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AOS 1 Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

what are nucleic acids made up of?

A

sub-units / monomers called nucleotides

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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.

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3
Q

what are the types of sugar in RNA and DNA nucleotides?

A

DNA = deoxyribose, RNA = ribose

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4
Q

what are the 5 types of bases?

A

adenine, thymine, uracil, cytosine and guanine

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5
Q

what are the 3 types of RNA?

A

transfer RNA (tRNA), messenger RNA (mRNA) and ribosomal RNA (rRNA)

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6
Q

what does mRNA do?

A

Carries the genetic message from the DNA from the nucleus to the ribosomes (to be translated)

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7
Q

what does rRNA do?

A

together with particular proteins, makes the ribosomes found in cytosol

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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

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9
Q

what are the 3 main steps in gene expression?

A

Transcription
RNA processing
Translation

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10
Q

what happens during transcription?

(3 steps)

A
  1. The DNA is unwound by the RNA polymerase binding to the promoter region as well as DNA helicase assisting
  2. 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
  3. A pre mRNA strand is made and released from the templated.
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11
Q

what are the 3 main steps in RNA processing?

A

Capping
Adding a tail
splicing

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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.

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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

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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.

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15
Q

what is alternate splicing?

A

exons can be removed enabling one gene to produce a multitude of proteins if required.

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16
Q

where does translation take place?

A

cytosol

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17
Q

what happens in translation?

(4 steps)

A
  1. mRNA moves to the ribosome where it is read in codons.
  2. 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.
  3. The ribosome then continues to make more amino acids and they are joined by peptide bonds.
  4. A codon that tells the ribosome to stop production is reached and the polypeptide is released from the ribosome.
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18
Q

what is the start codon

A

AUG

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19
Q

what are the 3 stop codons

A

UAA, UAG or UGA

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20
Q

what is the coding region?

A

the part of the gene that gives the information for making proteins

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21
Q

what is the flanking regions?

A

parts of the gene that isn’t the coding region

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22
Q

what is the coding region made up off?

A

exons and introns

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23
Q

what are the 2 flanking regions known as?

A

upstream and downstream

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24
Q

what are exons?

A

the part that contain the instructions for the synthesis of the protein and are both transcribed and translated

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25
Q

what are introns?

A

parts in the coding region that are transcribed but are cut out during RNA processing and therefore are not translated

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26
Q

what are the 3 sections of the upstream region?

A

promoter
operator
leader

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27
Q

what happens in the promoter region?

A

The promoter is where transcription factors and RNA polymerase binds to initiate transcription

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28
Q

what happens in the operator region?

A

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

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29
Q

what are the 4 parts of the leader region?

A

TrpL (1), then three attenuator regions (2, 3, 4)

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30
Q

what happens in the leader region?

A

further regulation of transcription

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31
Q

what is an operon?

A

group of linked structural genes with a common promoter and operator that is transcribed as a single unit

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32
Q

what are the two types of regulation of the trp operon?

A

repression and attenuation

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33
Q

what happens when trp is present in repression

(3 steps)

A
  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
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34
Q

what happens when trp isn’t present in repression

(2 steps)

A
  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
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35
Q

when there is trp present what happens in attenuation

(4 steps)

A
  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
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36
Q

when there isn’t trp present what happens in attenuation

(5 steps)

A
  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
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37
Q

what are polypeptides?

A

large molecules made up of amino acids

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38
Q

what are amino acids made up of

A

an amino group and a carboxyl group. The difference between amino acids are the R group

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39
Q

how do the amino acids join together to make the polypeptide?

A

Each peptide bond forms by the linkage of an amino group from one amino acid and a carboxyl group of another amino acid

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40
Q

what are the 4 levels of protein structure?

A

primary, secondary, tertiary, quaternary

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41
Q

what is a primary structure?

A

linear sequence of amino acids, each protein has a different primary structure and therefore different functions

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42
Q

what is a secondary structure?

