Biochemistry (Molecular ) Flashcards
USMLE STEP 1
DNA and cell
-There is a lot of DNA in a cell
and since the cell is only a few microns in diameter —-) it needs a way to package DNA into a small space inside +++
they do it by coiling DNA around histones
Histones :
-there is a few different types of histones : H2A ,H2B,H3,H4; they aggregate together and DNA wrapps around them to form NUCLEOSOME ,
There is another type of histone called H1 which is not in the nucleosome ,
but why does DNA wrapps around histones ???
the charge of DNA and histones :
-DNA is - (negatively ) charged
-Histone is + (positively ) charged
Euchromatin vs heterochromatin :
-Euchromatin :acetyle groups , transcriptionaly active(more accessible to the transcription machinery )
-Heterochromatin : more methylation , less acetylation , can’t be transcribed
histone methylation —) makes DNA MUTE ( transcription inactive )
histone Acetyl—–) makes DNA ACTIVE —) transcription active ++++
DNA abreviation :
-Deoxyribonucleic acid +++
DNA composition :
-DNA is composed of nucleotides
and each nucleotide is composed of :
_Phosphate group
_5-carbon sugar (deoxyribose )
_Nitrogenous base (A, G , C , T )
Mnemonic to remember the name of PYRIMIDINES :
'’CUT PYe ‘’
-Cytosin and uracil and Thymin are PYrimidine
Nucleotides bind together using phosphate and sugar groups
-5’——–) 3’ , 3’—–) 5’
DNA is antiparallel molecule
-The basis form hydrogen bonds between them
(A–T)
(C—G)
-know that hydrogen bonds are weaker than covalent bonds thus can easily been broken and reformed for transcription
basis form bonds according to the rule of complementary base pairing +++
Facts about DNA :
-superorganised molecule
-long molecule (over 2 meters along when fully stretched )
to make this DNA fit into a tiny nucleus inside the cell ,our cells relies on a few packaging tricks +++
we can wrap DNA around histones (because DNA is negatively charged by phosphate , and histone is positively charged , so they attracted and DNA get wrapped around histones
-Nucleosome = DNA around histones (histone + DNA )
nucleosomes get packaged as chromatin fibers
-Chromatin comes in 2 flavours :
_Euchromatin (nucleosomes are loosely packed , they are used to the transcription ++++ )
_ Heterochromatin( nucleosomes are densely packed , contains genes that cells rarely or never uses to make proteins , so they are not active for the transcription +++)
-the chromatin condenses to give 46 chromosomes ( mazal ma3reftch 3lach had 46 )
Nucleotide composition (DNA )
-Base + sugar (desoxyribose) +phosphate
NucleoSide : (DNA )
Base + sugar (desoxyribose )
A researcher is investigating the structure of chromatin and finds that DNA binds with several proteins to form a “bead on a string appearance” as detailed in the image below. Which of the following best describes the chemical interaction between DNA and protein that results in the formation of this molecular structure?
Response:
Bond between negatively charged phosphate and positively charged arginine and lysine residues
Major takeaway
The nucleosome is held together by ionic bonds between the negatively charged phosphate residues of DNA and positively charged lysine and arginine residues found on histones.
Main explanation
The nucleosome refers to a DNA-protein structure held together by negatively charged phosphate residues on nucleotides and positively charged arginine and lysine residues on histones. The nucleosome serves as the backbone for the tight packaging and coiling of DNA, which gives rise to chromatin.
Chromatin is composed of DNA (approximately 146 base pairs) that loops twice around a histone octamer, thus giving the appearance of a bead on a string. The histone octamer consists of two copies of each of the following histone proteins: H2A, H2B, H3, and H4. By forming tightly packed chromatin, the DNA is able to fit within the confines of the cell nucleus.
A researcher is studying the structure of the nucleus under an electron microscope. He detects an area of heterochromatin, at the periphery of the nucleus that he identifies as the inactivated X-chromosome (the Barr body). Which of the following cellular mechanisms best explains the appearance of this structure on electron microscopy?
Histone methylation
Major takeaway
Histone methylation refers to the process of adding a methyl group to histone subunits of the nucleosome. Methylation is largely responsible for the appearance of heterochromatin on electron microscopy.
Main explanation
Histone methylation is the process of adding methyl groups to histone subunits of the nucleosome (DNA, histone complex). Methylation is largely responsible for the appearance of heterochromatin (tightly packed DNA) on electron microscopy and contributes to the formation of the Barr body (inactivated X chromosome) in females.
In addition, the Barr body undergoes DNA methylation–a form of irreversible gene silencing without actually changing the sequence of DNA. Similar to histone methylation, DNA methylation causes tight coiling of DNA around histones. Both DNA methylation and histone methylation lead to the condensed and sterically inaccessible form of DNA called heterochromatin, which is located typically at the periphery of the nucleus.
In contrast, histone acetylation removes positive charge from histones; thereby, decreasing its binding affinity for negatively charged DNA and increasing the transcriptional activity of uncoiled DNA. Histone deacetylation has a similar effect to that of histone methylation. Deacetylation increases the positive charge of histones, thus enabling histones to bind more avidly to negatively charged DNA and decreasing transcription.
A researcher is studying the thermal properties of small sequences of deoxyribonucleic acid found in Gram-positive bacteria. Which of the following sequences of DNA will have the highest melting point?
Major takeaway
DNA sequences with a higher G-C content are more chemically stable and have a higher melting point, due to additional hydrogen bonds when compared to A-T base pairs.
