Genetics 𧬠Flashcards
What are purines?
-Adenine
-Guanine
-Xanthine
-Hypoxanthine
-What are pyrimidines?
-Uracil
-Thymine
-Cytosine
-What are the functions of nucleotides?
-Building block of nucleic acids.-Source of energy as ATP and GTP.
-Mediate the action of hormones as the work as second messenger like c.AMP and c.GMP.
-Co-Enzymes help the enzyme carry hydrogen like co-enzyme A and NAD and FAD.
-Chemical group donors like PAPS which donate sulphate for sulpholipids synthesis and SAM which is a methyl donor for transmethylation reactions.
-Activate chemical compounds like UDP-glucose for synthesis of glycogen and CDP-Choline and CDP-ethanolamine for synthesis of phospholipids.
-Synthetic analogues which happens by altering the base ring or the sugar part like allopurinol and Anti-Cancer where 5-Flourouracil is used to dec the synthesis of thymine decreasing the DNA synthesis which prevents cancer cells from growth.
How are the sugar and phosphate linked in the backbone?
By 3-5 phosphdiester bonds where one end is attached to the carbon atom N3 and the other end is attached to the other sugar at carbon N5
What are the characteristics of the primary structure of DNA?
βANS DPβ
A: alternating sugar phosphate units makes the backbone asymmetrical.
N: Nitrogenous bases are projected to the inside at right angle.
S: Sequence of nucleotides determines the coding structure (The genetic information).
D: DNA sequence is read from the 5 end to the 3 end by the latter abb. Of the bases.
P: Each backbone has to poles one is the 3 pole which has the hydroxyl and the other is the 5 end which has the phosphate group.
What are the characters of the secondary structure of the DNA (the physiological form)?
- The two helices are wounded around each other in the form of a Right-handed helix. (With diameter 2nm)
- They are antiparallel as they run in opposite direction-They are held by NBs.
What are the factors affecting the melting temperature of the DNA?
- The concentration of salt solution (direct)
- The ratio of CG base pair (direct)-Ph of the medium (inverse)
mRNA
-There are 105 different species.-It represents 5% of the RNA in the cell.
-They are responsible for transmitting the message of the DNA to the ribosome to be translated.
-Each protein has its own mRNA.
-It is divided into three parts which are untranslated leading part which ends in a cap,Translated coding sequence which is responsible for arranging the amino acids in the polypeptide chain ,Untranslated tailing part which ends in a poly-A tail.
-It is formed by RNA polymerase II
tRNA
-It is 50-60 different species.-It represents 15% of the RNA in the cell.
-It is formed by RNA polymerase III.-It is folded back on itself like hairpin in a clover-like appearance which is stabilized by base pairing.
What are the arms of tRNA?
D-Arm : It has a stem of 3-4 bp and ends in a loop which has diflourouracil (hence its name)
TΕͺC arm: it has a stem of 5 bp which ends in a loop containing thymine, psuedouridine and cytosine (Hence its name)
Anti-codon arm : it has a stem of 5 bp which ends in aloop that has 7 bases where the middle three represent the anticodon. (Hence its name)
The acceptor arm : it has a stem of 7 bp and it doesnβt end in a loop but with a sequence CCA and the 3 end is where the amino acid attaches.
What is the percentage of rRNA in the cell?
80%
Why is rRNA broken into smaller pieces?
- In order to combine with polypeptide chains forming the ribose.
What is the mammalian ribosome 80s composed of?
Consists of 2 subunits:- Large subunit 60s which consists of 50 polypeptide chain and 3 types of rRNA (5s-5.8s-28s)
-Small subunit 40s which consists of 30polypeptide chain and 18s rRNA .
What are the polymerases that form rRNA?
RNA polymerase I for 5.8s,18s and 28sRNA polymerase III for 5s
What are the components of RNA and what are its types?
-It consists of for nucleotides UMP,GMP,AMP and CMP which are linked by phosphodiester bonds.
And the types are:-mRNAtRNArRNAsnRNA
What is the stability of all types of RNA?
-mRNA is ranged between unstable to very stable
-tRNA is very stable
-rRNA is very stable
What are the characteristics of snRNA?
-30 different species.
-Less than 1% of the cellular RNA.
How long is the DNA of one cell in human and what is the diameter of the nucleus?
1.8 Meter - 6 Micrometer
What is DNA packaging?
- It is packing all the DNA in the Nucleus and still be functional.
What does Eukaryotic DNA look like?
- It is linear helix which is associated with proteins to form the chromosome.
When does DNA packaging take place?
In prophase in mitosis prior to being separated into two daughter cellsz
What do chromosomes form and what is chromatin?
-Chromosomes form the chromatin network and chromatin is Double helix DNA associated with proteins
What are chromosomes?
-They are DNA helices associated with histones and other structural proteins
What are the types of chromatin and when does it appear like that?
-It appears in interphase as Euchromatin and heterochromatin.Euchromatin is less densely packed so it shows gene expression while heterochromatin is densely packed thats why it shows no gene expression as it is not accessible to enzymes and factors
What are the proteins associated with DNA?
- Histone proteins:- They are proteins that contain high content of basic amino acids like lysine,arginine and histidine.
- They bind with the Phosphate group of the DNA as they are negatively charged.
