AOS 1 Flashcards
(115 cards)
1
Q
what are nucleic acids made up of?
A
sub-units / monomers called nucleotides
2
Q
what are nucleotides?
A
basic building blocks or sub-units of DNA and RNA consisting of a phosphate group, a base and a five-carbon sugar.
3
Q
what are the types of sugar in RNA and DNA nucleotides?
A
DNA = deoxyribose, RNA = ribose
4
Q
what are the 5 types of bases?
A
adenine, thymine, uracil, cytosine and guanine
5
Q
what are the 3 types of RNA?
A
transfer RNA (tRNA), messenger RNA (mRNA) and ribosomal RNA (rRNA)
6
Q
what does mRNA do?
A
Carries the genetic message from the DNA from the nucleus to the ribosomes (to be translated)
7
Q
what does rRNA do?
A
together with particular proteins, makes the ribosomes found in cytosol
8
Q
what does tRNA do?
A
carry amino acids to ribosomes that are free in the cytoplasm, where they are used to construct proteins
9
Q
what are the 3 main steps in gene expression?
A
Transcription
RNA processing
Translation
10
Q
what happens during transcription?
(3 steps)
A
- The DNA is unwound by the RNA polymerase binding to the promoter region as well as DNA helicase assisting
- This base sequence of DNA gained acts as a template for a mRNA strand to be made by RNA polymerase continuing moving along (3’ to 5’) bring complimentary nucleotides as it goes
- A pre mRNA strand is made and released from the templated.
11
Q
what are the 3 main steps in RNA processing?
A
Capping
Adding a tail
splicing
12
Q
What happens during capping?
A
The 5’ end of the pre-RNA has its G’s modified with a methyl cap (methyl guanosine). This capping protects the pre-RNA from enzyme attack and assists with stability, allowing it to attach to the ribosome.
13
Q
what happens during adding a tail?
A
A poly-adenine (A) tail with up to 250 A’s is also added to the 3’ end. The tail contributes to the stability of the mRNA and facilitates mRNA export from the nucleus
14
Q
what happens during splicing
A
the introns from the pre-RNA are spliced out allowing the exons to join together. This is done by spliceosomes which recognise the base sequences at the 5’ (GU) and 3’ (AG) that are the end of the introns.
15
Q
what is alternate splicing?
A
exons can be removed enabling one gene to produce a multitude of proteins if required.
16
Q
where does translation take place?
A
cytosol
17
Q
what happens in translation?
(4 steps)
A
- mRNA moves to the ribosome where it is read in codons.
- the amino acids are then brought to the mRNA by the tRNA. At one end of the tRNA it makes an anticodon, and at the other end it attaches to a specific amino acid.
- The ribosome then continues to make more amino acids and they are joined by peptide bonds.
- A codon that tells the ribosome to stop production is reached and the polypeptide is released from the ribosome.
18
Q
what is the start codon
A
AUG
19
Q
what are the 3 stop codons
A
UAA, UAG or UGA
20
Q
what is the coding region?
A
the part of the gene that gives the information for making proteins
21
Q
what is the flanking regions?
A
parts of the gene that isn’t the coding region
22
Q
what is the coding region made up off?
A
exons and introns
23
Q
what are the 2 flanking regions known as?
A
upstream and downstream
24
Q
what are exons?
A
the part that contain the instructions for the synthesis of the protein and are both transcribed and translated
25
what are introns?
parts in the coding region that are transcribed but are cut out during RNA processing and therefore are not translated
26
what are the 3 sections of the upstream region?
promoter
operator
leader
27
what happens in the promoter region?
The promoter is where transcription factors and RNA polymerase binds to initiate transcription
28
what happens in the operator region?
It is a binding site for repressor proteins, which are proteins that prevents RNA polymerase binding to a promoter, and thus transcription cannot be initiated
29
what are the 4 parts of the leader region?
