TERM TEST #2 Flashcards
What does the central dogma of molecular biology consist of?
its the universal information flow from DNA to protein in order to convert genotype to phenotype
In prokaryotes what does the Central dogma process look like?
Transcription and translation both occur in the cytoplasm in prokaryotes and therefore, both processes happen simultaneously
in Eukaryotes what does the central dogma process look like?
transcription and process of the precursor mRNA molecules occur in the nucleus and translation occurs in the cytoplasm
what is the one gene-one enzyme (protein) hypothesis?
in 1940s Beadle and Tatum hypothesized that genes encode enzymes that function at each step of a biochemical pathway needed to make an essential nutrient
- mutating a gene encoding an enzyme would cause a block in the metabolic pathway and the organism can no longer synthesize the needed nutrient (auxotroph)
what is an auxotroph?
An auxotroph is an organism that cannot synthesize a particular essential nutrient on its own and must obtain it from its environment. This inability is due to a mutation in a gene involved in the biosynthetic pathway of that nutrient.
information flow occurs in certain places on chromosomes called what?
genes
genes encode for two types of RNA which are?
- coding RNA (mRNA): codes for protein/polypeptide
- noncoding RNA: tRNA, rRNA, snRNA, microRNA: does not code for a protein
what is the genetic code?
nucleotide information to amino acid sequence
For the genetic code information is contained in what?
4 nucleotide bases in DNA (A,T,G,C) OR RNA (A,U,G,C) sequences
if a code has one-letter words how many combination?
4 combinations
if a code has two-letter words how many combinations?
16 combinations
if a code had three-letter words how many combination?
64 combinations
If DNA has a three-letter code it is known as a what?
Triplet
if RNA has a three-letter code it is known as a ?
codon
genetic code is what ?
universal (same code in prokaryotes, eukaryotes and viruses)
why is it that the universal code can allow foreign genes to be transferred and expressed in different host organisms
The universal genetic code means that the same codons specify the same amino acids in almost all organisms. This allows it to be transmitted to different host organisms because the host’s cellular machinery can read and translate the inserted genes correctly to produce the corresponding protein
How does green fluorescent protein used from jellyfish help with for research from scientists?
main application is to monitor the spatial and temporal expression of a protein
What are the key things we need to note about template and coding DNA strands?
in general for every gene, a RNA molecule is only produced (transcription) from one of the DNA strand (Template strand)
- the other DNA strand is the non template strand or coding strand (has same 5’to3’ orientation and sequence as mRNA molecules except uracil is substituted with thymine
- the template strand is always read from 3’-5’ by the RNA polymerase
-mRNA is synthesized in the 5’to3’ direction (by the RNA polymerase)
what the order for central dogma?
- DNA replication
- Transcription
- TRANSLATION
- PROTEIN
Transcription of a gene occurs off only …?
one of the DNA strands (template) in a 5’- 3’ direction
On chromosomal maps genes are shown on the coding strand true or false?
true
on a prokaryote what are the rings labelled?
Which came first DNA or RNA?
Likely RNA because able to store genetic information (code for amino acids like DNA) can also catalyze reaction (like an enzyme)
- DNA developed late 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
what can ribozymes do?
- they are ribonucleic acid enzymes they can catalyze their own synthesis and cleave RNA molecules (2 degree structure)
what is reverse transcription?
RNA—>DNA
- reverse transcriptase is in some viruses with RNA genomes (e.g retrovirsus)
- Viral RNA needs to be converted into viral DNA in order to integrate into the host’s chromosome
- the host’s transcription and translation machinery is hijacked to produce viral proteins from the viral DNA
- RNA based viruses enter the host cell
-viral RNA is reverse transcribed into DNA
-viral DNA integrates into the host genome
-Host cell machinery is used to produce viral proteins - an example is HIV
what are the different parts of Transcriptional regulation of Gene expression?
This is how you make RNA molecules from genes
1. Initiation
2. Elongation
3. Termination
What do organisms phenotypes depend on?
an organisms phenotype depends of cell number, type, and function
is it true every cell in an organism has an identical genome (DNA sequence)
yes
How is the differentiatiation of cells determined?
by which genes are turned on and off (transcription) in each cell type
what is regenerative medicine?
growing a desired tissue type by turning on/off the appropriate genes using molecular techniques
What does a Gene include?
includes a promoter and transcriptional unit
What is a promoter?