- There are five types of histones which are H1,H2A,H2B,H3 and H4.
- Non histone proteins:- Structural proteins which help in packaging the DNA.
- Enzymes that help in packaging, Replication and transcription.
- Regulatory proteins which help in transcription and replication.
What are the stages of packaging DNA?
1- Nucleosome
2- 11nm-chromatin fibril
3- 30nm-chromatin fiber
4- 700nm-chromatid
5- 1400nm-chromosome
β1-2-3 are Euchromatinβ
Nucleosome stage
-The DNA is wounded 1.75 turns (146 bp) around octamer proteins which consists of 2 molecules of each of (H2A - H2B - H3 - H4), These structures are connected together by linker DNA (50bp) associated with H1, This Structure protects The DNA from digestion by nucleases and it is 11-nm in diameter and 5 nm in lenght.
11nm - chromatin fibril
-The Nucleosomes are connected together by Linker DNA forming a string of nucleosomes βbeads-on-a-stringβ-packaging ratio is 10 folds.
-The Linker DNA and histone protein H1 make it more compact.
30-nm chromatin fiber
-The supercoiling of the Nucleosomes so that each turn contains 6-7 Nucleosomes-Stabilized by H1 histone-packaging ratio is 50 folds
700 nm chromatid
-The 30 nm fiber is supercoiled into twisted looped structure where each 6 loops are wrapped around scaffold protein (rosettes), The packaging ratio is 8000 folds, Each 30 rosettes form a loop of the coil that form the chromatid
1400 nm chromosome
-It is identified in prophase
-They are arranged according to their length and the site of centromere.
-packaging ration is 10000.
-Each chromosome consists of two sister chromatid.
The chromosme
-The centromere is rich in AT bp (106) which is bonded to certain proteins forming the kinetochore which forms a mitotic spindle.
-The centromere forms the arms where the short ones are called p and long are Q.
-At the ends of the DNA there are tandems 5β TTAGGG 3β which are called telomeres (many kilos bp long)
What are somatic cells?
Any cell which is not part of the germ line
What is the chromosome number in somatic cells?
Diploid chromosome set with two copies of each chromosome (23 pairs of chromosome)
What is the chromosome number in germ cells? (Sperm or ovum)
haploid (cell containing only one copy of each chromosome)
What is DNA replication?
Replication is:
- the process by which an identical copy of DNA is made.
- the duplication of the DNA content before mitosis i.e. the two DNA copies are distributed equally between the new daughter cells so that information can be preserved & given to offspring.
What are the general criteria for DNA replication?
βSTP 5 polymeraseβ
1) Replication is semiconservative (As each daughter DNA molecule contain):
ο² One old strand (one parent strand is conserved)
ο² One new strand (from free nucleotides in the nucleus)
2) Both strands serve as templates βsimultaneouslyβ.
3) Replication is bidirectional.
4) Direction of replication: synthesis of new DNA in direction β5β² β 3β²β.
5) Done by DNA polymerases Complex
What are the components of DNA replication?
1) DNA template: Double-stranded DNA.
2) Precursors: dATP, dGTP, dCTP, dTTP.
3) Cofactors: Mg++, Mn++, ATP.
4) Enzymes and proteins: DNA polymerase, other enzymes, and proteins.
Characterises of DNA polymerases
1) Can read the template strand (3β to 5β direction) to synthesize a new strand in the 5β to 3β direction.
2) Deoxyribonucleotides triphosphate serve as precursors (dAMP, dGMP, dCMP and dTMP).
3) It cannot initiate DNA synthesis; it needs an RNA primer to build a new DNA strand upon it.
4) In eukaryotes, there are five types of DNA polymerases: Ξ±, Ξ΅, Ξ², Ξ³, and Ξ΄.
What are major enzymes needed for DNA replication?
DNA helicase
DNA primase
DNA polymerases
Exonucleases
Nick-sealing enzymes
SsDB Proteins
What is the function of DNA helicase?
Required for the unwinding of dsDNA.
What is the function of DNA primase?
β (a subunit of DNA polymerase Ξ±)
β Required for synthesis of RNA primer.
What is the function of DNA polymerases?
β required for deoxy-nucleotide polymerization and repair.
What is the function of exonucleases?
Remove RNA primers.
What are the steps of DNA replication?
- Initiation or identification of ori
- Unwinding and separation
- Priming by primase
- Synthesis of two complementary DNA strands
- Excision of primers
- Ligation of DNA fragments
- Proofreading of newly synthesized DNA strands.
Initiation
β DNA replication starts at multiple sites (in Eukaryotes) called the origin of replication or (ori).
β These sites contain a short unique sequence of (rich in AT) base pairs (consensus sequence).
β DNA replication initiates at many different sites simultaneously and it is bidirectional.
Synthesis
β The DNA polymerases are responsible for the synthesis of both strands of DNA.
β The presence of a large number of DNA polymerases (more than 20.000) helps to decrease the time needed for replication in eukaryotic cells.
β DNA polymerase reads the template strand (3β to 5β direction) to synthesize a new strand in the 5β to 3β direction.
β Deoxyribonucleotides triphosphate serve as precursors (dAMP, dGMP, dCMP and dTMP).
β The different bases are arranged in the complementary strands according to the sequence present in the parental strands.