Main explanation
Deoxyribonucleic acid (DNA) is made up of nucleotide base pairs that bond together via hydrogen bonding. This chemical interaction underlies the base-pairing rules such that only adenine may hydrogen bond with thymine and only cytosine may hydrogen bond with guanine.
In general, DNA sequences with a higher guanine to cytosine base pair content are considered more chemically stable. This is due to the fact that guanine to cytosine base pairs contain three hydrogen bonds, whereas adenine to thymine base pairs contain two hydrogen bonds. Thus, DNA sequences with a higher G-C ratio will have a higher melting point. In the question stem above, choice A has the highest G-C content.
Note DNA and genes
each DNA is coding for a lot of genes (thousands of genes )
but there should be a process to control this process of genes
note on DNA and genes
DNA is wrapping around each histone (octamer ) twice = NUCLEOSOME ++++
nucleosome wrapped around very tightly giving CHROMATIN (either euchromatin or heterochromatin )
our DNA contains a lot of genes , and the cell function is related to the types of genes they code for = exactly to the protein they made +++ —) a cell can do its function by activating some genes and closing or silencing other genes
if this process is not made correctly , we can have a cell that does a lot of functions not related to it
so the final appearence of a cell depends on which genes are activated ++++(PHENOTYPE )
all of this happens through EPIGENETICS ++++
Definition of epigenetic :
Mechanism through wich we can selectively activate or silence genes without modifying the nucleotide sequence++++
in epigenetic , we can modify either Histone or DNA in a way that we activate the genes we want to express and we deactivate genes we want to delete ++
-we made this in :
1- HISTONES : histones can either release their DNA or lock down their DNA , in a result of easier or not easier transcription
so : _Acetylation : when we add a group of acetyl to the nucleosome —–) less attraction between DNA and histone —–) DNA loosen up from histones —-) easy transcription +++++
deacytelation is the contrary , we remove acetyl group , therefore increase attraction between DNA and histone , hard transcription
-methylation : if we add one group of methyl we loosen DNA ,
but if we add 2 or more methyl groups , we lock down DNA and therefore harder transcription ++++
_Epigenetic can include also direct modifications of the DNA +++ (we either activate a portion of dna genes or suppress them ) without changing genes sequence or modifying genes sequence +++
we can modify in the CpG sites by adding a methyl groupp to Cytosine (without modifying DNA sequence )
-DNA methylation —–) can silent the gene expression
Epigenetic changes are (reversible or not )
REVERSIBLE
(they can be changed throughout the life of the individual , and also related to some risk factors (diet , physical activity and others )))
Nucleotide synthesis :
-either from scratch (de nove synthesis )
-salvage pathway (recycles nucleotides that are already semi degraded ++)
An investigator is studying nucleic acids. Which of the following best differentiates a nucleotide from a nucleoside?
Presence of a phosphate group
Major takeaway
Nucleosides are made of a nitrogenous base and a five-carbon carbohydrate (deoxy)ribose. A nucleotide is simply a nucleoside with an additional phosphate group(s).
Main explanation
Nucleosides are composed of a nitrogenous base, either a pyrimidine (cytosine, thymine for DNA, uracil for RNA) or purine (adenine, guanine), and a five-carbon carbohydrate (deoxy)ribose. A nucleotide is simply a nucleoside with additional phosphate group or groups.
Polynucleotides containing the carbohydrate ribose are known as ribonucleotides or RNA. If the 2′ hydroxyl group (OH) is removed, the polynucleotide deoxyribonucleic acid (DNA) results.
A 27-year-old woman gravida 1 para 0 at 20 weeks gestation comes to her physician for follow-up. The physician ordered genetic testing for Lesch-Nyhan syndrome due to a positive family history and results positive for the mutation associated with this disease. Which of the following biochemical steps becomes impaired as a result of this mutation?
Hypoxanthine to inosine monophosphate
Major takeaway
Lesch-Nyhan syndrome is a genetic disorder due to an X-linked recessive mutation in the HPRT gene with a deficiency in hypoxanthine-guanine phosphoribosyltransferase (HGPRT), an enzyme that mediates the purine salvage pathway, where purines are recycled and used again in DNA and RNA synthesis. Without HGPRT, all purines are broken down into uric acid, resulting in hyperuricemia very early in life.
Main explanation
This patient has a family history of Lesch-Nyhan syndrome and is currently pregnant with a child who is also affected.
Lesch-Nyhan syndrome is an X-linked recessive disorder due to mutation in the hypoxanthine-guanine phosphoribosyltransferase-1 gene (HPRT1) on the X chromosome. This results in the absence of hypoxanthine-guanine phosphoribosyltransferase (HGPRT), an enzyme that is involved in the purine salvage pathway where purines are recycled and used again to make DNA and RNA.
Synthesis of purines to make DNA and RNA can be from scratch (de novo synthesis) or from recycling. The purine recycling pathway is also known as the purine salvage pathway. Here guanine is converted to GMP, and hypoxanthine is converted to IMP and then AMP. Then both AMP and GMP can be used again to make DNA. This step is mediated by the HGPRT enzyme.
In Lesch-Nyhan syndrome, HGPRT is absent. Leading to the inability of cells to recycle purines. This leads to the accumulation of hypoxanthine and guanine due to two mechanisms:
1. Inability to recycle guanine and hypoxanthine
2. Increased de novo synthesis of purines, which are then converted to hypoxanthine and guanine
Hypoxanthine and guanine will eventually be converted to uric acid; therefore, patients with Lesch-Nyhan syndrome develop hyperuricemia, usually very early in life.