DNA sequence (including TATA box) that specifies where transcription begins on the chromosome
where is the promoter located?
immediately “upstream” or 5’ of transcriptional start point of the non-template or coding DNA strand
- the promoter is then recognized and bound by the transcriptional machinery that initiate transcription
what is the transcriptional UNIT?
part of the gene that is copied into RNA
what is RNA polymerases? and what are the job of them
Synthesizes RNA transcript in a 5’ -3’ direction (adds new ribonucleotides to 3’-OH) while reading DNA template in a 3’to5’ direction
does not need a primer for initiation of RNA synthesis (different from DNA polymerases)
Unwinds and rewinds DNA helix during RNA synthesis
what are the three types of RNA. polymerases in eukaryotes?
- RNA pol I: rRNA
- RNA pol II: mRNA
- RNA pol III: tRNA
What is the job of the RNA pol I:
synthesize ribosomal RNA (rRNA) which is a key component of ribosomes used in protein synthesis
what is the job of RNA pol II?
RNA polymerase II’s job is to synthesize messenger RNA (mRNA) which carries the genetic code from DNA to the ribosomes for protein synthesis. It also synthesized some small nuclear RNAs (snRNAs) involved in RNA splicing
what is the job of DNA pol III?
RNA polymerase III’s job is to synthesize transfer RNA (tRNA), 5S Ribosomal RNA (5S rRNA), and other small RNAs, which are essential for protein synthesis and other cellular processes
What is transcriptional initiation ?
transcriptional initiation is mediated by direct interaction of DNA-binding proteins to specific regulatory sequences of the gene (rate determining step)
what are the two types of transcriptional initiation processes?
- general transcription factors
- transcriptional activator proteins
what is the job of the general transcription factors of the initiation process?
they bind to the promotor and recruit RNA polymerase II resulting in low basal level of transcription.
what is the job of the transcriptional activator proteins ?
they bind to enhancer regions distant from the promoter to cause DNA looping bringing mediator and RNA polymerase to the promoter resulting in high level of transcription
what is transcriptional elongation?
RNA polymerase moves along the template DNA (3’ to 5’)
- DNA is unwound in front of the moving RNA polymerase and reannealed behind in the transcription bubble
- Ribonucleotides are added to the 3’ end of the RNA transcript (synthesis continues in a 5’ to 3’ direction)
-growing RNA transcript is displaced from the DNA template strand to allow reannealing back into double stranded DNA
what is transcriptional termination?
- 5’ sequence in DNA template causes termination after transcribed into RNA
1. RHO-independent termination (prokaryotes)
2. RHO-dependent termination (prokaryotes)
3. cleavage and polyadenylation specific factor (eukaryotes)
explain the two transcriptional termination factors in prokayotes?
- rho-independent termination: terminator sequence in mRNA base pairs with itself to form G-C hairpin and causes RNA polymerase to stall and dissociate
- rho-dependent termination: terminator sequence in mRNA is recognized and bound by the Rho helicase which unwinds the RNA from the template DNA and RNA polymerase
what is cleavage and polyadenylation specific factor?
poly-A sequence in mRNA signals the CPSF to cleave the completed mRNA transcript signaling RNA polymerase to stop transcription
Compare and contrast the differences between DNA replication and transcription
DNA replication:
- DNA molecules are double stranded
-Replication occurs for the entire genome
-Replicates genome only once/cell cycle
- DNA polymerase requires a primer for initiation
- Daughter strand remains base paired with parental template strand
-synthesis of new DNA strand occurs in 5’-3’ direction
TRANSCRIPTION:
- RNA molecules are single strands
-Occurs at selected location in the genome (i.e genes)
-synthesis of RNA in multiple copies and copes vary throughout the genome
-RNA polymerase does not need a primer for initiation
RNA product does not remain base-paired to the template DNA
-synthesis of RNA occurs in 5’-3’ direction
What is the 3 steps to post-transcriptional Regulation of Gene expression
” processing of mRNA molecules for stability and proper translation “
1. 5’ Capping
2. 3’ Polyadenylation
3. Splicing
Is it true that the ends of prokaryotic and eukaryotic mRNAs are not translated ? (5’ and 3’ untranslated regions)
true
What do both 5’ UTR’s and 3’ UTRs regulate?
mRNA stability and translational efficiency
What is the 5’ UTR contained at a ribosomal binding site called in prokaryotes and eukaryotes? and what do they function in?
