topic seven Flashcards
(121 cards)
1
Q
eukaryotic dna is associated with what pH and what charge histones
A
alkaline and positively charged proteins called histones
2
Q
a nucleosome consists fo alength of dna of about how many base pairs
A
150 wrapped around 150 base paris
3
Q
dna is what charge and what pH
A
acidic and negatively charged
4
Q
how are nucelosomes linked
A
the dna strand from one nucelosome flows directly into the next. this section is called a DNA linker
5
Q
what is the repeat unit of eukaryoitc chromatin
A
nucleosomes
6
Q
what does base pairing
A
The hydrogen bonding between the purine and the pyrimidines (see Be aware box below). Two hydrogen bonds occur between adenine (A) and thymine (T), and three hydrogen bonds occur between guanine (G) and cytosine (C).
The slightly positive charge on T and a slightly negative charge on A, allow the two bases to bond together during complementary base pairing.
7
Q
which bases are the purines
A
guanine and adenine (2 rings in their structure)
8
Q
which bases are the pyrimidines
A
thymine and cytosine (they contain one ring in their structure)
9
Q
can eukaryotic dna be initated at various points along the dna molecule
A
yes
10
Q
rate of replication
A
approximately 100 nucleotides per second in eukaryotes while it can be as high as 1000 nucleotides per second for prokaryotes
11
Q
how many base pairs have to be replicated during the S phase of the cell cyle
A
3 billion airs per haploid set of chromosomes so 6 billion base paris have to be replicated
12
Q
- What does helicase do
A
binds to the origin of replication and breaks hydrogen bonds between base pairs to unwind the DNA double helix.
As helicase moves along the DNA molecule, it causes supercoiling and tension on the region ahead.
13
Q
- what do ssb’s do
A
Single-strand binding proteins then bind to the single strands formed to keep them apart to allow time for the DNA sequence to be copied. The two separated strands act as templates for the replication process.
14
Q
- waht does gyrase do
A
As helicase moves along the DNA molecule, it causes supercoiling and tension on the region ahead. This is relieved by the enzyme DNA gyrase, which moves in advance of helicase.
15
Q
which is the leading strand
A
the strand of DNA that is being replicated continuously in the 5’ to 3’ direction by continuous polymerisation at the 3’ growing tip.
16
Q
which is the lagging strand
A
the strand of DNA that is replicated discontinuously in small fragments in the 5’ to 3’ direction away from the replication fork.
17
Q
As free nucleoside triphosphates bind to the template
A
they lose their two extra phosphate groups to generate energy, which is used to add the nucleotide to the growing polynucleotide chain.
18
Q
what does dna polymerase III do
A
the enzyme that adds DNA nucleotides to the strands
19
Q
where can dna polymerase III add a nucelotide
A
to the 3’ OH group of the deoxyribose
20
Q
what is different for dna polymerase III on the lagging strand
A
the last nucleotide ends with a 5’ phosphate group. So, on the lagging strand, a DNA primase first makes short RNA primers (these primers are later removed by DNA polymerase I and substituted with a short DNA segment), which allow the DNA polymerase III to add DNA nucleotides to the 3’ OH of the RNA primer. Many such primers are made as a scaffold for the DNA polymerase III. It synthesises short DNA fragments called Okazaki fragments, which are joined together by DNA ligase to form a complete DNA strand. The result is two new strands, both based on the template of the old DNA molecule.
21
Q
whcih enzyme makes the short rna primers for the lagging strand
A
dna primase
22
Q
what removes the rna primers on the lagging strand
A
dna polymerase I
23
Q
how much of dna is non coding
A
more than 98% of the human genome
24
Q
regions of da that dont code for protines
A
regulators of gene expression
introns
telomeres
genes for trnas
25
Regulators of gene expression :
These are DNA sequences that regulate gene expression in various ways. For instance, promoters are sequences that occur just before genes and act as a binding point for the RNA polymerase enzymes that catalyse the transcription process. Other DNA sequences may act as binding sites for proteins that either increase or decrease the rate of transcription; these are known as enhancers and silencers, respectively.