β This can be completed by two different mechanisms on each strand: Leading and lagging
Unwinding
β This origin of replication is unwound to generate a βreplication bubbleβ forming V-shaped two replication forks by DNA helicase enzyme (ATP-dependent).
β This process starts at each replication fork & proceeds in both directions.
β The two strands of DNA are kept away and separated by the single-strand binding proteins (ssBP).
Priming
β DNA polymerases cannot initiate DNA synthesis by themselves.
β The primase utilizes the DNA strands as templates and synthesizes a short stretch of RNA as a primer for DNA polymerase (a starting part used
in DNA replication).
β One RNA primer is formed for the leading strand and multiple primers for the lagging strand.
What is the function of neck-sealing enzymes?
DNA ligase
In what direction is the leading strand synthesized?
In the direction of the fork.
Is the leading strand continuous or not?
Yes
How many primers are there in the leading strand?
One
In what direction is the lagging strand?
Opposite to the direction of the fork.
Is the lagging strand synthesized continuously or not?
No
How many primers are found in the lagging strand?
Many
Are the lagging strands formed from Okazaki fragments and what are they?
Yes and they are DNA + RNA primers
Excision of RNA primers
β Removal of RNA primers by Exonulceases.
β Once the primers are removed, DNA polymerases land at the 3β end of the preceding DNA fragment and extend the DNA over the gap.
Ligation of DNA fragments
β The final phosphodiester linkage between the 5β-phosphate group on the DNA chain and the 3βhydroxyl group on the adjacent chain is catalyzed by DNA ligase.
β This reaction requires ATP.
Proofreading
β As each nucleotide is added to the chain, the DNA polymerases (Ξ΄ and Ξ΅) check the complementary base on the template.
β DNA polymerases hydrolytically remove the misplaced nucleotide (by the 3β β 5β exonuclease activity) and replace it with the correct nucleotide.
What are post replication modifications do DNA replication?
β The post-replication modifications of the newly synthesized DNA occur while being packaged into chromatin by the methylation of the 5th C atom of cytosine residues on DNA.
β Changing methylation status of DNA (Hypomethylation or Hypermethylation) is reported in different tumors.
What is gene expression?
β The majority of genes are expressed as the proteins they encode.
β The process occurs in two steps :
ο² Transcription = DNA β RNA
ο² Translation = RNA β protein
What is the structure of genes?
β Composed of exons, introns, and different control elements:
ο² Exon β protein-coding sequence
ο² Intron β intervening sequence (non-protein coding sequences)
Eukaryotic RNA polymerase
β RNA polymerase read a DNA template in the 3β΅ to 5β΅ direction and synthesizes single-stranded RNA molecule in a 5β΅ to 3β΅ direction.
β It utilizes ribonucleoside triphosphates (NTP) as building units.
β Do not require a primer.
β Eukaryotes have several types of RNA polymerases.
β RNA polymerases have no known endonuclease or exonuclease activity. So, it has
no ability to repair mistakes in the RNA.
β There are three species of eukaryotic RNA polymerase: RNA polymerase I, RNA polymerase II, RNA polymerase III
What are then inhibitors of DNA replication?
β Inhibitors of eukaryotic DNA replication are used as anticancer chemotherapy: Some act on DNA and some are nucleotides analogues
Act on DNA:β Actinomycin D:
ο² inhibit the initiation of replication by binding the DNA template.
Nucleotide analogues:β Cytosine arabinoside (ara C)
β 5-fluorouracil (thymine analogue).
Transcription
1) Transcription, the synthesis of different types of RNA from a DNA template, is catalyzed by RNA polymerase.
2) DNA serves as the template for the synthesis of RNA much as it does for its own replication:
ο² The strand of DNA that is transcribed into RNA is called the template strand.
ο² The other strand of DNA is called the coding strand because it except for the change of U for T, its base sequence is identical to that of the RNA synthesized.
3) RNA is synthesized as a complementary strand from the DNA template strand, by the action of the enzyme RNA polymerase.
4) The basic mechanism of RNA synthesis is the same for all types of RNAs.
5) Eukaryotic RNA must travel from the nucleus to the cytoplasm for translation.
What are the required materials for DNA transcription?
1) Template DNA: Transcription unit (promoter region, transcription start site, transcribed region, termination region, and regulatory element).
2) Four ribonucleotide triphosphate (ATP, GTP UTP, and CTP).
3) RNA polymerase enzymes
4) Transcription factors
How is snRNA formed?
Mosy of it by RNA polymerase II but some with RNA polymerase III
What are the steps of DNA transcription?
Initiation
Elongation
Termination
Initiation of DNA transcription
β The binding of RNA polymerase to the promoter leads to local separation (unwinding) of the DNA double helix into template and coding strand.
β Several sequences are common to RNA polymerase II promoter and include:
ο² sequence formed of six nucleotides (TATAAA)
ο² The CAAT box (CCAATC) and the GC box (GGGCGG):
TATAAA
β’ located 25 to 35 base pairs upstream of the start point.
β’ It binds several proteins termed TFIID which is the first step in transcription.
CCAATC and GGGCGG
β’ They determine the frequency of transcription events.
β’ 70 to 80 base pairs upstream the start point.
β’ Each of these boxes has its specific binding protein or proteins.
