Genetics
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| How are the parts of nucleotides bonded? | C'1 of pentose to N'9 of purines and N'1 of pyrimidines. the bond is called N-glycosidic bond. And phosphate is bonded to pentose in C'3, or C'5. |
| What are RNA? | Single-stranded molecule that consists of one chain of ribonucleotides complementary to one of the DNa strands (transcribed) enzyme that synthesizes it is called RNA polymerase. |
| What is the difference between DNA and RNA (sugar/base/molecule/localization)? | Sugar (deoxyribose/ribose) base (thymine/Uracil) molecule (double helix,long/ single stranded, short) localization--eukaryotes (nucleus mitochondria chloroplast/nucleus, cytoplasm and mitochondria) ---prokaryotes (cytoplasm BOTH) |
| How does ligase function? | After removal of RNA primers,DNA polymerase polymerizes the gaps until a side of phosphate is present then the ligase ligates the two adjacent strands with phosphodiester bonds |
| What are the different types of RNA? | MRNA (messenger) single stranded that specifies aa in polypeptide chains through transcription and translation. it is synthesized on template transcribed non coding DNA strand it is the only coding RNA. tRNA (transfer) single stranded, particular arrangement resembles shape of cloverleaf. used in protein synthesis as an adapter between mRNA and aa, each tRNA is linked to an aa covalently and is so called charged tRNA rRNA; located in ribosomes. |
| What is gene expression? | Process by which a gene product is produced. |
| What are the steps of gene expression? | Transcription (copying genetic info through RNA) if the transcript RNA is mRNA, then the second step is translation into peptides. |
| What is the result of transcription? | Single stranded mRNA complementary to one of the DNA strands. |
| Talk about the process of transcription | DNA sense strand (or coding ) is the strand that is the same as the mRNA but the difference is in T and U, it contains promoters (with 5' end) which makes it impossible to be transcribed given that RNA polymerase reads only from 3'-5'. |
| What is the point of transcription? | First RNA nucleotide is transcribed at a point, designated vy "+1" |
| What is a gene consisting of in terms of organizaton? | Exons and introns, exons are the coding sequences while introns are not coded by RNA, a gene always begins and ends with an exon, exons and introns are separated by termination sequences. (terminators) |
| What are UTR sequences? | Genes that are transcribed but not translated, constituting the opening frame. |
| Is the whole DNA sequence transcribed? | Yes, but not all mRNA sequences are translated (only exons) |
| Describe the transcription process. | Intiation: RNA polymerase recognizes promoter binds to it and starts transcribing the template starting from transcription start site. Elongation: RNA are inserted to complement the transcribed strand and linked by amide bonds, from 5' to 3', direction of the DNA stranded is 3' to 5' Termination: when it encounters a specific nucleutide sequence acting as a termination signal, enzyme terminates, RNA is released from transcribed strand. |
| What is the difference between transcription of eukaryotes and prokaryotes? | Eukaryotes (in nucleus, has to go to ribosomes in the cytoplasm, processing (changes to make RNA possible to polymerize proteins) prokaryotes (no need for any additional processes d8re transcription translation. |
| What was the original view over genetic material carriers? | Originally, scientists didn't know whether chromosomes are made up of proteins or nucleic acids, so there was no idea of which carries the genetic material. |
| Who was the first do discover about carriers of genetic material? Name the experiment | Fredrick Griffith - Transportation experiment |
| What cells did Griffith use? | A bacterium called streptococcus pneomoniae which was responsible for pneumonia and death of mice |
| What are the kinds of the bacteria Griffith used? how do they differ? | Two kinds S which is virulent and is capsuled by a polysaccharide capsule and the stains form smooth colonies, and R which was avirulent and not capsuled and stains form rough colonies. |
| Talk about the procedures of the experiment of Griffith | Mice were injected first with living S and R bacterium, the one who was injected with S died whereas the one with R survived. Then a mice was injected with heat killed S bacterium, the mouse survived. Lastly the mouse was injected with both R and heat killed S bacterium, the mouse died |