26
introns
These are DNA base sequences found within eukaryotic genes that get removed at the end of transcription. They do not contribute to the amino acid sequence of the polypeptide made from the gene.
27
telomeres
These are repetitive sequences that protect the ends of the chromosome. Telomeres help ensure that DNA is replicated correctly. With every cell division, short stretches of DNA are lost from the telomeres.
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genes for trnas
These genes code for RNA molecules that do not get translated into proteins, but instead fold to form tRNA molecules that play an important role in translation.
29
what is a tandem repeat
a sequence of two or more DNA base pairs that is repeated in such a way that the repeats lie end-to-end on the chromosome
30
DNA profiling involves the following steps:
Collection of samples and extraction of DNA
Amplification (copying) of the DNA region containing tandem repeats by PCR
Separation of the DNA fragments using gel electrophoresis .
31
When DNA profiling is used to analyse the DNA of individuals, which parts of the DNA are used?
Short tandem repeats
32
DNA sequencing
the method used for deducing the precise order of nucleotides within a DNA molecule. Since all DNA molecules have the same sugar phosphate backbone, the main role of DNA sequencing is to determine the order of the four bases (adenine, guanine, cytosine and thymine) in a DNA strand.
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what is dna sequencing used for
dna profiling
paternity suits
forensics
cancer analysis
genome studies
34
Dideoxy Chain Termination Method
It is based on the fact that DNA polymerase needs a 3' OH group of the preceding nucleotide to add another nucleotide to the DNA strand. If a dideoxy nucleotide (a 'normal' DNA nucleotide but lacking the oxygen atom at the 3' OH group) is added to the mixture, and this nucleotide is built into the growing DNA strand, no further nucleotides can be added and the reaction stops.
35
how have modern dna sequencers make use of Dideoxy Chain Termination Method
add a fluorescent dye to the four dideoxynucleotides so that the base present when replication stops can be recognised
36
waht does dNTP stand for
deoxyribose nucleotide triphosphate
37
what does ddNTP stand for
dideoxyribose nucleotide triphosphate
38
X-ray diffraction is based on
the principle that X-rays are scattered when they pass through different material. The scattering is called diffraction, and patterns in diffraction indicate properties of the crystals. Since X-rays affect photographic film in the same way as visible light (turning it black), the scattering pattern can be visualised (shown) on a radiogram. Biological material, such as DNA, can be used in this technique.
39
what did the x ray diffraction radiogram show
the distance between the base pairs, as well as the turns of the helix (3.4 nm). Franklin was able to measure other features of the DNA molecule, including the distance between the repeats.
40
waht did hershey chase do
convince the scientific community that it was DNA, and not protein, that made up genetic material. They used a T2 bacteriophage, which is a virus that infects bacterial cells. This virus injects its DNA into the bacterial cell while its protein coat stays on the outside.
41
hershey chase experiment
Hershey and Chase used radioactive phosphorus and sulfur to label the DNA and protein in the viruses. Phosphorus is found in DNA but not protein, and sulfur is found in protein but not DNA. This was an elegant and simple way to determine what part of the virus entered the bacterium.
42
what did hershey and chase find
When bacteriophages containing radioactive phosphorus ( 32 P) were allowed to infect nonradioactive bacteria, all the infected cells became radioactive. Additionally, the next generation of bacteriophages, produced from the infected bacteria, were all radioactive.
However, when the bacteria were infected with bacteriophages labelled with radioactive sulfur ( 35 S) and the virus coats removed (by agitating them in an electric blender), almost no radioactivity could be detected in the infected cells.
These findings suggest that the DNA component of the bacteriophages is injected into the bacterial cell, while the protein component remains outside. Since the DNA entered the bacteria and caused the formation of radioactive bacteriophages, it showed that DNA was the genetic material.
