14.3, 14.7, 15, 16, 20 Flashcards
the application of tools of computation and analysis to the capture and interpretation of biological data AKA meaning from genomic sequence
Bioinformatics
The information content of the genome includes:
binding sites
Regulatory proteins bind _____
DNA
RNA polymerase binds _____
DNA
Ribosome binds _____
mRNA
tRNAs bind ______
each codon in mRNA
Spliceosome binds _____
primary RNA transcript
Translation-termination protein binds _______
mRNA
pola(A) polymerase binds _______
primary RNA transcript
You can predict protein coding genes based on genomic sequences - 5 elements
Find ORF
Predict binding sites
Evidences from cDNA and ESTs
Similarity search
Combined evidences
Will bioinformatics tools help to identify all the genes in a sequenced genome?
No because they use existing knowledge to find gene structures, so an unknown gene will be difficult to predict
Human genome is predicted to have 25,000 protein-coding genes, but the detected protein products are much more than that. Why?
- Alternative splicing
- Post-translation remodification
Transcriptome
The set of RNAs expressed in cells, tissues, or organisms
Proteome
The complete set of proteins expressed in a cell, tissue, or organism
Interactome
The complete set of proteins expressed in a cell, tissue, or organism
Steps of RNA-seq
- Isolation
- Oligo dT enrichment
- Sample prep
- Fragmentation
- Sequencing
- Mapping
Two-hybrid test
A method for detecting protein-protein interactions, typically performed in yeast
______ isolates the DNA and its associated proteins in a specific region of chromatin so that both can be analyzed together.
ChIP
Types of reverse genetics (3 types)
- Reverse genetics through random mutagenesis
- Reverse genetics by targeted mutagenesis
- Reverse genetics by phenocopying
___________ provide general ways of experimentally interfering with the function of a specific gene without changing its DNA sequence.
RNAi-based methods
What reverse genetic approach can be applied to nonmodel organisms?
Phenocopying
What reverse genetic approach can be used for targeted gene knockout?
Targeted mutagenesis
Point mutation that involves the swapping of one nucleotide for another during DNA replication.
Base substitutions
occurs when an extra base pair is added to a sequence of bases or when a base pair is deleted from a sequence.
Base insertion/deletion
a change in the DNA sequence that codes for amino acids in a protein sequence, but does not change the encoded amino acid
synonymous mutation
the amino acid replaced is similar in function and shape to the amino acid being replaced.
missense mutation (conservative)
a completely different kind of amino acid is added to the chain (ex: polar replaced with non-polar)
missense mutation (non-conservative)
a mutation in which a sense codon that corresponds to one of the twenty amino acids specified by the genetic code is changed to a chain-terminating codon.
nonsense mutation
DNA replication error includes: (2 things)
Base substitutions
Indel
naturally occurring damage to DNA
spontaneous lesions
the release of purine bases from nucleic acids by the hydrolysis of N-glycosidic bonds
depurination
the removal of an amino group from an amino acid or other compound.
deamination
spontaneous lesions (3 examples)
- depurination
- deamination
- oxidatively damaged base
the misalignment of DNA strands during the replication of repeated DNA sequences
Replication slippage
Example of indel mutation
Fragile X syndrome (Trinucleotide-repeat diseases)
MOLECULAR BASIS OF INDUCED MUTATIONS (4 things)
Base modification by alkylating agents
Base damage by bulky adducts
Incorporation of base analogs
Binding of intercalating agents
Base can be damaged by ______ and _______
ultraviolet light and ionizing radiation
repairs non-bulky damage to bases
Base excision repair (BER)
the main pathway used by mammals to remove bulky DNA lesions such as those formed by UV light, environmental mutagens, and some cancer chemotherapeutic adducts from DNA
Nucleotide excision repair (NER)
detects and eliminates bulky damages in the entire genome, including the untranscribed regions and silent chromatin,
Global genome nucleotide excision repair (GG-NER )
operates when damage to a transcribed DNA strand limits transcription activity.
