The Central Dogma Theory Flashcards
What does DNA use as an intermediate for protein synthesis?
RNA
What is the process of synthesizing an RNA molecule from DNA template that will dictate the synthesis of a protein?
Transcription
Where does transcription take place?
Cell nucleus
What are the 3 general regions found in all genes?
1.) Promotor region
2.) Coding region
3.) Terminator region
What does the promotor region of a gene contain?
The consensus sequence
What happens in the coding region of a gene?
It is transcribed into mRNA. Transcription begins.
What happens in the terminator region?
It specified the end of transcription.
What is the template strand?
The strand of DNA that is transcribed into RNA.
AKA anti-sense strand
What is the template strand’s complimentary partner?
The non-template strand
What is the main key enzyme for transcription?
RNA polymerase
What does RNA polymerase do?
Moves along the DNA, unwinding the DNA helix just ahead of the active site for polymerization.
RNA polymerase catalyzes a new ____________ bond on the newly forming strand of RNA
Phosphodiester
In which direction does RNA polymerase work in?
5’ –> 3’
At what rate does RNA polymerase make mistakes? What about DNA polymerase?
1 for every 10^4 nucleotides
1 for every 10^7 nucleotides
What are the 4 steps of DNA transcription?
1.) Initiation
2.) Elongation
3.) Processing
4.) Termination
What helps the RNA polymerase recognize where to start?
Initiation factors
In prokaryotes what is the initiation factor?
Sigma factor
In eukaryotes, what is an important general transcription factor?
TFII
In step A of initiation, TFII recognized and binds a __________________ in the promotor region.
Consensus sequence
What is the TATA box?
A specific DNA sequence found in the promoter region of genes that plays a pivotal role in transcription initiation by serving as a binding site.
What is the TFII that is specific to the TATA box?
TFIID
What happens during steps B-D of initiation?
B. Other transcription factors join
C. RNA polymerase II joins
D. Transcription initiation complex is complete and transcription can begin
What are 2 other binding sites on DNA that influence initiation of transcription, other than TATA box?
1.) Repressor proteins bind upstream sequences called silencers (aka negative regulatory elements) **They inhibit gene transcription
2.) Transcriptional activator proteins bind upstream are called enhancers (aka positive regulatory elements)
**Increase the rate of transcription by attracting RNA polymerase II enzyme
During elongation, and RNA polymerase begins transcribing DNA, what happens?
Most general transcription factors (TFII) are released.
What happens to the transcription factors when they are released?
They are available to initiate another round of transcription with new RNA polymerase molecule
________ moves downstream along the DNA, transcribing the coding region.
RNA polymerase
Various ____________ factors are needed to help reduce the likelihood that RNA polymerase dissociating from DNA before it reaches the end of the gene
Elongation
What helps the RNA polymerase navigate the chromatin structure?
Chromatin remodeling complexes.
What partially disassembles & reassembles nucleosomes as an RNA Polymerase passes through?
Histone chaperones
As DNA polymerase moves along the DNA double helix it generates ___________.
Supercoils
In eukaryotes ________________________ removes super-helical tension.
DNA topoisomerase
How does DNA topoisomerase relieve super-helical tension?
By breaking the phosphodiester bond
In what 3 mains ways in the pre-mRNA transcript processed?
1.) Splicing
2.) Capping the 5’ end
3.) Polyadenylation of 3’ end
Once all pre-mRNA processing is complete, what is the transcript called?
mRNA
What is added to the 5’ end of the transcribed pre-mRNA for the 7-methyl guanosine cap?
A modified guanine nucleotide
Does the capping at the 5’ end occur early or late?
Early, once ~25 nucleotides of RNA have been transcribed
The 5’ cap facilitates export of the mRNA into the ________ and is also involved in ______________.
Nucleus/translation
Both ______ and ________ sequences are transcribed into __________.
intron, exon, RNA
Introns are then removed in a process called ____________.
RNA splicing
What is splicing performed by?