Elongation of DNA transcription
β Sequential addition of ribonucleoside monophosphate.
β They are inserted in RNA molecules according to the bases pairing rule, PPI (pyrophosphate) is released (RNA is complementary to DNA template strand).
β Elongation of the RNA chain continues until a termination region is reached.
Termination of DNA transcription
β Termination of transcription is started when RNA polymerase meets the terminator (termination signal is reached)
What are post-transcriptional modifications?
β Primary mRNA is modified into mature mRNA in the nucleus by:
ο² Capping
ο² Tailing (addition of polyadenylate 3β tail)
ο² Splicing (Removal of the intron).
What is the definition of capping?
β It is the addition of 7 methyl guanosine triphosphate to the 5β end of mRNA.
What is the function of capping?
β protect the 5ΚΌ end of mRNA from attack by 5ΚΌ ribonucleases.
β it is important for initiation of translation through binding with the specific cap-binding protein
What is tailing?
β Addition of up to 200 adenine nucleotides at the 3β end by the action of poly-A- polymerase enzyme.
What is the function of tailing?
β Protect the 3ΚΌ end mRNA from attack by 3ΚΌ ribonucleases
β It increases the efficiency of translation.
How is splicing done?
β Done by several small nuclear RNA (snRNA)
What happens to the remainder of the transcript?
Degraded.
What are the inhibitors of DNA transcription?
β Act on DNA template: e.g. Actinomycin D
β Bind to RNA-polymerase: e.g. Ξ±- amanitin (eukaryotic RNA Polymerase II inhibitor).
What is central dogma?
The two-step process (transcription and translation) by which the information in genes flows into proteins: DNA β RNA β protein.
What is the genetic codon?
ο Three adjacent nucleotides in the 5 Μ-3 Μdirection on mRNA constitute a genetic codon or triplet codon.
ο One genetic codon codes for one amino acid.
What are the characters of genetic codons?
ο There are 20 amino acids
ο Each amino acid has specific codons (1 or more) ο Each codon consists of 3 nucleotides
ο There are 64 codons (43):
ο² 61 codons: sense codons codes for 20 aa
ο² 3 codons: nonsense codons or termination codons (UAA, UAG, UGA)
ο AUG (which encode for methionine) act as an initiation codon for translation
What are the characteristics of the genetic code?
βCTSURN1β
1- Colinear: bases of the codon in mRNA are read from 5β to 3β end.
2- Triplet: Triplet sequence on mRNA that specifies certain a.a.
3- Specific: a specific codon always codes for the specific a.a.
4- Universal: It is the same for all species i.e. plants, animals.
5- Redundant (degenerate): a given a.a may have more than one codon that specifies the same a.a. They are different in the 3rd base.
6- Non-overlapping & commaless (Without interruption): read from a fixed starting point as a continuous sequence bases, taken 3 at a time without punctuation between the codons, The genetic codons should be read continuously without spacing or overlapping.
What is the definition of translation?
The synthesis of protein using mRNA as the template, in other words, to translate the nucleotide sequence of mRNA into the amino acid sequence of protein according to the genetic code.
What are the requirements for protein synthesis?
βmRNA+tRNA+Ribosomes+A.A+ATP+AATSE+Protein factorsβ
1) A ribosome: protein-synthesizing machinery.
2) mRNA: carries the information needed for arranging the amino acids in the proper order of the specific protein.
3) tRNA: which carries the amino acids to the proper place in the polypeptide chain. 4) Amino acids: the building units of the protein.
5) Aminoacyl-tRNA synthetase enzyme: which connects the amino acids to the specific carrier tRNA.
6) Protein factors: initiation factors (IF), elongation factors (EF) & releasing factors (RF).
7) A source of energy: in the form of ATP and GTP.
What are the subunits of the ribosome?
β The prokaryotic 50S and 30S ribosomal subunits form a 70S ribosome.
β The eukaryotic 60S and 40S ribosomal subunits form an 80S ribosome.
What are the binding sites of the ribosome?
β The ribosome has 2 binding sites for tRNA molecules, the A and P sites in addition to the E site.
β During translation:
ο² A site binds an incoming aminoacyl-tRNA.
ο² The P site codon is occupied by peptidyl-tRNA.
ο² This tRNA carries the polypeptide chain of amino acids that have already been synthesized.
tRNA characters
ο The tRNA carries amino acids during translation.
ο There is at least one specific tRNA for each amino acid.
ο Some amino acids (those having > one codon) may be carried by > one tRNA type.
ο When a tRNA carries an amino acid it is said to be charged, and when an amino acid is carried by a tRNA it is said to be activated.
What are the steps of translation?
1) Activation of aa: synthesis of aminoacyl-tRNA
2) Initiation: formation of the initiation complex
3) Elongation: polypeptide chain synthesis
4) Termination: release of the polypeptide chain
Activation of amino acids
ο Amino acids to be used in the synthesis of a protein must be at first activated [the amino acid binds to its specific tRNA by ester bond].
ο The enzyme is responsible for charging tRNA by its specific A.A is known as aminoacyl tRNA synthetase (there are at least 20 different aminoacyl tRNA synthetases).
ο 2 high-energy bonds (from 1 ATP) are needed for a.a activation.
Initiation of DNA translation
ο Assembly of the translation machinery before peptide bond formation.
