape so it is no longer complementary to substrate and enzyme can’t bind to active site so no ES complexes form

313
Q

Does max rate of reaction stay the same or decrease with presence of non-competitive inhibitor

A

It reduces and the Vmax is lowered

314
Q

What may adding more substrate do if non-competitive inhibitor is present

A

It may allow reaction to reach a new lower rate but even very high concentration of substrate won’t allow rate of reaction to return to its uninhibited max

315
Q

What happens the greater amount of inhibitor molecules present

A

Greater degree of inhibition as more enzymes are distorted and either can’t form ES complexes it can’t complete the catalytic reaction involving ES complexes

316
Q

Do non-competitive inhibitors bind reversibly or irreversibly to allosteric site

A

Some reversible but most are irreversible

317
Q

What is one way enzyme catalysed reactions may be regulated

A

By end product inhibition

318
Q

What is end product inhibition

A

After catalysed reaction has been completed product molecules stay tightly bound to enzyme, this way enzymes can’t form more of the product that the cell needs and this is an example of negative feedback

319
Q

What do many metabolic process such as respiration and photosynthesis involve

A

A series of enzyme catalysed reactions as product of one enzyme catalysed reaction becomes substrate for the next within the metabolic pathway

320
Q

What does cells not needing to accumulate too much end product mean

A

Product of last enzyme catalysed reaction in metabolic pathway may attach to a part of the first enzyme in the pathway, but not as its active site, this binding changes the shape of the first enzymes active site preventing pathway from running

321
Q

What is it when the 1st enzymes active shape changes in a metabolic pathway

A

It is non-competitive inhibition but reversible

322
Q

After the first enzymes had been changed on a metabolic pathway how is it reversed

A

When the concentration of the product within the cell falls, the molecules will detach from enzyme 1 and allow its active site to return to its normal shape

323
Q

What increases efficiency of metabolic reactions without increasing substrate concentration and how

A

Multi-enzyme complexes as they keep the enzyme and substrate molecules in the same vicinity and reduce diffusion time

324
Q

What does many metabolic reactions being carried out in certain regions or organelles of the cell do to reactions efficiency

A

It increases its efficiency of metabolism, some enzymes within organelles are bound into the organelle membranes

325
Q

How do many toxins(poisons) exert their effect

A

They inhibit/inactivate enzymes

326
Q

How does potassium cyanide (KCN) work

A

Highly toxic as it inhibits aerobic respiration and catalase

327
Q

What happens when KCN is ingested

A

It is hydrolysed to produce hydrogen cyanid which is a very toxic gas that can readily dissociate into H+ and CN- ions

328
Q

What to CN- ions do once they have be made from hydrogen cyanide dissociating

A

They bind irreversibly to an enzyme found in mitochondria and inhibit final stages of aerobic respiration, as final stage is inhibited, earlier stages cannot run and aerobic respiration stops

329
Q

What does venom of a green mamba contain

A

A chemical that inhibits the enzyme acetylcholinesterase which is important in neuromuscular synapses tissue break down the neurotransmitter, acetylcholine

330
Q

What happens if acetylcholinesterase is inhibited

A

Acetylochtine says attached to receptors on muscle membrane and keeps muscle contracted which causes paralysis as movement depends on muscle being able to contact and relax alternately, also if muscle is involved in breathing and is paralysed victim suffocates

331
Q

How does aspirin work

A

Salicylic acid binds to enzymes that catalyse formation of prostaglandins, so it prevents formation of these and they are cell signalling molecules produced by cells when tissues are infected or damaged

332
Q

What do prostaglandins do

A

They make the nerve cells more sensitive to pain and increase swelling during inflammation

333
Q

What does aspirin do in terms of blood clots

A

Reduces risk of blood clots in blood vessels and many people take it to reduce risk of strokes

334
Q

Why can’t children U12 take aspirin

A

It can damage their stomach lining

335
Q

Where is ATPase inhibitors found and what does it do

A

Extract from foxglove leaves used to treat heart failure and atrial arrhythmia (abnormal beat of atria)

336
Q

What are ATPase inhibitors now called

A

Cardiac glycosides or digitalis, digitoxin, digitalin or digoxin

337
Q

How to cardiac glycosides work

A

They inhibit sodium potassium pump in cell membrane of heart muscle cells and allow more Ca2+ ions to enter the cell, calcium ions increase muscle contractions and this strengthens heartbeat

338
Q

What are ACE inhibitors

A

Medicinal drugs that inhibit angiotensin converting the enzyme (ACE) which normally operates in a metabolic pathway that ultimately increases blood pressure

339
Q

What are ACE inhibitors used for

A

To lower blood pressure in patients with hypertension who can’t take beta-blockers, to treat heart-failure and to minimise risk of a second heart attacks and help prevent strokes in patients who have suffered a myocardial infarction

340
Q

Why is patients blood pressure checked when taking ACE inhibitors

A

Only a small does can lower blood pressure too much so it is checked incase it falls to low

341
Q

What are protease inhibitors

A

Like amprenavir and ritonavir, they are used to treat some viral infections

342
Q

How do protease inhibitors work

A

They prevent replication of virus particles within host cells by inhibiting protease enzymes so viral coats can’t be made

343
Q

Do protease inhibitors inhibit by competitive or non-competitive inhibition

A

Competitive

344
Q

What are many anti viral drugs like zidovudine and Abacavir used to treat

A

Patients how are HIV+

345
Q

What type of inhibitors are anti-viral drugs used to treat HIV and how does this work

A

They are nucleoside reverse transcriptase inhibitors as they inhibit enzymes involved in making DNA using viral RNA as a template

alevel biology (25 decks)

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