43
In trying to determine whether DNA or protein is the genetic material, Hershey and Chase made use of which of the following facts?
DNA contains purines, whereas protein includes pyrimidines.
DNA contains sulfur, whereas protein does not.
DNA contains phosphorus, whereas protein does not.
DNA contains nitrogen, whereas protein does not.
DNA contains phosphorus, whereas protein does not.
44
waht is epigenetics
DNA contains purines, whereas protein includes pyrimidines.
DNA contains sulfur, whereas protein does not.
DNA contains phosphorus, whereas protein does not.
, Correct answer
Your answer
DNA contains nitrogen, whereas protein does not.
45
In epigenetic changes, the DNA sequence itself is not altered, but
some of the bases are altered. most often, a cytosine base is methylated (a methyl group is added) by the enzyme DNA methyl transferase. Another factor that favours methylation is when cytosine (C) is followed by guanine (G). This CpG (the 'p' stands for phosphate linking the two bases) combination is often seen in or near the promoter region of a gene, and when methylated, gene expression will be shut down.
46
The CpG is called an
epigenetic tag and can be passed to daughter cells during mitosis in the body. This means that these tags are copied during DNA replication.
47
what can affect methylation
Many environmental factors, such as pollution, diet, temperature or stress
48
During DNA replication
methylation of the dna does not change
49
Which is the best description of epigenetics?
Investigating how non-coding DNA functions to regulate gene expression.
Investigating methylation patterns in DNA
Investigating how the environment affects phenotype
Investigating phenotypic changes due to gene expression rather than DNA sequence changes
Investigating phenotypic changes due to gene expression rather than DNA sequence changes
50
where does rna polymerase start to make a copy of mrna
the promoter, located at the 5' end adjacent to the coding region
51
3 stages of transcription
intiation
elongation
termination
52
initaiton transcription
Initiation starts when RNA polymerase binds to the DNA at the promoter region and the double helix unwinds
53
elongation transcription
Elongation is when mRNA becomes longer as nucleotides are added to the 3' OH group. Note that, similar to replication, transcription progresses in a 5' to 3' direction.
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termination transcription
Termination is when the mRNA synthesis is complete and the complex of DNA, RNA polymerase and mRNA disassembles.
55
which way do replication and transcription progress
5' to 3'
56
which strand does rna make first
antisense dna strand
57
where does rna polymerase form covalent bonds between
the growing mrna molecule and th ribonuleotides
58
why does translation being immediately in prokaryoutes
there is no nuleus or nuclear membrane
59
in eukaryotes what is it claled when the mrna needs to be prepared for translation
his process is called post-transcriptional modification of mRNA. The reason for this extra step is the introns and exons in eukaryotic genes. Introns are DNA sequences in eukaryotic genes that contain no coding information. Sometimes they contain controlling sequences that regulate the transcription of the gene. Exons are the DNA sequences that code for a polypeptide.
60
post transcriptional modification
these steps are transcription (synthesis of pre-mRNA ) ,
addition of a 5' cap and
a poly-A tail (which protect the mRNA molecule from degradation) and, finally,
splicing, which involves removing (excising) the introns and joining (ligating) the exons to form mature mRNA.
61
spliceosome
a large ribonucleoprotein (RNP) complex made up of five small nuclear ribonucleoproteins (snRNPs) and several proteins. It acts as an enzyme in the splicing process to remove introns and bind exons together. (You are not expected to know this definition for the exam.)
62
spliceosome removing introns and exons to form mature mrna
Splicing allows several proteins to be synthesised from the same gene
63
waht is alternative pslicing
differnt splicing produces different polypeptides
64
how does the promoter directly affect transcription
by controlling whether or not rna polymerase can access the gene
65
define promoter
a short DNA sequence situated just before a gene, which acts as a binding point for the RNA polymerase enzyme. The promoter is a good example of non-coding DNA with a function.
