module 4 Flashcards
nuclear lamina
- inner surface of nuclear envelope
- provides mechanical support
- composed of lamins: members of the super family of the polypeptides that assemble into the intermediate filaments of the cytoplasm.
How do the base pairing relationships of DNA bases account for the uniform width of the double helix
- Purines are made up of two rings and include Adenine and Guanine.
- Pyrimidines structure includes a single ring and bases that are pyrimidines are Cytosine and Thymine.
- Pyrimidine can only bind to the purine via hydrogen bonding (Adenine forms double bond with Thymine and Cytosine forms triple bond with Guanine)
- double helix a uniform width of ~2nm
semiconservative rreplication
Semiconservative replication means that newly synthesized double helix is composed of one old parental strand and one new daughter strand.
semidiscontinuous replication
- DNA synthesis only occurs in 5’->3’ direction
- one of the strands (leading strand) will be synthesized in the continuous manner
- other (lagging strand) is synthesized in fragments called Okazaki fragments (they are later linked together by enzyme DNA ligase).
outline the lowest level of chromatin organization in eukaryotic cells
- nucleosome:
- composed of 8 core histone molecules around which approximately 1.8 turns of negatively supercoiled DNA is wrapped
- 8 histone molecules are composed of two each of H2A, H2B, H3 and H4
- histones are organized into 4 dimeric complexes, each of which binds ~27 base pairs (contact occurs in the minor groove)
- The H1 linker histone binds where DNA enters and exits the nucleosome. H1 histone molecule and the histone core interact with 168 base pair of DNA.
- Nucleosome are attached to one another along the strand of DNA and are coiled by looped domains around proteins. When the loops fold over onto themselves, the become really condensed and this allows tight packing of the chromosome.
What is the experimental evidence suggesting that DNA replication in eukaryotic chromosomes begins at many sites along the DNA
proven in the autoradiographic experiment. Cells were incubated in [3H] thymidine for a short period of time prior to the preparation for the autoradiography. The black silver grains showed the place where the radioactive DNA precursor was incorporated. The initiation of replication begins in the center of each incorporated thymidine. During the S phase, it was noted that ~10-15% or replicons were engaged in the simultaneous replication at any point in time. There was noted to be a correlation between proximity or replicons and the time of replication.
facultative heterochromatin
Facultative heterochromatin is a heterochromatin that has been specifically inactivated during certain stages. This inactivation is less permanent in comparison to the constitutive heterochromatin.
Random inactivation of one of the two X chromosome in the female is the example of the facultative chromatin. This ensures that both male and females have the same number of active X chromosome and synthesize the equivalent amounts of products encoded by X-linked genes. However, the inactivated chromosome can be reactivated if it has been passed on to the male offspring
Despite the numerous checks present in the cell to prevent the placement of the wrong nucleotide in a replicating DNA, a few mistakes can be made. Why is this beneficial in the long term
The change in the nucleotide can lead to the mutation, or changes to the genetic make up that can be passed on to the offspring. Even though mutation is often associated with negative consequences (for example when it causes improperly folded protein and leads to the disease), there are mutation that are beneficial for the specie (for example some mutation in bacterial genome lead to the development of the antibiotic resistance that protects the specie). Moreover, that is genetic mutations that leads to evolutionary changes in the species (species converged, diverged, adapted). Mutations enabled such a great variety of species to evolve that we have today
telomeres
- caps at the end of linear chromosomes
- only present in euk
- protect ends of chromosomes from degradation (protection from nucleases and other destabilizing agents)
- prevent fusion b/ chromosomes ends
- Important factor in limiting # of times the cell can divide
- Required for the complete replication of the chromosome
- Facilitate interaction between ends of the chromosome and nuclear envelope in some types of cells
- Shortening of telomeres is responsible for crisis in which normal cell stops dividing after about 50 divisions.
Which enzyme is responsible for maintaining chromosome length in most eukaryotes
Telomerase is responsible for maintaining chromosome length in most eukaryotes because it maintains length of telomeres by adding G-rich repetitive sequence.
