Unit 2: Decoding Genetic Information Flashcards
(109 cards)
1
Q
What is the Central Dogma?
A
This is the flow of information from the DNA to the RNA and finally the protein.
2
Q
What is an auxotroph?
A
This is the nutrients that the organism needs in order to attain the enzymes or fuel that it lacks in due to a genetic mutation.
3
Q
What is a codon?
A
This is the necessary set of 3 nucleotides that code for the amino acid and once the amino acids are all linked together the result is a polypeptide chain, and then the protein.
4
Q
What is the coding strand?
A
Only one DNA strand acts as the template for the synthesis of mRNA and the other DNA strand does not contribute however the mRNA and the coding strand are identical in the orientation and the order of the nucleotides the only difference between the DNA coding strand and the daughter RNA strand is that in RNA uracil is used whereas in DNA thymine is used.
For simplicity when writing the daughter RNA strand just look at the coding strand and replace the T’s with U’s.
5
Q
What direction is the DNA template strand read in?
A
3’ to 5’
6
Q
What direction is the mRNA strand read in from the perspective of the daughter strand?
A
5’ to 3’
7
Q
What direction are the amino acids added?
A
5’ to 3’
8
Q
What came first the RNA or DNA? How do you know?
A
It is likely that the RNA came first because because RNA can encode for amino acids like DNA and catalyze reaction like an enzyme. DNA developed later with advantages over RNA such as more stable and double stranded allows the complementary strand to be used as a template to repair the damaged strand.
9
Q
What is a ribozyme?
A
It is a ribonucleic acid enzyme that can catalyze their own synthesis and cleave RNA molecules.
10
Q
What does the phenotype depend on?
A
- ) Cell number
- ) Cell type
- ) Cell function
11
Q
What is the structure of a gene?
A
It includes the promoter and the transcriptional unit.
12
Q
What is the promoter?
A
The DNA sequence that includes the TATA Box that specifies where transcription begins on the chromosome and is located upstream of the transcription start point of the coding strand.
13
Q
What is upstream?
A
3’ of the template strand and 5’ of the coding strand.
14
Q
What is downstream?
A
5’ of the template strand and 3’ of the coding strand.
15
Q
What initiates transcription?
A
Once the promoter is recognized and bound by the transcriptional machinery such as RNA polymerase and transcription factors.
16
Q
What is the transcriptional unit?
A
This is part of the gene that is copied into RNA.
17
Q
What are the types of RNA polymerase?
A
- ) RNA polymerase I = rRNA
- ) RNA polymerase II = mRNA
- ) RNA polymerase III = tRNA
18
Q
What is the role of RNA polymerase?
A
- Synthesize RNA transcript in the 5’ to 3’ direction
- Unlike DNA replication a primer is not needed
- Unwinds and rewinds the DNA helix
19
Q
What is transcriptional initiation?
A
- ) General transcription factors bind to the promoter and recruit RNA polymerase II resulting in a low basal level of transcription.
- ) Transcriptional activator proteins bind to enhancer regions distant from the promoter to cause SNA looping bringing mediator nd RNA polymerase to the promoter resulting in high level of transcription.
20
Q
What is transcriptional elongation?
A
- RNA polymerase moves along the template
- DNA is unwound in from of the moving RNA polymerase and reannealed behind the transcription bubble
- Ribonucleotides are added to the 3’ end of the RNA transcript
- The growing RNA transcript is displaced from the template strand
21
Q
How does termination of transcription take place in prokaryotes?
A
- ) Rho-independent termination in DNA terminates the mRNA sequence by forming a G-C hairpin and causes RNA polymerase to stall and dissociate.
- ) Rho-dependent termination terminates the mRNA sequence and it gets bound by the Rho helicase which unwinds RNA from the template DNA and RNA polymerase.
22
Q
How does termination of transcription take place in eukaryotes?
A
Cleavage and polyadenylation specific factor where the pol-A sequence in mRNA signals the CPSF to cleave the completed mRNA transcript thus separating it from the RNA polymerase and the template DNA strand.
23
Q
What are the main differences between RNA and DNA?
A
- RNA is single-stranded while DNA is double-stranded.
- DNA replication occurs for the entire genome while RNA synthesis occurs at select locations of the genome.
- DNA replicates genomes only once per cell cycle while RNA synthesis occurs in multiple copies throughout the genome.
- DNA polymerase needs an RNA primer for the lagging strand but RNA polymerase does not need one.
- RNA products detach from the template DNA while the DNA template and daughter strand remain attached.
24
Q
What is the main similarity between RNA and DNA?
A
The synthesis of both DNA and RNA occurs in the 5’ to 3’ direction.