| What conclusions can be made by Griffiths experiment? | Substances inside heat killed S bacterium caused the R bacterium to transform into S bacterium, forming a capsuled virulent bacterium which killed the mouse. |
| After the transportation experiment, Who were the scientists that made a breakthrough? | Avery, Macleod and McCarty |
| What was the aim of their experiments? | To discover the substance that caused the transformation in Griffith's experiment |
| Talk about the procedure of Avery, Macleod and McCarty's experiment. | First S cell extracts was isolated, heat killed, then added with R cells, then some S cells were added into R cells but with protease that digest proteins, then they added them with RNase which digest RNA, then with DNase which digest DNA. |
| What results were obtained and what conclusions were discovered? | Transformation occurred in all tubes except the one with DNase, meaning that the substance that carries genetic information are DNA, however they were inconclusive since DNA might still just be catalyzing agents |
| In general, what is DNA? | DNA is deoxyribonucleic acids that carry genetic information , a polymer of two helical anti-parallel chain that are essential for the cell's life |
| What are nucleosides? | The combination of a nitrogenous base and pentose |
| WWhat are nucleotides? | They are the main subunits that polymerize to form DNA. they are made up of nitrogenous bases, pentose and phosphate. |
| What are the main kinds of nitrogenous bases? | Nine member double ring purine (Adenine and Guanine), and six member single ring pyrimidines (Cytosine, Thymine, Uracil). |
| What is the main difference between RNA and DNA? | The difference is in the pentose, where in C'2 of DNA the carbon is bonded to two hydrogen atoms however in RNA it is bonded to one hydrogen and one hydroxyl group. So RNA contains ribose, while DNA contains Deoxyribose. |
| How are nucleotides named(TWO WAYS) | They are named according to the nitrogenous base attached (adenylic acid- guanylic acid- cytidylic acid- deoxythymidylic acid- uridylic acid) or nucleoside mono-tri-diphosphate. |
| How are nucleosides named | (adenosine- cytidine- guanosine) |
| How are mononucleotides bonded together? | Through phosphodiester bond between phosphate and two sugars of both mononucleotides one at C-3' and one on C-5'. |
| What are the two types of bonded nucleotides? | Oligonucleotides (30 mono and less) and polynucleotides. |
| What conclusions did Chargaff give concerning DNA structure? | A & T are equal, C & G are equal , (A+G)=(C+T), (A+T)!=(C+G) |
| Who were first to discover the real structure of DNA? | Watson and Crick |
| What is the main structure of DNA? | Two long antiparallel polynucleotide chains coiled around a central axis (hydrophobic nitrogenous bases) forming a right-handed double helical shape, H-bonded in the middle, distance between two nucleotides is 0.34 nm, distance of a complete turn in helical structure is 3.4nm (10 nucleotides) diameter of 2nm |
| What is the mode of DNA replication? | Semi-consevative |
| Describe the process of replication | Helicase unwinds helical shaped of DNA forming the origin of replication. Primase adds RNA primers on with 3'-OH ends necessary for the commencation of DNA polymerase to be able to synthesize DNA. DNA polymerase starts synthesizing DNA complement of both strands of parents, Because the two strands are antiparallel, continuous synthesis in the direction of the replication fork is possible along only one strand called the leading strand, whereas in the other strand the synthesis is discontinuous called lagging strand. RNA primers are removed by ligase, gaps temporarily created must be filled with DNA polymerase leaving some gaps. The gaps left after synthesis are filled and must be joined to the adjacent DNA strand by ligase. |
| What is the origin (eye) of replication? | The sum of both forks done by helicase to unwound the DNA helix shape |
| How is the replication process? and why? | Bidirectional, since replication forks are expanding in both directions of the replication bubble |
| How is DNA synthesis catalyzed? | By DNA polymerase III |
| Describe the DNA synthesis process. | Helical shape of double strands is unwitted by helicase, then RNA primers attach to the cite of polymerizing for the DNA polymerase to act. Synthesis occurs on one direction at first because the two strands are bidirectional, the other strand is complemented discontinously. |