66
what is an operon
a set of genes all linked to a single promoter
67
what is an operator
a sequence of DNA in prokaryotes that allows a cell to regulate whether a gene is transcribed or not. This stops the binding of RNA polymerase with the promoter. Thus, the genes of the lac operon are not transcribed.
68
Repressor proteins may
block the transcription of specific genes, which plays an important role in the differentiation process.
69
activator proteins bind to
enhancers silencers to increase the rate of transcription
70
repressor proteins bind to
silencers to decrease the rate of transcription
71
In response to the presence of certain food sources, prokaryotes can do which of the following?
Turn off translation of their mRNA
Alter the level of transcription of certain genes
Inactivate their mRNA molecules
Increase the number of their ribosomes
Alter the level of transcription of certain genes
72
Which of these options is NOT a DNA sequence to which proteins can bind in order to regulate gene expression?
Silencer
Repressor
Promoter
Enhancer
repressor: It is not a DNA region, but a protein that can bind to DNA regions such as operators or silencers. The other three options are all DNA regions that have regulatory functions for gene expression when proteins bind to them.
73
when hsitones bind to dna, they block
rna polymerase
74
how can the tails fo histone proteins be acetylated
adding an acetyl grouo (-CH3COO-)
75
Histones can also be methylated. Instead of adding an acetyl group (–CH 3 COO - ), a ___ group is added
methyl -CH3
76
Methylation can have a positive or a negative effect on transcription, depending on
where the histones are located on the genome.
77
DNA that is methylated is usually not
expressed
In other words, the genes that have methylated cytosine nucleotides are shut down. Methylation lasts for a long time. It causes the inactivation of the second X chromosome in females.
78
translation starts when
mature mrna binds to a small ribsoosal subunit at the mrna binding site
79
translation consists of 3 stages
intiiation
elongation
termination
80
preparation for translation
At initiation, the mRNA binds to a small ribosomal subunit. Next, the anticodon of the initiator tRNA binds to the codon of the mRNA. Finally, the large ribosomal subunit joins to complete the assembly of the translation complex. Now that each component is in its correct location, the process of translation can start.
81
what is an aminoacyl-trna
When a tRNA molecule binds to its corresponding amino acid it forms a complex called an aminoacyl-tRNA. (This is discussed in more detail in the next section.)
82
the space filled by the initiatior trna is called the
p site
83
what does e stand for
exit
84
what does p stand for
peptidyl-trna binding
85
what does a stand for
aminoacyl-trna binding site
86
the e site is wehre
the trna moves after transferring its amino acid to the growing polypeptide chain, ready to exit the ribosome.
87
the a site is where
the incoming trna with its attached amino acid binds,
88
the p site is where
trna from the a site moves after its amino acid forms a peptide bond with the growing polypeptide chain
89
step one of elongation
A new aminoacyl-tRNA comes in and binds to the A site. This aminoacyl-tRNA carries a specific amino acid that matches the codon on the mRNA and the anticodon of the tRNA.
90
step two of elongation
the new amino acid is joined to the existing polypeptide chain by a peptide bond.
91
step three of elongation
the tRNA that was bound to the polypeptide chain is now ready to be recycled as it is no longer bound to an amino acid.s
92
step four of elongation
the ribosome translocates (moves) the tRNA holding the growing amino acid chain from the A site to the P site. This shifts the 'empty' tRNA to the E site, where it can leave the ribosome and be recycled. Now the whole process can start again until the ribosome reaches the termination codons: UAG, UAA or UGA.
93
waht happens intermination
Once the termination codon is reached, a release factor binds in the A site and causes the disassembly of the components of the translation complex. All of these components can be reused for another translation complex. This stage of translation is called termination.
94
Which of these statements describes the A site of the ribosome?