A

folded amino acid sequences depending on the R group

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43
Q

what are the 3 types of secondary structures

A

Alpha helix, Beta-pleated sheet and Random coiling

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44
Q

what is an alpha helix

A

secondary structure in proteins that appears as a tight twist

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45
Q

what is a beta-pleated sheet?

A

secondary structure in proteins that appears as folded sheets, with a change in direction of the polypeptide chain

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46
Q

what is random coiling?

A

secondary structure in proteins that does not fit in as either a alpha helix or beta-pleated sheet

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47
Q

what are tertiary structures?

A

total irregular 3D folding held together by ionic or hydrogen bonds forming a complex shape

48
Q

what is a quaternary structure?

A

A structure in which two or more polypeptide chains interact to form a protein

49
Q

what do catalysts (enzymes) do?

A

speed up the rate of chemical reactions without the catalyst itself being used up in the reactions

50
Q

what is the basic function of enzymes?

A

increase the rate of almost all the chemical reactions and to do this within the prevailing conditions of temperature and pH within cells

51
Q

What is a proteome

A

The complete array of proteins produced by a single cell or an organism in a particular environment.

52
Q

what happens at the ribosome?

A

translation

53
Q

what happens in the rough endoplasmic reticulum?

A

transporting some of the proteins to various sites within a cell.

54
Q

what does the Golgi apparatus (complex) do?

A

packages proteins into vesicles for export from the cell through exocytosis

55
Q

what do vesicles outside of the golgi apparatus do?

A

move to the plasma membrane of the cell, where they fuse with it and discharge their protein contents to the exterior through exocytosis

56
Q

What is reverse transcription?

A

the process in cells by which an enzyme makes a copy of DNA from RNA

57
Q

when is reverse transcription used?

A

when only specific genes or small sections of DNA are required to be synthesised, we use mRNA instead of DNA

58
Q

what are the steps in reverse transcription

(5 steps)

A
  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
Q

what enzyme is used to use mRNA as the template to build the single stranded DNA in reverse transcription?

A

reverse transcriptase

60
Q

what are restriction enzymes?

A

cleave (cut) DNA at specific recognition sequences known as restriction sites, splitting DNA into smaller fragments

61
Q

what is another name for restriction enzymes?

A

endonucleases

62
Q

what is a restriction site

A

a particular order of nucleotides

63
Q

what do restriction enzymes create when cutting?

A

blunt and sticky ends

64
Q

how are blunt ends cut?

A

at points directly opposite each other

65
Q

how are blunt ends rejoined together (ligated)

A

the DNA fragments are joined directly together through the use of DNA ligase

66
Q

how are sticky ends cut?

A

cut one strand at one point but cut the second strand at a point that is not directly opposite, leaving over hanging ends.

67
Q

how are sticky ends joined together (ligated)

A

The DNA ligase enzyme connects the single-stranded DNA together via the sugar-phosphate backbones

68
Q

what enzyme is used to glue DNA that has been cleaved back together

A

ligase (DNA ligase)

69
Q

where does ligase join DNA together?

A

sugar–phosphate backbones

70
Q

what is polymerase chain reaction (PCR)

A

is a technique used to amplify a segment of DNA accurately and quickly

71
Q

what is the main enzyme used in PCR and why is it used over others

A

Taq polymerase, because it can withstand great heat needed for the breakdown of DNA (heat resistant)

72
Q

what are the 3 main steps in PCR?