Spliceosomes
Spliceosomes require a special form of RNA _______ and proteins complexed into _________.
snRNA (small nuclear RNA), snRNP (small nuclear ribonucleoprotein)
___________ is referred to a spliceosome once it has complexed with the pre-mRNA.
snRNP
Splicing allows the same gene to produce a variety of different _______________.
Proteins
95% of human genes are _______ in more than one way.
Spliced
During step 4, the 3’ end of the mRNA molecule is specified by signals encoded in ______.
DNA
Once signals are transcribed into RNA and then bind to proteins. What do these proteins facilitate?
The cleavage of mRNA from RNA polymerase
What do Poly A tails (Poly- A Polymerase (PAP) do for the mRNA?
Protect it from degradation and facilitates export from the nucleus
True or False. The steps of transcription in prokaryotes are the same as in eukaryotes.
True
In what ways is the mRNA transcript produced in prokaryotes different from eukaryotes? (3)
1.) No processing is required for the prokaryotic mRNA (no 5’ cap, splicing, or poly-A tail)
2.) No export from nucleus (thus translation can begin right away)
3.) mRNA transcript is polycistronic (codes for more than one protein)
What does polycistronic mean?
Codes for more than one protein
Mature mRNA is exported from the nucleus through ___________.
Nuclear pore complexes
The mRNA sequence is decoded in sets of how many nucleotides? What are they called?
3, codons
Once in the cytosol, what is the mature mRNA translated into?
Protein
How many possible combinations of 3 nucleotides are there?
64
Since mRNA is interpreted in 3-nucleotide codons, the correct polypeptide sequence depends on what?
The correct reading frame
What are the 3 molecules needed for translation?
1.) mRNA transcript
2.) tRNA (bound to the correct AA-“charged tRNA)
3.) Ribosomes (a large and small subunit)
True or false. The cell makes a variety of tRNAs, each corresponding to all of the 20 amino acids.
False. Each corresponding to one of the 20 AA
Which enzyme catalyzes the attachment of correct amino acid to tRNA?
aminoacyl-tRNA synthetase
What molecule is protein synthesis performed by?
Ribosome
What helps maintain correct reading frame and ensure accuracy of codon - anticodon interaction?
Ribosomes
What is the ribosome complex composed of?
Various ribosomal proteins and ribosomal RNA (rRNA)
What are the 2 subunits of the ribosomal complex?
Small ribosomal subunit (SSU) and large ribosomal subunit (LSU)
Translation is divided into what 3 steps?
1.) Initiation
2.) Elongation
3.) Termination
What are the 4 substeps involved in the elongation step of translation?
1.) tRNA binding
2.) Peptide bond formation
3.) Large subunit translocation
4.) Small subunit translocation
What is the first codon translated on the mRNA?
AUG
AUG is the codon for which AA?
Methionine
Where is methionine always the first AA in all newly made proteins?
At their N-terminus
What side of the mRNA does the small ribosome bind to?
The 5’ end
True or False.
The 5’ 7-methyl guanosine cap helps with recognition of the 5’ end
True
How does the scanning mechanism in initiation work? What form of energy does this require?
The small ribosome moves along the mRNA (from 5’ to 3’) scanning for the first AUG.
ATP hydrolysis
When do the large ribosomal subunits assemble to complete the ribosome complex?
After the initiation factors dissociate
What is the ribosome-binding site called in prokaryotes?
Shine-Dalgnaro sequence
What are the 4 steps of elongation?
A.) tRNA binding
B.) Peptide bond formation
C.) Translocation of large subunit
D.) Translocation of small subunit
In elongation, where does the newly charged tRNA bind to?
The A site of the ribosome complex
The __________end of the polypeptide chain is released from the tRNA at the _____ site & joins the AA linked to the tRNA at the A site.
Carboxyl end, P site
When the polypeptide chain goes from the p site to the a site, what enzyme catalyzes this?
Peptidyl transferase
What are the different functions of the small ribosomal subunit compared to the large ribosomal subunit?