The site containing the tRNA that holds the growing polypeptide
The site where a tRNA attached to an amino acid enters the ribosome
The site where the initiator tRNA binds during initiation
The site from which tRNA molecules without amino acids exit the molecule
The site where a tRNA attached to an amino acid enters the ribosome
95
is trna rna or dna
single stranded rna that folds on itself
96
one loop on the trna contains
a sequence called the anticodon, which can decode and bind to an mrna codon
97
what happens when a trna recognises and binds to its corresponding codon of mmrna in the ribosome
the trna transfers the appropriate amino acid to the end of the growing polypeptide
98
The triplet of bases at the amino acid binding site of tRNA is:
5' CCA 3'
99
How many permanent loops does a tRNA molecule have?
3
100
describe th subunits of eukaryotic ribosomes
a small subunit which binds mrna and a large subunit with three trna binding sites
101
what enzyme is involved in ensuring trna molecules are loaded with the correct amino acid corresponding to the codon on the mrna
aminoacyl-trna synthetase (1 corresponds to each amino acid) (20)
102
what is the specificity of a amino acid and a trna activating enzyme based on
This specificity is based on a match between the shape of the anticodon of the tRNA and the enzyme, as well as the match between the shape of the particular amino acid and the enzyme, thus illustrating the concept of enzyme–substrate specificity
103
phosphorylation when phosphates are removed from ATP molecules energy is released for use by the cell.
aminoacylation of a trna molecule
104
which proteins are synthesised on the bound ribosomes attached to the er
Proteins that function inside the endoplasmic reticulum (ER), Golgi apparatus, lysosomes and plasma membrane, or that are destined to be exported outside of the cell
105
when does translation start
once te mrna attaches itself to the ribosome
106
what does the signal recognition particle do
The SRP then binds to the SRP receptor protein on the endoplasmic reticulum. This allows the polypeptide to enter the rough endoplasmic reticulum (RER) as it grows in length.
107
what happens when translation ends and the translation complex disassembles
the whole polypeptide is taken into the RER
108
proteins that are translated on free ribosomes are destined to function in the
mitochondira, chloroplasts, cytoplasm or nucleus of the cell
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Bound ribosomes synthesise proteins mainly meant for
secretion or for use in lysosomes.
110
Free ribosomes produce proteins for
use mainly within the cell.
111
why is there no seperation between the areas of the cell where transcription and translation take place, due to
the absence of a nuclear membrane
112
To allow the production of polypeptides and hence proteins at a faster rate, multiple ribosomes can attach to the same
mrna.
the structure formed is called a polysome
113
primary structure
The primary structure of a protein refers to the sequence (order and identity) and the number of amino acids in the polypeptide. It is maintained by peptide bonds between the subunits.
114
secondary structure
The secondary structure is formed when the polypeptide chain folds back on itself into α -helices or β -pleated sheets. It is stabilised by hydrogen bonds between –NH groups (from the peptide bonds) and –C=O groups on another peptide bond, further along in the same chain.
115
tertiary structure
further folding of the polypeptide, stabilised by itneractions between r group.
116
quaternary structure
more than one folded polypeptide chain. subunits joined together via strong bonds similar to those in the tertiary structure.
117
hat do quarternary proteins also often have
a non-protein molecular unit, called a co-factor or prosthetic group that is tightly attached to their polypeptides. In the case of hemoglobin, heme is the iron-containing prosthetic group that helps the protein to transport oxygen.
118
a protein with a prosthetic group attached is called
a conjugated protein
119
What aspects of protein structure are stabilised or assisted by hydrogen bonds?
Secondary, tertiary, and quaternary structures, but not primary structures
120
Aminoacyl-tRNA synthetases often associate with a Mg2+ ion in order to function properly. When a protein associates with a prosthetic group as in this example, what is it called?
Conjugated protein
121
Tertiary structure of proteins depends primarily on which structural component of amino acids?
r groups