ο Ribosome assembles with the other 2 types of RNAs forming the initiation complex:
1) The 2 subunits of the ribosome binds to the mRNA strand.
2) 1st tRNA binds to mRNA.
Elongation of DNA translation
ο Elongation is a cyclic process involving several steps and is catalyzed by elongation factors.
What are the stages of elongation in DNA translation?
1) Binding of the new aminoacyl tRNA to A site:
ο² tRNA brings the correct new amino acid to A- Site
2) peptide bond formation:
ο² Formation of a peptide bond between the old and the newly added amino acid according to codon-anticodon recognition
3) Translocation:
ο² Release of tRNA from P-Site
Binding of new amino acyl-tRNA to the A site
ο Entry of a new amino acyl-tRNA to the empty A site on the ribosome requires proper codon recognition (acc. to the complementary bases of both codon and anticodon).
βOne GTP is needed for this processβ
Peptide-bond formation
ο The COOH of the aminoacyl-tRNA in the P site binds with NH2 of new aminoacyl-tRNA in the A site.
ο This reaction is catalyzed by the peptidyl transferase enzyme present inside the 60s subunit.
Translocation
ο After the peptide bond formation, the ribosome moves 3 nucleotides towards the 3ΚΉ end of mRNA.
ο This requires eEF2 and GTP.
ο Results of translocation:
- Release of uncharged tRNA from E (exit) site.
- Transfer of the newly formed peptidyl-tRNA from A site to occupy P site.
- The A site becomes free (can be occupied by another new aminoacyl-tRNA according to the codon-anticodon recognition).
What is the energy needed for the formation of one peptide bond?
For each new peptide bond formed 4 high energy phosphate bonds are cleaved:
ο² 2 (from 1 ATP) for activation
ο² 1 GTP for binding of aminoacyl-tRNA to A site
ο² 1 GTP for translocation
Termination of DNA translation
ο Elongation of polypeptide chain continues until A site is occupied by one of the 3 non-sense codon (UAA, UAG, UGA), stop signal of translation.
ο Releasing factors (RF) appear in A site and can recognize all three termination codons.
ο RF + GTP + peptidyl transferase promotes the hydrolysis of the bond between the peptide chain and tRNA occupying the P site.
ο This hydrolysis leads to:
- Release of both peptide and tRNA.
- Dissociation of 80s ribosomes into 40s and 60s subunit.
Polyribosome
Because of the length of the nucleotide sequence of most mRNAs, more than one ribosome can translate the same mRNA at the same time.
When do post-translational modifications take place?
ο Many polypeptide chains are modified either while they are still in the ribosome or after their synthesis is completed.
What does the process of post-translational modification include?
1) Folding
2) Trimming
3) Covalent modification
Protein folding
Folding of polypeptide primary structure of protein molecule to get secondary, tertiary and quaternary structure if present to become functioning.
What is trimming?
Removal of part of the peptide chain.
What is the aim of trimming?
Conversion of inactive protein to an active one:
- many proteins are formed as large precursors molecules that are functionally inactive and part of the chain must be removed to release the active molecule.
What are examples of trimming?
-proinsulin is converted into insulin.
-Zymogen of GIT: e.g. inactive pancreatic trypsinogen becomes active trypsin.
Covalent modification
- Proteins may be activated or inactivated by covalent attachment of a variety of chemical groups e.g.
- Phosphorylation: addition of phosphate group to the protein
- Hydroxylation: addition of Hydroxyl group to the protein as in the maturation of collagen
- Carboxylation: addition of carboxylic group to the protein as in the activation of some clotting factors
- Glycosylation: addition of CHO part to the protein.B
How can the translation process be regulated?
-At the level of initiation
-At the level of elongation
Regulation at the level of initiation.
-by control activity of initiation factors (IF-2)
Example:
- Interferon (anti-viral drug) stimulates IF-2 phosphorylation β inhibits translation β to decrease viral protein synthesis Stop the virus from growing and dividing.
-increasing Heme globin synthesis by preventing phosphorylation of IF-2.
RegulationοΏΌ of translation at the level of elongation
Diphtheria toxin inhibits elongation factor 2 (EF-2) β inhibits host protein synthesis.
erythromycin
Some antibiotics as erythromycin inhibit the translocation step, so decrease bacterial protein synthesis.
Many mechanisms that control protein synthesis explain the pathophysiology of some diseases:
Diphtheria toxin inhibits EF-2 β inhibition of protein synthesis β leads to cell death
What is the cell cycle?
the series of events that take place in a cell involving cell growth and cell division and produce two daughter cells.
What are the stages of the cell cycle?
Interphase and cell division
Why is interphase called the resting stage and is it the longest part of the cellβs life cycle?
It is called by this name because the cell doesnβt divide in it and yes it is the longest phase in the cellβs life cycle.
What is interphase?
It is the period between two successive cell divisions.
What are the stages of interphase?
G1 (1st gap) stage.
β’ S (synthesis) stage.
β’ G2 (2nd gap) stage.
What is the def. of G1?
It is the gap between previous mitosis and s-stage
What are the events that take place in G1?
Growth of the newly formed daughter cell, After growth: cells pass to (S).
What is the number of chromosomes in G1?
46 S-chromosome
What is the definition of S-stage?
