מולקולרית Flashcards
Where would histone proteins migrate in SDS-PAGE?
A. Catode
B. Anode
A. Catode
–> Catode îs negatively charged, therefore, we can understand from it that histones are positively charged
how many alpha helices comprise histones?
1. 3
2. 5
3. 4
4. 2
- 3
Histones are made of 3 aloha helices and 2 loops, and contain many positively charged AA (mainly arginine (Arg, R), lysine (Lys, K)); the + AA make histones positive
A researcher would like to extract H2 and H3. what solution should she use?
1. an isotonic solution
2. a strong base solution
3. a strong acid solution
5. a weak base solution
- a strong acid solution
Histones are positively charged due to high presence of arginine and lysine AA which, due to their positive charge in neutral pH, make the protein very alkaline. therefore, in order to dissolve histones of type 2 and 3 one should use a strong acid solution.
What are the common types of histones?
H1 (most variable); H2A, H2B, H3 and H4 (most conserved)
What are nucleosomes made of (structure)
1. An octamer of 2 copies of each histone) and a copy of H1 attached to it
2. a heterodimer made of 2 different histones
3. a homodimer made of t copies of a histone of a certain type
4. a hexamer - made of 2 copies of H3 and H4 and 1 of each isoform of H2 (A and B)
- An octamer of 2 copies of each histone) and a copy of H1 attached to it
How long is the DNA sequence that is wrapped around a single nucleosome?
147 bp + and linker of 40 bp; the DNE is looped around the histone 1.7 times in the left hand direction through the minor groove and leaves the major groove exposed
What is the role of histone proteins?
To help reduce the volume of the DNA molecule by folding the DNA into the nucleosomes (made of histones) and generate chromatin thereby
True or False:
Histone modification is inherited through the parents’ genome
False-
Histone modification (modification of the DNA by histones) is considered an epigenetic process; this means it is involved in the process of genome regulation. epigenetic modification can be inherited but is not encoded in the genome person; therefore, it is heavily influences by environmental factors
what are chromatin remodelers?
chromatin remodeling is the enzyme-assisted process to facilitate access of nucleosomal DNA by remodeling the structure, composition and positioning of nucleosomes. Chromatin remodelers are complexes of large diamers (made of 10 proteins) which change chromatin structure by reducing its affinity under energy investment utilising ATP molecules. (ATPases)
What are 4 types of covalent modification?
- Methylation - twists heterochromatin by recruiting chromatin regulating complexes; (done by HMT and removed by de-methylases)
- Phosphorylation - oosens the bond between DNA and the histone by adding a negative residue to serin
- Ethylation - loosens the bond between DNA and the histone by removing the positive residue of lysin; (done by HATs)
- De-ethylation - tightens the bond between DNA and the history by returning the + charge of lysin (done by HADAC)
How is HP1 recruited for methylation?
trimethylation of K9 on the H3 tail recruits HP1 which recruits more methyl-transferases (HMTs) that methylate the following tails.
What is the difference in hydrogen bonds between A-T and G-C BPs?
A-T have 2 H-bonds; G-C have 3 H-bonds
What is the direction of the DNA tails?
during replication it is read in direction 5’-3’;
tail 5’ contains the positive phosphate group and 3’ tail contains a negative OH- group
DNA directionality (5’/3’) is important for replication as it only progresses in the 5’ to 3’ direction. However, the replication fork is bi-directional; one strand is oriented in the 3’ to 5’ direction (leading strand) while the other is oriented 5’ to 3’ (lagging strand). The two sides are therefore replicated with two different processes to accommodate the directional difference.
The replication process
a semi conservative process in which the DNA double helix is replicated in the 5’ to 3’ direction into 2 double helices; The first step for the process is the opening of the DNA double helix, and creation of a replication fork.
- Primer binding: on the leading strand; the primer binds at the 3’ end of the strand.