Shine Dalgarno sequence in prokaryotes and Kozak box sequences in eukaryotes that function in translational initiation
What is the open reading frame (ORF) ?
is the region of mRNA that is translated and includes that start and stop codons at the borders
where does post-transcriptional modifications of eukaryotic pre-mRNAs take place?
the newly transcribed mRNA (pre-mRNA) undergoes processing in the nucleus to produce mature translatable mRNA.
What is the 5’ CAP in the post-transcriptional modification of eukaryotic pre- mRNA?
a modified guanosine triphosphate is added to the 5’ end of the mRNA and acts as a ribosome binding site and protects mRNA from degradation
What is the Poly (A) tail in the post-transcriptional modification of eukaryotic pre- mRNA?
a long (50 to 250) sting of adenine nucleotides added to the 3’ end of the mRNA by poly-A polymerase to protect the mRNA from being degraded and increase translational efficiency
What is the Introns in the post-transcriptional modification of eukaryotic pre- mRNA?
are removed/sliced during pre-mRNA processing produce translatable mRNA
what is the process of postranscriptional processing from pre-mRNA to mRNA
- newly- transcribed precursor mRNA (pre-mRNA) is not ready to be translated into a protein
- needs to be converted to a translatable mRNA (mature)
- addition of 5’CAP and Poly-A tail
-pre-mRNA has a mix of alternating coding segments and UTRs (exons) and non-coding segments (introns) - removal of introns by splicing to generate the open reading frame consisting of a continuous strech of codons and UTRs
- mRNA is exported from nucleus into the cytoplasm to associate with ribosomes
what is mRNA splicing ?
removal of introns from pre-mRNA and joining of exons to make mature mRNA
What needs to be removed in the pre-mRNA for it to become a mature one?
non-coding segments (introns) need to be removed in pre-mRNA with UTRs and exons (contains codons) remaining in mRNA
what is splicing carried out by, and what is it made out of?
- splicing is carried out by spliceosome which is made up of five noncoding RNAs (snRNA) complexed to several proteins (small ribonucleoprotein particles or snRNPs)
in point form explain the process of mRNA splicing?
- bind to intron-exon junctions
- loop introns out of the pre-mRNA (lariat strucure) bringing exons closer together
- clip the intron at each exon boundary releasing the lariat structure
- join adjacent exons together
what is alternative splicing?
generating different proteins from one gene
- one gene sequence made by moving exons to make proteins from single gene
- splicing can occur in different combinations to generate two or more different mRNA from a gene and therefore several related protein products (isoforms)
what are isoforms?
they are different versions of the same protein that are produced from a single gene through alternative splicing
- different isoforms are made in different tissues from the same gene producing tissue-specific phenotypes
what is a result that can occure from alternative splicing
it can dramatically increase the number and variety of proteins that can be encoded by the genome
what percent of human genes are alternatively spliced?
~75%
what is an example of alternative splicing ?
it can happen in tropomyosin
Explain what happens to microRNAs and siRNAs in postranscriptional regulation by RNA interference
- microRNAs (miRNAs) are transcribed by RNA polymerase II
- small interfering RNAs (siRNAs) can also be transcribed and may come from foreign origins ( this means comes from outside the organism, such as viral RNA )
explain the processing of miRNA/siRNA precursors in post transcriptional regulation by RNA interference
precursors of miRNA/siRNA are cleaved into 21-23 base pair double- stranded RNAs by the Dicer RNase enzyme
explain the difference between transcriptional and post transcriptional regulation?
transcriptional regulation involves the control of mRNA synthesis at the DNA level, including chromatin remodelling and promoter strength, while posttranscriptional regulation involves mRNA processing and stability, including 5’ CAP, poly-A tail, and RNA interference
for a particular rRNA molecule, where are the 5’ and 3’ ends?