It is the stage of chromosomal duplication.
What are the events that take place in S-stage?
DNA duplication
What is the number of chromosomes in the S-stage?
92 S-chromosome
What is the definition of the G2 stage?
It is the stage between S-stage and the next mitosis.
What are the events that take place in G2?
The pairing of each two identical s-chromosomes and the duplication of centrioles.
What are the steps of cell division?
Cell division consists of two phases: karyokinesis (a nuclear division that divides the genetic material in the nucleus), followed by cytokinesis (cytoplasmic division).
What are the types of cell division?
1)Mitosis (indirect cell division)
2)Meiosis (reduction cell division).
Mitosis
-happens in somatic cells
-Gives 2 daughter cells
-have the same numbers of chromosomes which is 46 s chromosome
Meiosis
-happens in germ cells of testes and ovaries
-gives 4 daughter cells
-each of them has half the number of chromosomes in parent cells which is 23 S-chromosome
What is mitosis?
It is the type of division in which there is production of two daughter cells, each has the same number of chromosomes as the mother cell (46 s - chromosomes)
What are the stages of mitosis?
1)Prophase.
2)Metaphase.
3)Anaphase.
4)Telophase.
What are the events that happen In the Early prophase?
Fragmentation of ER, Golgi, and disassembly of the cytoskeleton.
* Mitotic spindle formation: Continuous microtubules arise between the pairs of centrioles (MTOCs) and grow gradually causing:
A)Formation of an eccentric spindle.
B) Gradual elongation of the cell.
What are the events that happen in the Late prophase of mitosis?
Nuclear membrane breaks.
Nucleoli disintegrates
The spindle becomes central.
The d -chromosomes lie in the inter-tubular spaces of the spindle.
They become more condensed with the appearance of kinetochores.
What are the events of the metaphase of mitosis?
Formation of chromosomal microtubules.
Single chromosomes arrange in the center or equator of the cell and show the highest degree of condensation.
What are the events that take place in the anaphase of mitosis?
Splitting of the sister chromatids of each d-chromosome at the centromere.
Movement of each set of chromosomes toward the opposite pole of the cell.
What are the events that take place in the telophase of mitosis?
Cytokinesis: Formation of Contractile ring and cleavage furrow which deepens gradually until the separation of the two daughter cells
Nuclear membrane forms at each end of the cell around the chromosomes.
Nucleolus reform.
Chromosomes become less tightly coiled & appear as chromatin again.
The net result is the production of two daughter cells, each having 46 s β chromosomes.
What is the definition of meiosis?
It is the type of division in which there is production of 4 cells, each one has (haploid) number of chromosomes (23 s - chromosomes).
What are the stages of meiosis?
- 1st Meiotic division.
- 2nd Meiotic division: the same as mitosis.
N.B: no S stage in the interphase between both meiotic divisions.
What are the substages of prophase I of meiosis?
A) Leptotene phase: D-chromosomes appear as thin threads.
B) Zygotene phase: Homologous d-chromosomes are paired with formation of synaptonemal complex and called bivalents.
C) Pachytene phase:
-Chromosomes condense and become thicker and shorter.- Crossing over occurs between chromatids to allow exchange of genetic material.
D) Diplotene phase:
-Chromosomes are more condensed and appear as tetrad.
- Chromosomes are separated except at chiasmata
E) Diakinesis: * Disappearance of nuclear envelope & nucleoli. * Formation of the spindle.
Compare between mitosis and first meiosis
Compare between the three categories of specialized cells and give examples.
What is the result of meiosis?
In β: production of 4 viable spermatids.
In β: production of one viable ovum and 3 non-viable polar bodies.
What is DNA?
What provides the key to genetic diversity among living organisms?
Different arrangements of NUCLEOTIDES in a nucleic acid (DNA) provides the key to DIVERSITY among living organisms.
What is a chromosome and how many chromosomes do humans have?
What are genes?
Describe the experiment of plant hybridization done by the father of genetics Mendel
What is heredity?
Transmission of genetic information from parent to offspring
What is genetics?
The science of heredity (branch of biology that deals with heredity and variation of organisms).
What is Genome?
the entire set of genes in an organism
What is a locus?
Each gene has a specific site on a certain chromosome (fixed positions).
What are alleles or alternative forms?
The forms of the gene found at a particular locus, One allele is inherited from father and the other from mother.
What are homozygous alleles?
Both alleles of a pair are the same TT, tt
What are heterozygous alleles?
Both alleles of a pair are not the same Tt
What are dominant alleles?
the allele of a gene that masks or suppresses the expression of an alternate allele; the trait appears in the heterozygous condition.
What are recessive alleles?
an allele that is masked by a dominant allele; does not appear in the heterozygous condition, only in homozygous.
What is a trait?
Any genetically determined characteristics of the individual
What does genotype mean?
the genetic makeup of an organisms. alleles carried by anindividual eg. RR, Rr, rr. (internal information)
What does phenotype mean?
- the physical appearance of an organism (Genotype + environment) (external appearance).
- physical characteristic or appearance of an individual
Give an example that illustrates basic terms of genetics
Trait: eye colour
Genotype: BB. Bb, bb
phenotype: brown or blue
Dominant allele: B
Recessive allele: b
What are Mendelβs principles?