25
What is Rho?
This is a helicase molecule.
26
What is post transcription?
The maturation of the transcribed mRNA strand which is the precursor (pre) mRNA to form the mature mRNA.
27
What is the point of having Untranslated Regions (UTRs)?
These regions provide the mRNA with stability and translation efficiency as the 5' UTRs contain a ribosome binding site or (Shine Dalgamo in prokaryotes) and (Kozak Box in eukaryotes) which initiate translation.
28
What is the function of the 5' cap?
This is a modified guanosine triphosphate that is added to the 5' mRNA end to allow ribosomes to bind to the correct place on the mRNA (ribosomes read in the same direction mRNA are made 5' to 3') and to protect the mRNA from degradation.
29
What is the poly-A tail?
This is a long strand of adenine nucleotides added to the 3' end of the mRNA by poly-A polymerase to protect the mRNA from degrading and translational efficiency.
30
Why is the RNA molecule more unstable than the DNA molecule?
RNA is more unstable than DNA because instead of deoxyribose sugar it has ribose sugar which is more unstable and instead of being double-stranded it is single-stranded.
31
What benefit can the poly-A tail serve by being at the 3' end?
The RNA is not simply linear it wraps around therefore even if the poly-A tail is at the 3' end the poly-A tail is close to the 5' end and can assist the translation and prevent degradation that way.
32
What is an intron?
These are non-coding or Untranslated Regions.
33
What is an exon?
These are coding segments.
34
What is endonuclease?
An enzyme that breaks down a nucleotide chain into two or more shorter chains by cleaving the internal covalent bonds linking nucleotides.
35
What is exonuclease?
An enzyme that breaks down a nucleic acid by removing nucleotides one by one from the end of a chain.
36
How does mRNA splicing take place?
1. ) Bind to an intron-exon junction.
2. ) Loop introns out of the pre-mRNA by forming a lasso and bringing the exons closer together.
3. ) Clip the intron at each exon boundary releasing the lasso structure using the spliceosome.
4. ) Join the adjacent exons together.
37
What is the open reading frame?
The region of mRNA that is translated includes the start and stop codons at the border.
38
What are the steps in post transcription?
1. ) The newly transcribed precursor mRNA or pre mRNA is not ready for translation as it is not mature enough.
2. ) Add the poly-A tail and the 5' cap.
3. ) Pre-mRNA has alternating exons and introns.
4. ) Remove the introns by splicing to generate an open reading frame consisting of a continuous stretch.
5. ) Then mature mRNA is exported from the nucleus.
39
What is a spliceosome?
This is what carries out the splicing and it consists of 5 noncoding RNAs or snRNA and several small ribonucleoprotein particle or snRNPs and it is responsible for clipping the intron lasso during splicing.
40
How does the spliceosome know where to splice?
There is a specific sequence of the nitrogen bases at the exon-intron junction that informs the spliceosome where to cut.
41
What is an isoform?
These are the protein products that result from splicing since you can have different mRNAs from a gene by cutting the exons out at different location and have different protein products as a result of the splicing.
42
What is alternative splicing?
It is the cutting of different exons and the introns in order to increase the number and variety of proteins.
43
Are fewer genes more beneficial than more genes?
It is believed that fewer genes are better because it requires less regulation and fewer potential problems can take place whereas more genes have a higher potential for problems and mistakes.
44
What do the line and box represent in this transcript map?
In this transcript map, the lines represent the introns and the boxes represent the codons.
45
How does RNA interfere in post transcription?
1. ) siRNA and microRNA are synthesized.
2. ) siRNA and microRNA bend to form a loop or hairpin structure and the dicer RNAse come and cleave the 21-23 base pair removing the loop and leaving behind the double strands of the mRNA and the dicer stays connected to the double strands.
3. ) Then the protein complex RISC comes and unwinds the double strands of the microRNA or siRNA and one of the strands leaves and breaks down while the other serves as the complementary to the mRNA target strand.
4. ) Then the target mRNA binds to the complementary strand formed by the siRNA or the microRNA thus stopping gene expression and inducing the degradation of the mRNA strand.
46
What is RISC?
This is the RNA-induced silencing complex and it consists of other complex proteins such as microRNA and siRNA which are used as a template to identify the complementary mRNA strand and then cleaves the mRNA by activating RNAse.
47
What is microRNA?
This is a small non-coding molecule that is transcribed by RNA polymerase III and its goal is to silence gene expression by stopping translation by binding to the 3' untranslated region of the mRNA and it is used in post-transcription.
48
What is siRNA?