You are studying a particular tRNA. When charged with its amino acid, it is able to participate in protein synthesis. When interacting with the ribosome, it always enters the ribosome and associates with the P site. Which amino acid is attached to the tRNA? Explain your answer.
The start codon that initiates translation is AUG that codes for Methionine (in eukaryotes, but N-formyl-methionine in prokaryotes). Activated tRNA (with a small ribosomal subunit) binds to the 5’ end of the mRNA and moves along mRNA (in 5’ ->3’ direction) until it finds start codon and attaches to it. This will follow by the binding of the large ribosomal subunit powered by ATP hydrolysis. The start codon will be in the P site of the ribosome, while the next codon will be placed into the A site
RNA pol III
synthesizes for tRNA and rRNA 5S
Why is a degenerate genetic code beneficial, i.e., if only one triplet codon exists per amino acid, why would this be a problem (i.e., from an evolutionary perspective)
Genetic code is degenerate means that most amino acids are encoded by more than 1 codon (except M and T). In this case, if we have a point mutation for example in the last base, there is a good chance that this mutation will not lead serious consequences since it will still code for the same amino acid. Degenerate genetic code prevents generation of the non-coding triplets or premature termination of translation. Therefore, the polypeptide produced are more likely to be functional and of required length because of this property of the genetic code
It makes sense that DNA, the stable genetic material of most organisms, should be sequestered in a specific area of the cell to protect it and prevent it from potential damage. On the other hand, the mRNA, the working copy of the genetic code, is relatively short-lived or unstable. Why is the latter advantageous to the cell?
Because mRNA is short lived and unstable it permits more regulated and efficient translation rates and gene expression to respond to the needs of the organism and environmental changes. For example, this helps to prevent unnecessary production of the proteins if the organism already has the necessary level of that protein (this ensures we are not wasting energy for unnecessary processes). If the mRNA was as stable as DNA, the organism would be constantly producing proteins even when we don’t need them. The degradation of the mRNA is beneficial process that controls and regulates production of only necessary levels of the proteins.
RNA world and evidence for this phenomenon
- This is a belief that in the past RNA performed double role as the main carrier/storage of the genetic information and had enzymatic functions
- The discovery of the ribozyme was the evidence for the RNA world hypothesis because it proved that RNA not only carries genetic information , but has catalytical activity to it (ribozymes are catalytic RNAs that mediate cell splicing and they are believed to be the first enzymes evolved on Earth). Ribozymes permitted splicing of the RNA without assistance of any other enzymes.
- The presence of introns, exons and gene shuffling allowed for various new combination of genes that would create new proteins
What is the most prominent difference between prokaryotes and eukaryotes, and how does this difference influence the flow of genetic information from transcription to translation?
- eukaryotes is the presence of membrane bound organelles (such as nucleus)
- organization of chromosomes are different (prokaryotes have circular chromosome, while eukaryotes have linear chromosome)
- In prokaryotes, transcription and translation occurs simultaneously since both processes occur in the cytoplasm
- in eukaryotes, transcription occurs in the nucleus first prior any processing of pre-mRNA happens. Pre-mRNA undergoes addition of 5’ cap, poly(A) tail at 3’ end and removal of introns (removed introns remain in the nucleus and are digested) and splicing of exons together. The mature mRNA is then moved out of the nucleus through the nuclear pore into the cytoplasm in order to initiate translation via the assembly of tRNA-ribosomal complex.