- Principle of Dominance
- Principle of Segregation
- Principle of Independent Assortment
Describe Mendelβs principle of dominance
One allele masked another; one allele was dominant over the other.
* Each trait is controlled by 2 factors (alleles), one factor (dominant) may mask the other factor (recessive) preventing it from having an effect.
Describe Mendelβs principle of segregation
When gametes are formed, the alleles for each gene segregate from each other so that each gamete carries only one allele for each gene.
Describe Mendelβs principle of independent assortment
the alleles for one trait separate independently of the alleles for other traits during gamete formation
What is punnett square?
It is a chart that allows to easily determine the expected ratios of possible genotypes in the offspring of two parents.
What is the definition of a family pedigree and what is its importance?
β’ A family pedigree shows how a trait is passed from generation to generation within a family.
β’ A pedigree can show\whether a Mendelian trait is autosomal or x-linked trait/ dominant or recessive.
What are other types of inheritance that Mendel never considered?
β’ Incomplete Inheritance
β’ Codominance
β’ Multiple Alleles
β’ Polygenic Traits
β’ Sex-linked
What does of the heterozygous offspring in case of incomplete inheritance display?
and give an example for it
β’ The heterozygous offspring displays a THIRD Phenotype!! (intermediate in phenotype)
β’ A good example of incomplete dominance in humans is hair type.
β’ There are genes for straight and curly hair, and if an individual is heterozygous, they will typically have the phenotype of wavy hair.
Describe multiple alleles theory and give an example for it
Genes often exist in several different forms and are therefore said to have multiple alleles.
Example: Human Blood group (A, B, O, or AB)Multiple allele A, B, and O, A and B dominant / O recessive,[3 alleles & 4 phenotypes]
describe co-dominance theory and give an example for it
Both traits are dominant and show up in the phenotype together. [Co means βtogetherβ]they both influence the phenotype.
Both alleles of a gene are expressed in the phenotype.
in human; AB blood group
Describe polygenic inheritance and give an example for it
β’ Traits controlled by interaction of two or more genes (multiple genes) are said to be polygenic traits.
β’ E.g. skin color and height.
β’ Skin color is a common example of a polygenic trait it is governed by 6 loci and at least 12 alleles.
Describe sex-linked genetics
Sex is determined by sex chromosomes X and Y
XX= female, XY = male
The X chromosome contains many important genes that are unrelated to sex determination, These genes are required for both males and females
A male receives ALL of his X-linked genes from his mother while a female receives her X-linked genes from both parents.
Remember the following notes about Sex-linked Inheritance
When will males or females show X-linked recessive disorders?
- Males will show this trait if they have the recessive allele on the X chromosome
- Females will show this trait if they have the recessive allele on both X chromosomes
Give an example of X-linked recessive disorders
(Homozygous recessive)
* Hemophilia: Inability to have clotting of blood, XhColor blindness: Xc
What is the definition of DNA mutation?
It is a permanent change of base sequence of nucleotides in the genetic code
What are the types of DNA mutation?
It may be:- gross at the level of the chromosome,
- small at DNA level.
- Germinal occurring in germ cells and can be passed on to future generations
- Somatic occurring in somatic cells and cannot be transmitted to offspring.
What is the effect of DNA mutation?
β Once the gene has been mutated or changed, the mRNA transcribed from that gene will now carry an altered message.
β The resulting polypeptide will now contain a different sequence of amino acids.
β Then, the function of the protein made by folding this polypeptide will probably be changed or lost.
What are the (classes) causes of mutations?
1) Spontaneous mutations (molecular decay)
2) Induced mutations caused by mutagens
What is Spontaneous mutations (molecular decay)?
Mistakes happen spontaneously during DNA replication or repair
What is Induced mutations caused by mutagens?
Induced Mutations occur when cells are exposed to external mutagens.
What are the types of mutagens?
physical, chemical and biological
What are the physical mutagens?
β Ionizing radiation (gamma and X-rays)
β Non-ionizing radiation:- Ultraviolet radiation- Electromagnetic radiation (Mobile phone, satellite, computer)
What are chemical mutagens?
β Cigarette smoke
β Free radicals and oxidizing agents
β Aflatoxin (leading to liver cancer)
β Heterocyclic amines (found in over-cooked food)
β some of Chemotherapy and antibiotic drugs.
What are biological mutagens?
β Hepatitis C virus (HCV) β Hepatocellular carcinoma
β Human papilloma virus (HPV) β cancer cervix
β Human Herpes virus (HHV) β sarcoma
β H pylori β cancer stomach
What is the classification of mutations?
1)Structural classification (according to structural change in the DNA)
2)Functional Classification
What is the structural classification of mutations?
What is the functional classification of mutations?
β Small scale Mutation (1-20 base mutation):
1- Point Mutations (Base substitution)
2- Frame shift mutations
3- Splicing Mutation
4- Regulatory Mutation
β Large scale Mutation (ranged from Exon to whole gene):
1- Transolcations
2- Inversion
3- Duplication
4- large deletion
What are the types of point mutations?