5’ ends are the furthest away from rRNA molecule
Non polar amino acids
R groups usually contain -CH2 or -CH3
What is the 3 degree structure of the protein structure?
Is the 3-D structure of a single polypeptide and is composed of interactions between amino acid side chains
What is the structure of tRNA?
2-D and 3-D shaped: tRNA has a two-dimensional cloverleaf shape and a three-dimensional L-shape
- self- complementarity : tRNA folds into these shapes due to the complementary base pairing within the molecule itself
Explain the charging process cycle?
Step 1: the amino acid and ATP bind to the aminoacyl-tRNA synthetase enzyme
Step 2: the amino acid is activated by the ATP, forming an aminoacyl-AMP intermediate
Step 3: the tRNA binds to the enzyme, and the amino acid is transferred to the tRNA
Step 4: the charged tRNA (aminoacyl-tRNA) is released from the enzyme, ready to participate in protein synthesis
What are the steps in Translation initiation in eukaryotes?
- the initiator tRNA^Met is brought to the P-site of the small ribosome subunit. This process requires GTP, which provides energy
- The complex of initiator tRNA^Met and the small ribosomal subunit is recruited to the capped 5’ end of the mRNA. this complex scans along the mRNA in a 5’ to 3’ direction until it reaches the first 5’-AUG-3’ start codon
- complementary base pairing occurs between the anticodon of the initiator tRNA^Met and the start codon of the mRNA. The large ribosomal subunit then binds to the small subunit to form the initiation complex. This complex is now ready to accept the first tRNA in the A site
FInal step: GTP is hydrolyzed to GDP, signalling the start of translation
it goes A,P E
What are the steps of translation elongation?
- the correct aminoacyl tRNA (carrying an amino acid) enters the A site of the ribosome. This step requires a helper protein called elongation factor (EF-GTP)
- the anticodon of the tRNA must match the codon on the mRNA in the A site.
- Peptide bond formation
- an enzyme called peptidyl transferase, located in the large ribosomal subunit, forms a peptide bond
- this bond forms between the amino acid on the tRNA in the A site and the growing polypeptide chain on the tRNA in the P site - Translocation of the Ribosome
- the ribosome moves (translocates) along the mRNA
- as it moves, the tRNA in the A site, now with the growing polypeptide chain, shifts to the P site
- the empty tRNA that was in the P site moves to the E site, where it is released from the ribosome - the ribosome in now ready to accept the next animoacyl tRNA in the A site, corresponding to the next codon on the mRNA
- this cycle repeats, elongating the polypeptide chain one amino acid at a time
what is the job of termination during translation?
releases a completed polypeptide from the ribosome
what is post-translational regulation of gene expression?
“modification of proteins with chemical groups for activity and degradation”
1. phosphorylation
2. Ubiquitination
3. proteolysis
what is epigenetics?
post translational modification of histones that affect transcription
- changes in the gene transcription can occur without altering the DNA sequence itself. This is part of what is called epigenetics
compare translational regulation to posttranslational regulation
translational regulation: control of protein synthesis (rate of translation initiation or formation of the initiation complex)
post-transcriptional regulation: control of protein abundance and activity (availability of functional proteins)
what are germ-line mutations?
mutation originally occurred in gametes and therefore
becomes heritable
ex. sex influences trait
what are somatic mutations?
can occur in all other cell types except gametes and therefore, not heritable
- mutations occur in a progenitor cell and all other daughter cells will express the mutation
-somatic mutations are expressed as sectors (size depends on time of mutation)
ex. cancer tumors are an example
what is a base substitution as a small- scale mutation?
single nucleotide change as a result of point mutations
what is insertion as a small- scale mutation?
one or more base pairs in a sequence during DNA replication usually resulting in a frameshift mutation
what is deletion as a small- scale mutation?
one or more base pairs skipped during DNA replication usually resulting in frameshift mutations
what is a transitions as a small- scale mutation?
purine to purine or pyrimidine to pyrimidine changes
what is a transversions as a small- scale mutation?
purine to pyrimidine or pyrimidine to purine changes