TrpL (1), then three attenuator regions (2, 3, 4)
30
what happens in the leader region?
further regulation of transcription
31
what is an operon?
group of linked structural genes with a common promoter and operator that is transcribed as a single unit
32
what are the two types of regulation of the trp operon?
repression and attenuation
33
what happens when trp is present in repression
| (3 steps)
1. trp binds to the repressor protein causing a configurational change in its shape, allowing it to be active
2. This allows the repressor to bind at the operator
3. RNA polymerase is unable to bind to the promoter and transcription does not occur. Thus the operon is OFF
34
what happens when trp isn't present in repression
| (2 steps)
1. the repressor is unable to bind to the operator (as it is still in an inactive form)
2. RNA polymerase can bind to the promoter and start transcription of the structural genes; thus, the operon is ON
35
when there is trp present what happens in attenuation
| (4 steps)
1. trpL can be quickly translated. When the ribosome translates this region quickly (to the leader peptide), it will quickly detach from the mRNA
2. This allows a hairpin loop to form between the mRNA produced in regions 1 and 2.
3. A terminator hairpin loop between the mRNA in regions 3 and 4 is also able to form.
4. the RNA polymerase detaches from the DNA, transcription is stopped
36
when there isn't trp present what happens in attenuation
| (5 steps)
1. trpL is translated slowly
2. As the ribosome translates the gene, the ribosome pauses at the trp codon to wait for enough tryptophan to be available to produce the leader polypeptide
3. the ribosome stays attached to region 1, and therefore no hairpin loop can form between the mRNA in regions 1 and 2, but one will form between 2 and 3
4. this hairpin loop does not cause the RNA polymerase to detach and prevents the terminator hairpin of regions 3 and 4 forming
5. RNA polymerase continue remains attached to the trp operon, transcription and translation can occur
37
what are polypeptides?
large molecules made up of amino acids
38
what are amino acids made up of
an amino group and a carboxyl group. The difference between amino acids are the R group
39
how do the amino acids join together to make the polypeptide?
Each peptide bond forms by the linkage of an amino group from one amino acid and a carboxyl group of another amino acid
40
what are the 4 levels of protein structure?
primary, secondary, tertiary, quaternary
41
what is a primary structure?
linear sequence of amino acids, each protein has a different primary structure and therefore different functions
42
what is a secondary structure?
folded amino acid sequences depending on the R group
43
what are the 3 types of secondary structures
Alpha helix, Beta-pleated sheet and Random coiling
44
what is an alpha helix
secondary structure in proteins that appears as a tight twist
45
what is a beta-pleated sheet?
secondary structure in proteins that appears as folded sheets, with a change in direction of the polypeptide chain
46
what is random coiling?
secondary structure in proteins that does not fit in as either a alpha helix or beta-pleated sheet
47
what are tertiary structures?
total irregular 3D folding held together by ionic or hydrogen bonds forming a complex shape
48
what is a quaternary structure?
A structure in which two or more polypeptide chains interact to form a protein
49
what do catalysts (enzymes) do?
speed up the rate of chemical reactions without the catalyst itself being used up in the reactions
50
what is the basic function of enzymes?
increase the rate of almost all the chemical reactions and to do this within the prevailing conditions of temperature and pH within cells
51
What is a proteome
The complete array of proteins produced by a single cell or an organism in a particular environment.
52
what happens at the ribosome?
translation
53
what happens in the rough endoplasmic reticulum?
transporting some of the proteins to various sites within a cell.
54
what does the Golgi apparatus (complex) do?
packages proteins into vesicles for export from the cell through exocytosis
55
what do vesicles outside of the golgi apparatus do?
move to the plasma membrane of the cell, where they fuse with it and discharge their protein contents to the exterior through exocytosis
56
What is reverse transcription?
the process in cells by which an enzyme makes a copy of DNA from RNA
57
when is reverse transcription used?