- Prokaryotic cells transcribe a group of proteins (operon)
- eukaryotic mRNA can only produce one protein during transcription
structure of heterochromatin
- Remains condensed during interphase
- Usually in the periphery of the nucleus
- Does not participate in transcription
- Deacetylated
constitutive heterochromatin
Remains in the compacted state in all cells at all times
Represents permanently silenced DNA
In regions that flank telomeres and centromeres
DNA consists primarily of repeated sequences
Has relatively few genes
Can spread and affect nearby genes
Inhibit genetic recombination b/ homologous repetitive sequences
Leads to DNA duplication and deletion
euchromatin
- Dispersed, active state
- Has methyl groups attached
- Exhibit normal level of acetylation
- Transcriptionally active
mechanism of nuclear import of proteins
- Proteins needed for transcription and translation, snRNA
- Via proteins: importins
- Steps:
- Protein w/ nuclear localizing signal bind to importin
- Formation of complex that accosiates w/ cytoplasmic filament
- Moves thru the pore
- In the nucleoplasm interacts w/ Ran-GTP and dissociates
- Importin beta is associated w/ Ran-GTP -> moved into the cytoplasm
- Ran-GTP is hydrolyzed
- Ran-GDT is moved into the nucleus->Ran-GTP
- Importin alpha moved into the cytoplams
nuclear export
- mRNA, tRNA, ribosomal subunits, snRNA
- Via protein: exportin
- Via Ran-GTP/GDP cycles
- Ran-GTP promoted assembly of export complexes
- Proteins to be moved out have nuclear export signal
How does the nuclear pore complex regulate the movement of maretials into the nucleus?
The proteins that pass thru the pore contain nuclear localizing signal (NLS).
How id the method of regulating the movement of molecules in and out of the nucleus similar to the process that targets proteins in the cytoplasm?
NLS is similar to the signal recognition particle that targets proteins in the cytoplasm
W&C DNA model
- DNA is composed of two chains of nucleotides
- DNA strand wind into the R-handed helix and each strand follows a clockwise path
- Chains are antiparallel - they run in opposite direction (one is 5->3 and the other must be 3’->5’)
- Sugar-phosphate backbone is on the outside of the molecule
- P gives DNA a -ve charge (causes DNA strand to have polarity)
- Bases are stacked one on top of the other
- Hydrophobic interactions and van der Waals forces give stability to the helix
- Two strands are held together by H bonding
- Width of double helix is 2 nm
- A pyrimidine is always paired with purine in the other chain
- A forms DB w/ T and G forms TB w/ C
- Spaces b/ adjacent turns of the helix from major and minor grooves that spiral around the outer surface of the double helix
- Makes one complete turn every 10th residue
- Strands are complementary to one another: A on one strand bonds only to T on the other strand, while C binds only to G.
DNA as genetic material must fulfill these functions:
- Storage of genetic info:
* Must containd the info needed to assemble all of the proteins that are synthesized by an organism - Replication and inheritance :
- Must have infor for synthesis of new DNA strans
- Transmission of genetic info from one cell to another and from one individual to another
- Expression of genetic info :
- It directs cellular activities
- Info in the DNA must be used to direct the order by which specific AA are incorporates into a polypeptide chain
How do polytene chromosomes of insect differ from normal chromosomes?
Polytene:
- Have puffs that are generated by endoreplication where DNA is transcribed into RNA (multiple rounds of replication generate thousands of strands per chromosome)
- Allows for direct visualization of gene expression
Normal chromosomes do not show puffs
DNA ligase
Links Okazaki fragments
Seals gaps after the removal of primer
dna gyrase
- Aka topoisomerase II
- Relieves mechanical strain that builds up during replication in E.coli
- Removes supercoils ahead of the replication fork by cleaving both strands of the DNA duplex
primase
- Adds RNA primer @ 5’ end of both strands
- Initiates synthesis of each Okazaki fragments
- Type of RNA pol
helicase
Uses E from ATP hydrolysis to unwind DNA duplex and break H bonds
SS DNA binding protein:
- Aids helicase in DNA unwinding
- Bind selectively to ss DNA and keeps it in a extended state preventing it from becoming reqound
DNA pol I:
High accuracy
Low error rate
5->3 polymerase (synthesis, adds base)
5->3 exonuclease (removes bases from 5’ end of primer)
3->5 exonuclease (proofreading)
Function: main repair, replication, adds @ primer