This is a small double-stranded molecule that is transcribed by RNA polymerase III it stands for short interfering RNA and its goal is to silence the gene expression by acting as a hairpin structure to prevent the translation of the pre-mRNA and it is used in post-transcription.
49
How does the length of the RNA determine the direction of its synthesis?
Wherever on the DNA that has shorter RNA protruding is the start of the transcription because not that many genes have been transcribed thus it is the 3' of the template strand and the 5' of the daughter strand. Then the area where the RNA is longer is the 5' end of the template and the 3' end of the daughter strand.
50
How does the length of the RNA determine the direction of its synthesis?
For a protruding RNA molecule from the template DNA strand, the part connected to the DNA is the 3' end and the part of the RNA that is further away from the DNA strand is the 5' end since nucleotides are added to the 3' end.
51
What makes up amino acids?
- Amino group
- Carboxyl group
- R group
- Hydrogen
- Central carbon
52
What causes variation among amino acids?
The R group is unique for the amino acids.
53
What are the different types of amino acids?
1. ) Nonpolar amino acid = R group contains CH2 or CH3
2. ) Uncharged polar amino acid = R group contains O or OH
3. ) Charged amino acid = R group contains acids or bases
4. ) Aromatic amino acid = R group contains a carbon ring with alternating double and single bonds
54
What are the special functional amino acids?
1. ) Methionine is the first amino acid in the polypeptide
2. )Proline causes a kink or bends in the polypeptide
3. ) Cysteine bridge contributes to the structure of the polypeptide
55
What are the levels of protein structures?
1. ) Primary amino acid sequence
2. ) 2nd Degree structure
3. ) 3rd Degree structure
4. ) 4th Degree structure
56
What is a tRNA?
This is the middle component between the mRNA and protein synthesis it is what connects the two.
57
What is an anticodon?
This is the complementary 3-nucleotides to the codons which are the 3-nucleotides of the mRNA nucleotides.
58
How is tRNA charged?
The tRNA is charged by the addition of tRNA to the receptor on the tRNA this process is called Aminoacyl-tRNA synthetase.
59
What is the genetic code?
These are the 61 sense codons that code for an amino acid each codon is for a specific amino acid.
60
What are the rules of the genetic code?
1. ) The codons are read from the 5' to 3' end
2. ) Codons are nonoverlapping and the message does not contain gaps
2. ) Message is translated in a fixed reading frame set by the start codon: +1, +2, or +3 whichever of these are able to encode for AUG. The goal is to start at +1, +2, or +3 in order to get the AUG codon.
61
What are the components of the ribosome?
1. ) Large subunit -50S that contains a larger number of rRNA and proteins as well as the peptidyl transferase.
2) Small subunit - 30S that contains fewer rRNA and proteins as well as the decoding center where tRNA are read and decoded for the codon.
62
What are the 3 binding sites in the ribosome?
1. ) A or aminoacyl site where the charged tRNA binds.
2. ) P or peptidyl site where the tRNA attaches to the growing peptide chain.
3. ) E or exit site where the tRNA that carried the amino acid can now leave.
63
How does translational initiation occur?
1. ) The initiator tRNAMET is brought to the small ribosome subunit through the expense of energy called GTP.
2. ) The small ribosomal subunit is recruited to the capped 5'end and scans the mRNA in the 5' to 3' direction.
3. ) The anticodons are paired to their complementary codons.
64
How does translational elongation occur?
1. ) The charged tRNA or the aminoacyl tRNA binds to the A-site.
2. ) The peptidyl transferase in the large subunit forms a peptide bond between the carboxyl group of the growing polypeptide and the amino group of the amino acid in the A site.
3. ) Ribosome translocation in which the tRNA with the polypeptide shift from the A to P site and the uncharged tRNA shift from P to E site where it is ejected.
4. ) The next codon of the mRNA is now in the A site and the next amino acid tRNA can be loaded by EF-GTP.
65
How does translational termination occur?
1. ) There are 3 stop codons at the end of the protein-coding sequence.
2. ) When the ribosome reaches the stop codon the release factor binds the A-site and stimulates peptidyl transferase to cleave the polypeptide from the p-site tRNA.
66
What is the release factor?
These are the stop codons that are not recognized by tRNA but are by proteins.
67
How are proteins regulated?
1. ) Phosphorylation is the addition of a phosphate to a protein by kinase to activate or inhibit activity.
2. ) Ubiquitination is the addition of ubiquitin molecules to proteins to proteins and target them for destruction by the proteasome.
3. ) Proteolysis is the specific protein cleavage that can induce activity.
68
What is epigenetics?
These are changes that are made to the gene transcription without changing the DNA sequence and the genome.
69
What is an anticodon?