The small ribosomal subunit is responsible for finding and attaching to the messenger RNA (the finder)
The large ribosomal subunit plays a crucial role in the actual process of protein synthesis (the builder)
Elongation factors enter and leave the ribosome during each cycle & are coupled with _______________.
GTP hydrolysis
A ______ codon marks the end of tranlation. What are the 3?
Stop/ UAA, UAG, UGA
What binds to ribosomes with a stop codon in the A site?
Release factors
What enzyme catalyzes the addition of a water molecule rather than AA
Peptidyl transferase
Once full translated, what happens next? 3 possibilities.
1.) Protein is folded into specific 3-D shape
2.)May be modified in the ER.
3.)Sent to its proper cellular location
Where does the synthesis of proteins occur?
On polyribosomes (or polysomes)
True or False. Just one initiation takes place on each mRNA molecule being translated.
False. Multiple initiations
True or false.
Polysomes help speed up the rate of protein synthesis
True
What is the structural unit for DNA packaging?
nucleosome
_________ are highly dynamic structures regulated by a host of nuclear proteins.
histones
_________ can reposition nucleosomes on DNA to either expose or obscure gene regulatory elements
Chromatin remodeling complexes
__________ can carry out histone modification such as methylation, acetylation, or phosphorylation.
Chromatin writer complexes
Which step of protein synthesis are histones a part of?
transcript regulation
What are the 2 types of histone modification?
1.) Histone acetylation tends to open chromatin & increase transcription
2.) Histones and DNA can both be methylated
What enzyme performs histone acetylation?
histone acetyltransferases (aka HAT)
____________ reverses the changes made during histone acetylation and promotes chromatin condensation.
deacetylation
_________ can promote transcriptional activation or repression.
DNA methylation (and it typically results in transcriptional silencing.
The longer an mRNA last in the cytosol, the more protein can be made via ____________.
translation
Which protein receptor brings iron into a cell?
transferrin
Proteins needed for intracellular cytosolic use are translated on free __________ in the cytosol.
ribosomes
Proteins destined for lysosomes, ER, cell membrane or secretion need to be directed to the ______ _______ for translation. This process is called ______________.
rough ER, co-translational transfer
A signal peptide sequence is translated, which binds a signal _____ _______.
Signal recognition particle (SRP)
Binding of SRP (starts/stops) translation and directs the ribosome to the RER when it binds to a SRP receptor
stops
If a protein needs to be inserted into a cell membrane, it will contain a _________.
stop transfer sequence
When the stop transfer sequence comes into contact with the translocator, translation is paused.
Translocator will discharge the polypeptide into the phospholipid bilayer of the ER membrane.
_________rule states that the number of purines must equal the number of pyrimidines.
Chargaff’s
What forces are needed to stabilize the DNA double helix?
- H-bonds between complementary base pairs
- Sugar phosphate backbone
- Base stacking
Nucleotides are joined together along the sugar phosphate backbone with which bond type?
phosphodiester bond
Consider the negative charge between phosphate groups within the sugar phosphate backbone, what stabilizes the negative charges from repeling one another?
Mg2+
_________ are the structural unit for packaging DNA
Nucleosomes
Nucleosomes are composed of:
How many base pairs wrapped around a histone core
147 base pairs: Octamer of H2A, H2B, H3 and H4
H1 linker protein
________ is a complex of DNA + tightly bound protein
chromatin
Chromatin can be found either as densely packed __________ or dispersed _______________
heterochromatin/euchromatin
In it’s most condensed form, DNA is packaged into ___________
chromosomes
Which cell types in the human body are haploid, meaning they contain how many copies of each chromosome?
sperm cells in males and egg cells (ova) in females
Autosomal chromosomes are chromosomes 1 to ____ and they form _________ pairs
22/homologous
What is the name of the non-coding sequence removed during splicing?
intron
________ is a segment of DNA containing the instructions for making a particular protein
gene
________= coding sequence of a gene
_________ = non-coding sequences of a gene
exon
intron
98.5% of the human genome (does/ does not) encode protein
does NOT