A
  1. Denaturing
  2. Annealing
  3. Extension
73
Q

what are the 2 steps involved in denaturing

A
  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
Q

what is the optimal temperature for denaturing to occur at and for how long

A

around 94 for a minute

75
Q

What happens in annealing

A

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
Q

what is the optimal temperature for annealing to happen and for how long

A

55 for 2 mins

77
Q

What happens in extension

A

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
Q

what is the optimal temperature for extension to happen and for how long

A

72 for one minute

79
Q

whats the difference between DNA and RNA polymerase

A

DNA polymerases synthesise DNA strands by adding (DNA) nucleotides (deoxyribose, ACTG)
RNA polymerases synthesise RNA strands by adding (RNA) nucleotides (ribose, AUCG)

80
Q

what is gel electrophoresis

A

a technique for sorting a mixture of DNA fragments through an electric field on the basis of different fragment lengths

81
Q

what are some uses for gel electrophoresis

A

to help solve crimes, determine paternity and identify bodies in events such as natural disasters

82
Q

what are the 6 steps in gel electrophoresis

A

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
Q

why do smaller fragments move further in gel electrophoresis

A

the smaller fragments are able to better move and weave through the porous agarose gel compared to larger fragments

84
Q

what is DNA profiling

A

a technique for identifying DNA from different individuals based on variable regions known as short tandem repeats (STRs)

85
Q

what are STRs

A

short tandem repeats, sequences of just two to seven base pairs are repeated over and over

86
Q

how are STRs used in DNA profiling

A

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
Q

what is a plasmid

A

a small, circular, double-stranded DNA molecule, separate from the cell’s chromosomal DNA that exist naturally in bacterial cells

88
Q

what is a recombinant plasmid

A

plasmids that carry foreign DNA

89
Q

what are the 4 steps in making recombinant plasmids

A
  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
Q

what needs to happen after making a recombinant plasmid

A

needs to be transferred into a bacterial cell (bacterial transformation)

91
Q

what is bacterial transformation

A

process in which bacterial cells take up segments of foreign DNA that become part of their genetic make-up

92
Q

how can the success rate of bacterial transformation be increased

A

by heat shock or electroporation

93
Q

why is heat shock and electroporation used

A

to increase the chance of bacteria to take up the recombinant plasmid as chances are low

94
Q

what happens in electroporation

A

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
Q

what happens in heat shock

A

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
Q

what is a vector

A

an agent or vehicle used to transfer pathogens or genes between cells and organisms

97
Q

what is gene cloning

A

the process which a gene of interest is located and cloned to produce multiple copies

98
Q

what is recombinant DNA

A

DNA that is formed by combining DNA from different sources, often from different kinds of organisms

99
Q

what are recombinant proteins

A

proteins that are expressed by recombinant DNA present in an organism

100
Q

what are the 5 simple steps in creating insulin separately

A
  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
Q

CRISPR Cas9 definition

A

a tool for precise and targeted genome editing that uses specific RNA sequences to guide an endonuclease

102
Q

what is Cas9

A

a restriction enzyme, that will cut at the right positions based on the gRNA (guide) also known as sgRNA (synthetic/single guide RNA)

103
Q

what is CRISPR

A

short, repeated segments of DNA, with each repeated segment being separated by a length of spacer DNA.

104
Q

what are spacers?

A

a region of non-coding DNA between genes

105
Q

what are the 4 main steps that CRISPR Cas9 uses when cutting DNA

A
  1. Targeting
  2. binding
  3. cleaving
  4. DNA repair
106
Q

What happens in the targeting step?

A

Cas9 will locate and bind to a common sequence in the genome known as the PAM sequence

107
Q

what is the PAM sequence

A

a sequence of bases (NGG, N is any nucleotide) that is in the genome

108
Q

what happens in the binding step

A

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
Q

what happens in the cleaving step?

A

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
Q

what happens in the DNA repair step?

A

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
Q

what are GMOs

A

are organisms that has had their genome altered using genetic engineering technology

112
Q

what does GMO stand for

A

genetically modified organism

113
Q

what may GMOs involve

(2)

A
  • addition of gene segment
  • silencing of gene
114
Q

what are transgenic organisms

A

sub-group of GMOs, that contain genetic material from different species

115
Q

what are some uses for GMOs for plants

(3)

A
  • increased photosynthesis efficiency
  • greater crop yield
  • faster growth rates

Biology 3&4 (7 decks)

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