The codons consist of 3 nucleotides on an mRNA strand the complement of those mRNA codons is the anticodons which are antiparallel to the codons.
70
What methods do epigenetics include?
1. ) Modifications to the histone to allow the DNA to repel due to the repulsion and allow for binding potential.
2. ) Methylation of histone tails can activate or repress transcription.
3. ) The chromatin remodeling complex displaces nucleosomes to allow the promoter to bind to the transcription factor.
71
What is translational regulation?
The control of protein synthesis it is the rate of the translation initiation or the formation of the initiation complex.
72
What is posttranslational regulation?
The control of protein abundance and activity.
73
What is a mutation?
These are changes to the nucleic acid sequence and can be inherited or not inherited depending on the location of the mutation. These changes can lead to changes in the phenotype that could be advantageous, harmful or neither.
74
Which mutations are inherited?
The mutations that occur in the germline or the gametes such as the egg and sperm cell then become heritable.
75
Which mutations are not inherited?
The somatic mutations are the mutations that occur in all other cells except the gametes therefore it is not heritable.
76
What is a base substitution?
A single nucleotide changes.
77
What is an insertion?
One or more base pairs are added to the sequence during DNA replication.
78
What is a deletion?
One or more base pairs are skipped during DNA replication.
79
What are transitions?
Purine to purine changes or pyrimidine to pyrimidine changes.
80
What are transversions?
Purine to pyrimidine or pyrimidine to purine changes.
81
What is a missense(nonsynonymous) mutation?
When the codon changes and the amino acid also changes.
82
What is a nonsense mutation?
When the codon changes and the amino acid is a stop codon.
83
What is a silent(synonymous) mutation?
The codon changes but the amino acid is the same.
84
What is a frameshift mutation?
The insertion or deletion of a small number of base pairs that alter the reading frame.
85
What is deletion?
Loss of genes.
86
What is duplication/amplification?
Increasing the dosage of genes.
87
What is translocation?
Interchange of genetic parts from nonhomologous chromosomes.
88
What is inversion?
Reversing the orientation of a segment of the chromosome.
89
What is a spontaneous mutation?
These are naturally occurring mutations that are caused by replication error and spontaneous lesions such as depurination and denimation of bases.
90
What is an induced mutation?
Natural (environmental) or artificial agents or mutagens that cause the mutation such as chemicals that can damage bases.
91
What is a wild-type allele?
This is the normal form of the gene found in nature or the standard gene sequence.
92
What is a loss of function allele?
Mutations that reduce or eliminate the gene function or expression.
93
What is a gain of function allele?
Mutations that enhance the gene function or expression.
94
What is the cell cycle?
This is the process in which the cell grows, replicated DNA, and forms daughter cells.
95
What is the G1 and G2 phase?
These are the gap phase where the proteins and necessary material are made for cell division.
96
What is the S phase?
The phase where DNA replicates.
97
What is a CDK?
This is the cyclin-dependent kinase which is bound to its regulatory cyclin subunit in each phase of the cell cycle that can allow the progression past the checkpoints.
98
What is cyclin?
This is the regulatory complex that determines the activation of CDK.
99
What are the 3 checkpoints?
1. ) DNA damage a the G1/S phase.
2. ) DNA replication at the G2/M checkpoint.
3. ) Spindle connection at the prometaphase/metaphase point.
100
What is P53?
This is the break that inactivates CDK and stops the cell cycle.
101
What is cancer?
This is the process of mass cell division and is a result of the altered expression of multiple genes due to mutations.
102
What is an oncogene?
This is the positive regulator or a gain of function gene that supports cancer when it is active. The regulators include CDK and cyclin.
103
What is the tumor suppressor gene?
This is a negative regulator or a loss of function gene when active the tumor is suppressed when inactive the tumor can thrive and grow.
104
What are homologous chromosomes?
These are chromosome pairs that have the same order and number of genes however the alleles could be different.
105
What are the stages of mitosis?
1. ) Prophase
2. ) Prometaphase
3. ) Metaphase
4. ) Anaphase
5. ) Telophase
106
What are the stages of meiosis I?
1. ) Prophase I
2. ) Prometaphase I
3. ) Metaphase I
4. ) Anaphase I
5. ) Telophase I
107
What are the stages of meiosis II?
1. ) Prophase II
2. ) Prometaphase II
3. ) Metaphase II
4. ) Anaphase II
5. ) Telophase II
108
What is recombination?
During prophase I the process of crossing over occurs where the genes of the non-sister chromatids are exchanged and this exchange must be precise otherwise there will be a loss or gain for the other chromosome.
109
Which meiosis determines the ploidy?
Meiosis I determines the ploidy as it is the reductional division.