What causes frameshift mutations?
it is due to additions or deletions of one or more nucleotides lead to alter the reading frame (reading sequence) and the resulting amino acid sequence may become completely different from the wild type
What causes Splicing mutation?
it is due to alteration of exon-intron junction sequences, which interfere with mRNA splicing which may lead to the production of abnormal proteins.
describe regulatory mutation
β it is a mutation in regulatory element which lead to abnormal level of gene expression
β It ranges from abnormal high expression level to no expression level
Describe translocations βDNA mutationsβ
large DNA segment moves to new location.
Describe inversion βDNA Mutationβ
Orientation of DNA segment reverses.
Describe duplication βDNA mutationβ
Repetition of a portion of a chromosome.
What are the clinical applications for mutation?
1) Diagnosis of genetic diseases
2) Carrier detection.
3) Prenatal diagnosis
4) prognosis of some diseases
5) Gene therapy
What is molecular hematology?
It is the study of the molecular basis of benign (e.g anemia) and malignant (e.g leukemia) hematological disorders.
What is the best example for point mutation?
Benign disorders e.g hemoglobinopathies are the best example for point mutation
What are hemoglobinopathies ?
It is a group of disease related to abnormal hemoglobin synthesis e.g:
1) Sickle cell Disease (SCD)
2) Beta thalassemia.
3) Alpha thalassemia.
What is the nature of sickle cell disease (SCD)?
It is an autosomal recessive disease
What characterizes sickle cell disease?
- Chronic hemolytic anemia
- Presence of abnormal insoluble hemoglobin S (Hb S)
- Presence of a missense point mutation in the codon 6 of beta globin gene (GAGβGTG), changing the 6th amino acid of the beta chains from glutamic acid to valine (Glu 6 Val)
- This leads to polymerization of hemoglobin and distortion of the red blood cells into a sickle shape.
What are other names for Beta Thalassemia?
Cooleyβs Anemia, Mediterranean Anemia
What characterizes Beta Thalassemia?
Ξ²-thalassemia is characterized by reduced synthesis of the hemoglobin beta chain that results in:
- microcytic hypochromic anemia,
- reduced amounts of hemoglobin A (HbA)
- increase amount of HB A2 and HB F
What causes Ξ²-thalassemia?
The Ξ²-thalassemia can be caused by more than 200 different gene mutations on chromosome 11.
What types of mutation do Ξ²-thalassemia mutations include?
all types of mutation (point mutation, frame shift, regulatory, splicing, or even large deletion)One patient may have one or more of these mutations.
What is the nature of Ξ±- thalassemia?
β It is an autosomal recessive disease
What is the result of Ξ±- thalassemia?
β result in decreased alpha-globin production resulting in an excess of Ξ² chains in adults.
β The excess Ξ² chains form unstable tetramers (called Hemoglobin H or HbH of 4 beta chains) which have abnormal oxygen dissociation curves
What causes Ξ±- thalassemia?
It results from a large (exon or gene) deletion mutation in Ξ±1-globingene on chromosome 16
What are the causes of DNA damage?
Exogenous
β Physical agents: X-ray, U.V.R.s
β Chemical agents: as Nitrous acid
Endogenous
β Spontaneous
β During replication
What are the types of DNA damage?
1) Alteration or removal of one base
2) Alteration or removal of two bases or more e.g. thymine dimer which causes a kink or distortion in DNA helix.
What happens if the damage wasnβt repaired?
If the damage is not repaired, a permanent mutation occurs which may result in a hereditary disorder
What are the main steps for DNA repair?
Recognition of the lesion: This is the function of an endonuclease, which cleaves the damaged strand to form a cut (nick).
Excision of damaged DNA: The damaged part is removed by exonuclease.
Filling of the gap with the correct nucleotide: This is catalyzed by a DNA polymerase beta.
Ligation: This is catalyzed by DNA ligase
What are the mechanisms of DNA repair?
β The most common mechanisms of DNA repair are:
1) Mismatch repair (replicative errors).
2) Excision repair (correct the effect of exogenous agents): this mechanism includes:
ο² Base excision repair (BER).
ο² Nucleotide excision repair (NER).
Mismatch repair(replicative errors)
β It corrects errors occurring during DNA replication.
β During replication, specific enzymes(DNA nuclease complex) scan the newly synthesized strand.
β Three enzymes are involved in this mechanism:
1) If a mismatch is detected, it is Cut by nuclease
2) Gap is filled by DNA polymerase beta
3) DNA ligase Seals the break
Excision repair
β The most common type of repair
β It corrects DNA damage caused by exogenous agents either chemical or physical.
β It includes:
ο² Base excision repair (BER)
ο² Nucleotide excision repair (NER)
What are the diseases related to defects in DNA repair?
β Diseases related to defect in Mismatch Repair:
ο² Hereditary Non-Polyposis Colon Cancer (HNPCC)
β Diseases Related to defect in Nucleotide Excision Repair:
ο² xeroderma pigmentosum (XP)
ο² some cancers
ο² neurodegenerative diseases
What is the nature of Xeroderma pigmentosum (XP)?
It is a rare autosomal recessive disease.
Compare between base excision repair and nucleotide excision repair
What causes xeroderma pigmentosum?
It is due to absence of UV-specific endonulease enzyme and defective correction of thymine dimmer (Nucleotide excision repair defect).
What characterizes xeroderma pigmentosum?
It is characterized by marked sensitivity to sun light (ultraviolet) with subsequent development of:
- skin damage
- multiple skin cancers
- premature death