when only specific genes or small sections of DNA are required to be synthesised, we use mRNA instead of DNA
58
what are the steps in reverse transcription
| (5 steps)
1. mRNA is isolated from cytosol
2. Poly-A tail is added to the mRNA
3. a primer is added and binds to this tail, then the DNA lengthens from nucleotides being added
4. polymerase is added, catalysing the building of the complementary DNA strand
5. the double stranded DNA is produced
59
what enzyme is used to use mRNA as the template to build the single stranded DNA in reverse transcription?
reverse transcriptase
60
what are restriction enzymes?
cleave (cut) DNA at specific recognition sequences known as restriction sites, splitting DNA into smaller fragments
61
what is another name for restriction enzymes?
endonucleases
62
what is a restriction site
a particular order of nucleotides
63
what do restriction enzymes create when cutting?
blunt and sticky ends
64
how are blunt ends cut?
at points directly opposite each other
65
how are blunt ends rejoined together (ligated)
the DNA fragments are joined directly together through the use of DNA ligase
66
how are sticky ends cut?
cut one strand at one point but cut the second strand at a point that is not directly opposite, leaving over hanging ends.
67
how are sticky ends joined together (ligated)
The DNA ligase enzyme connects the single-stranded DNA together via the sugar-phosphate backbones
68
what enzyme is used to glue DNA that has been cleaved back together
ligase (DNA ligase)
69
where does ligase join DNA together?
sugar–phosphate backbones
70
what is polymerase chain reaction (PCR)
is a technique used to amplify a segment of DNA accurately and quickly
71
what is the main enzyme used in PCR and why is it used over others
Taq polymerase, because it can withstand great heat needed for the breakdown of DNA (heat resistant)
72
what are the 3 main steps in PCR?
1. Denaturing
2. Annealing
3. Extension
73
what are the 2 steps involved in denaturing
1. DNA is heated to 94 degrees
2. separation happens by raising the temperature of the PCR mixture, the hydrogen bonds between the complementary DNA strands break
74
what is the optimal temperature for denaturing to occur at and for how long
around 94 for a minute
75
What happens in annealing
Short segments of single-stranded DNA, known as primers, are added, binding to the 3' ends (target DNa sequences) initating DNA synthesis. These primers bind to their complementary sequences on the single-stranded template DNA
76
what is the optimal temperature for annealing to happen and for how long
55 for 2 mins
77
What happens in extension
The polymerase (Taq polymerase) uses the primers as a starting point and extending the primers, synthesising the new strands of DNA by adding nucleotides
78
what is the optimal temperature for extension to happen and for how long
72 for one minute
79
whats the difference between DNA and RNA polymerase
DNA polymerases synthesise DNA strands by adding (DNA) nucleotides (deoxyribose, ACTG)
RNA polymerases synthesise RNA strands by adding (RNA) nucleotides (ribose, AUCG)
80
what is gel electrophoresis
a technique for sorting a mixture of DNA fragments through an electric field on the basis of different fragment lengths
81
what are some uses for gel electrophoresis
to help solve crimes, determine paternity and identify bodies in events such as natural disasters
82
what are the 6 steps in gel electrophoresis
1.The DNA sample (fragments) is combined with DNA loading dye
2. it is then placed in a well at one end of a slab of aragose gel
3. This agarose gel is immersed in a buffer (salt) solution
4.The gel is then exposed to an electric field with the positive (+) pole (anode) at the far end and the negative (−) pole (cathode) at the starting origin. The DNA is attracted to the positive pole
5. Smaller fragments move through the agarose gel faster compared to larger fragments
6. fragments appear as bands on a gel which can be interpreted in various ways
83
why do smaller fragments move further in gel electrophoresis
the smaller fragments are able to better move and weave through the porous agarose gel compared to larger fragments
84
what is DNA profiling
a technique for identifying DNA from different individuals based on variable regions known as short tandem repeats (STRs)
85
what are STRs
short tandem repeats, sequences of just two to seven base pairs are repeated over and over
86
how are STRs used in DNA profiling
The number of repeats of an STR marker can vary between people and each variation is a distinct allele, so people with the same amount of repeats will match with certain DNA that is found