- Elongation: DNA polymerases are responsible for creating the new strand by a process called elongation; because replication takes place only in 5’ to 3’ direction the process is continuous;
–> The lagging strand begins replication by binding with multiple primers. Each primer is only several bases apart. DNA polymerase then adds pieces of DNA, called Okazaki fragments, to the strand between primers. This process of replication is discontinuous as the newly created fragments are disjointed;
- Termination: exonucleases remove all RNA primers from the original strands. These primers are then replaced with appropriate bases. Another exonuclease “proofreads” the newly formed DNA to check, remove, and replace any errors. Another enzyme called DNA ligase joins Okazaki fragments together forming a single unified strand; then the ends of the original strands consist of repeated base sequences, signalling temination. these sequences are called telomers and are considered caps of the DNA that prevent adjacent chromosomes from fusing; A special type of DNA polymerase enzyme called telomerase catalyzes the synthesis of telomere sequences at the ends of the DNA. once both strands have their telomeres on, the DNA coils to form the double helix shape.
What does DNA helicase do?
DNA helicase: Unwinds and separates double-stranded DNA as it moves along the DNA. It forms the replication fork by breaking hydrogen bonds between nucleotide pairs in DNA.
How many types of DNA polymerase are there and what is the difference between them?
5 types in humans and in bacteria.
In bacteria: polymerase 3 is the main replication enzyme, while polymerase 1, 2, 4, and 5 are responsible for error checking and repair. DNA polymerase 3 binds to the strand at the site of the primer and begins adding new base pairs complementary to the strand during replication.
In eukaryotic cells, polymerases alpha, delta, and epsilon are the primary polymerases involved in DNA replication
Name the enzymes involved in replication
DNA helicase- creates the replication fork by breaking H+ bonds; function requires ATP
DNA primase - generates primer for the initiation of the replication process
DNA polymerase- the main replication enzyme
Topoisomerase- Unwinds and rewinds DNA strands to prevent the DNA from becoming tangled or supercoiled.
Telomerase - (type of DNA polymerase) catalyzes the synthesis of telomere sequences at the ends of the DNA
Exonuclease - removes bases (primers) at from the end of the strands and proofreads the sequences.
DNA ligase - joins Okazaki fragments together, reconnects the 2 strands to generate the double helix
How much space does the DNA occupy in the nucleus?
10%
What covalent modifications affect the density and coiling of the chromatin?
Methylation and methylation
What is the role of barrier proteins?
Barrier Proteins Remodel and Modify Chromatin To Restrict Silenced Domains
In transcription, what is the difference between cis and trans elements?
Trans elements are areas that encode regulatory proteins and can bind to cis proteins.
Cis elements are areas on the DNS that bind the regulatory proteins (trans) that attach to the transcription complex
What are transcription factors (TFs)?
TFs are proteins that that control the rate of transcription of genetic information from DNA to mRNA, by binding to a specific DNA sequence. The function of TFs is to regulate—turn on and off—genes in order to make sure that they are expressed in the desired cells at the right time and in the right amount throughout the life of the cell and the organism; there are approx. known 1600 TFs
What are activators and repressors?
Specific factors that bind TFs and activate or repress their activity.
What are prokaryotic the homologues to eukaryotic cytoskeleton filaments ?
FtsZ - homologous to tubulin, assembles into a ring at the future site of bacterial cell division (also called the Z ring)
MreB, Mrl - homologoud to actin, contribute in constructing the cytoskeleton and shape of staph and spiral bacteria, and form a scaffold for constructing peptidoglycan wall (similar to the role of microtubule in cellulose cell wall in plants). They are also involved in separating the chromosomes; thus, they are very dynamic and mutations in these can cause severe impairments in bacterial cells.
ParM - homologous to actin; encoded on bacterial plasmid that also contains genes for antibiotic resistance; arrangement of ParM into filaments contributes to plasmid division after multiplication of the daughter cells.
TabZ- homologous to tubulin, fulfils a similar role to ParM in some bacteria.
Crescentin - homologous to intermediate filaments; known to be present in at least 1 type of bacteria, contributes to the croissant shape if the bacteria.