Transcription-coupled nucleotide excision repair (TC-NER)
Repair is restricted to the newly synthesized strand, which is identified in bacteria by the lack of DNA methylation and in eukaryotes by a DNA replication factor.
Mismatch repair (MMR)
the process by which cells copy DNA containing unrepaired damage that blocks progression of the replication fork
Translesion synthesis (TLS)
TLS polymerases can unblock the replication fork but cannot ______________ and is error-prone.
synthesize long stretches of DNA
a pathway that repairs double-strand breaks in DNA that does not require a homologous template to guide repair
Nonhomologous end joining
not as error-prone as NHEJ, primarily functions in S and G2 phases of the cell cycle.
Homologous recombination (HR)
What is the ultimate source of genetic variation?
DNA mutations
McClintock’s experiments: the Ds element.
The chromosome broke (dissociated) repeatedly in the same position on maize chromosome 9 during kernel development.
Ds is a genetic element that can jump around the genome or break chromosomes in the presence of ____
Ac
Ac provides functionality that enables Ds to _____
move
Ac encodes an enzyme called _______ that catalyzes the excision of Ds from a chromosome and its insertion in a new location
transposase
Ac is an ________ transposable element.
autonomous
Ds is a ________ transposable element.
nonautonomous
Evidence that E. coli has a transposon called an
insertion sequence (IS)
Transposase encoded by one of the two IS elements.
Composite transposons
A transposase and a resolvase are encoded within the transposon itself.
Simple transposons
the transposable element is duplicated during the reaction, so that the transposing entity is a copy of the original element.
replicative transposition
the transposon is completely removed from the genome and reintegrated into a new, non-homologous locus, the same genetic sequence is conserved throughout the entire process.
conservative (nonreplicative) transposition
Signature of transposon insertion:
(2 things)
Inverted repeats
Direct repeat
a type of genetic component that copy and paste themselves into different genomic locations by converting RNA back into DNA through the reverse transcription process using an RNA transposition intermediate
Retrotransposons
any of a family of RNA viruses that have an enzyme (reverse transcriptase) capable of making a complementary DNA copy of the viral RNA, which then is integrated into a host cell’s DNA. The family includes a number of significant pathogens, typically causing tumors or affecting the function of the immune system, e.g. HIV.
retrovirus
How did this experiment prove that retroposon transpose through a RNA intermediate?
made plasmid using a Ty element whose promoter activated by galactose, and an intron in its coding region. Transposition frequency increased by adding galactose (txn increase) and saw newly transposed Ty DNA lacked the intron sequence. Because intron splicing occurs only during RNA processing, there must have been an RNA intermediate in the transposition event.
Retrotransposons move via an intermediate that is:
single-stranded RNA.
like simple transposons of bacteria (its ends are short 31-bp inverted repeats and it encodes a single protein—the transposase).
P elements
______________ encode a transposase that cuts the transposon from the chromosome and catalyzes its reinsertion at other chromosomal locations.
DNA transposons (Ac and P element)
Most of ____________ is either transposable elements or decayed transposable elements.
repetitive DNA
_____% human genome (transposable elements)
50
_____ interspersed elements are autonomous
Long
_____ interspersed elements are nonautonomous
short
Diseases caused by transposable elements in the human genome
hemophilia A by LINE and hemophilia B, neurofibromatosis, and breast cancer by SINE (Alu).
Differences in the genome sizes of different plant species correlate primarily with the number of _____________
LTR-retrotransposons.
retrotransposons insert between genes, centromeric heterochromatin, tRNA genes, at sites where they do not _____________
interfere with the production of tRNAs.
Piwi complex guides the degradation of mRNAs complementary to the transposons that compose the pi-cluster.
piRNA
Principle of variation
variations exists among individuals within a population
Principle of heredity
offspring resemble their parents more
Principle of selection
some forms are more successful at surviving and reproduction than others in a given environment
Things learned from the HbS example:
(3 things)
Evolution can and does repeat itself;
Fitness is a very relative, conditional status;
Natural selection acts on whatever variation is available, and not necessarily by the best means imaginable