87
what is a plasmid
a small, circular, double-stranded DNA molecule, separate from the cell’s chromosomal DNA that exist naturally in bacterial cells
88
what is a recombinant plasmid
plasmids that carry foreign DNA
89
what are the 4 steps in making recombinant plasmids
1. DNA of the plasmid is cut using a specific cutting enzyme in order to create sticky ends
2. foreign DNA fragments are prepared using the same endonuclease so that the foreign DNA has sticky ends complementary to the cut plasmid (mostly done through reverse transcription)
3. foreign DNA fragments and the plasmids are mixed, and, in some cases, their ‘sticky ends’ pair by using weak hydrogen bonds. A recombinant plasmid has been created
4. The joining enzyme, ligase, is added and this makes the joins permanent through covalent bonding
90
what needs to happen after making a recombinant plasmid
needs to be transferred into a bacterial cell (bacterial transformation)
91
what is bacterial transformation
process in which bacterial cells take up segments of foreign DNA that become part of their genetic make-up
92
how can the success rate of bacterial transformation be increased
by heat shock or electroporation
93
why is heat shock and electroporation used
to increase the chance of bacteria to take up the recombinant plasmid as chances are low
94
what happens in electroporation
Cells are briefly placed in an electric field that shocks them and appears to create holes in their plasma membranes, allowing the plasmid entry
95
what happens in heat shock
The bacterial cells are suspended in an ice-cold salt solution and then transferred to 42 °C for less than one minute. This treatment appears to increase the fluidity of the plasma membranes of the bacterial cells and increases the chance of uptake of plasmids
96
what is a vector
an agent or vehicle used to transfer pathogens or genes between cells and organisms
97
what is gene cloning
the process which a gene of interest is located and cloned to produce multiple copies
98
what is recombinant DNA
DNA that is formed by combining DNA from different sources, often from different kinds of organisms
99
what are recombinant proteins
proteins that are expressed by recombinant DNA present in an organism
100
what are the 5 simple steps in creating insulin separately
1. cut with endonucleases
2. add insulin genes using ligase
3. transformations of bacteria with plasmids and expression of proteins
4. extract protein (insulin + B-galactosidase) from bacteria
5. purify both A and B and combine each to each other
101
CRISPR Cas9 definition
a tool for precise and targeted genome editing that uses specific RNA sequences to guide an endonuclease
102
what is Cas9
a restriction enzyme, that will cut at the right positions based on the gRNA (guide) also known as sgRNA (synthetic/single guide RNA)
103
what is CRISPR
short, repeated segments of DNA, with each repeated segment being separated by a length of spacer DNA.
104
what are spacers?
a region of non-coding DNA between genes
105
what are the 4 main steps that CRISPR Cas9 uses when cutting DNA
1. Targeting
2. binding
3. cleaving
4. DNA repair
106
What happens in the targeting step?
Cas9 will locate and bind to a common sequence in the genome known as the PAM sequence
107
what is the PAM sequence
a sequence of bases (NGG, N is any nucleotide) that is in the genome
108
what happens in the binding step
Cas9 unwinds the DNA, and if the DNA at that location matches with the 20 strands of gRNA then it will bind together with complimentary base pairing
109
what happens in the cleaving step?
Binding triggers Cas9 to change shape and gives the signal to cleave both strands of DNA upstream of PAM.
This disables the viral DNA
110
what happens in the DNA repair step?
the cell will try and repair the DNA, leading to mutation (error prone). Disabling the gene
Or scientists will add another sequence or modify the specific sequence allowing for knocking out genes or replacing faulty ones with healthy ones
111
what are GMOs
are organisms that has had their genome altered using genetic engineering technology
112
what does GMO stand for
genetically modified organism
113
what may GMOs involve
| (2)
- addition of gene segment
- silencing of gene
114
what are transgenic organisms
sub-group of GMOs, that contain genetic material from different species
115
what are some uses for GMOs for plants
| (3)
- increased photosynthesis efficiency
- greater crop yield
- faster growth rates