| What do we call the strand that gets polymerized first? the one that gets discontinously? | Leading strand, Lagging strand |
| What does DNA ligase do? | It attaches the nucleotides by phosphodiester bonds without polymerizing new nucleotides |
| What are primers? | Primers are ribonucleic acids (oligonucleotides) that are nessecary for the initiation of polymerizing complementary nucleotides to the old strands. |
| What is primase? | They are enzymes that adds RNA primers with 3'-OH ending for DNA polymerase to start |
| What are Okazaki fragments? | The fragments of lagging strand that get polymerized discontinously |
| What is transcription? | The process by which RNA molecules are synthesized on a DNA template. |
| What is the final result of transcription? | Single stranded mRNA molecule complementary to template DNA strand. |
| What is the gene expressed strand called? | DNA sense strand (coding strand) |
| Where is the promoter located? | At 5' OH of the sense strand. |
| How does RNA polymerase synthesize RNA? | It reads from 3' to 5' of the template strand and synthesizes antiparallel (5'- 3') , in the same sequence and sense as the sense strand (only replacing T with U) |
| What is a promoter? | A regulatory sequence that regulates initiation of transcription located at 5' upstream (before transcription) region from point of initial transcription of a gene |
| What is the "+1" region? | First nucleotide transcribed (transcription start site) |
| Where is the terminator region? | At 3' OH of gene (non-transcribed strand) |
| What is present between the initiation site and termination site? | Exons and introns (starts with an exon and ends with one) |
| What are exons and introns? | Exons= coding sequences, introns=non-coding sequences (translated to amino acids via translation) |
| What are regions that are transcribed but not translated called? | UTR (un translated regions) |
| What is the open reading frame? | Exons (mRNA molecules) |
| Talk about the initiation phase of transcription. | RNA polymerase recognizes the promoter, binds to it and starts transcribing the template from transcription site. |
| Talk about the elongation phase of transcription. | Subsequent nucleotides complements are inserted and linked through phosphodiester bonds, from 5' P to 3' OH direction of moving w.r.t template is 3' 5' |
| Talk about the termination phase of transcription | Enzyme transverses the entire gene until it reaches termination signal sequence. At that point, RNA is released from DNA template and polymerase dissociates. |
| What is the difference between eukaryotic and prokaryotic transcription? | Eukaryotes (within the nucleus and towards the cytoplasm ribosomes, processing of RNA transcript to form mRNA by adding cap to 5' end, and removing introns and ligating exons, and addition of poly A tail to 3' end) Prokaryotes (no need for going from place to place, no processing) |
| Give a major characteristic of nuclear genetic code. | Nearly universal with minor exceptions. |
| What is a genetic code? | Its the encoding of primary polypeptide synthesis, contains a sequence of codons read from 5' to 3', 64 codons (4^3) 61 are sense (specify an amino acid) there is a start codon (AUG) and three stop codons not recognized by tRNA (UAA UAG UGA) |
| List the main characteristics of genetic code. | Linear form each aa corresponds to three ribonucleotides (triplet codon) unambiguous code (each triplet codes one aa) degenerate (residancy) aa can be encoded by more than one codon the code contains start and stop signals commaless codes nonoverlapping code (each nucleotide is part of one triplet) |
| What do ribosomes translate? | ORF (open reading frame- starting with 5' P AUG-met and ending with stop codon UAA UAG UGA 3'OH) |
| What is translation? | Biological polymerization of polypeptides according to mRNA codes, It occurs in the ribosomes that serve as a workbench for translation, mRNA serves as an intermediate in transfer of DNA genetic information. |
| Describe tRNA used in translation | Charged tRNA, having three single stranded loop regions, 4 double stranded (intramolecular interaction) stem regions and a binding site for amino acid on CCA 3'OH end (3'OH is connected to the carboxyl group of the aa) |
| What is an anticodon? | 3 consecutive ribonucleotides that attach tRNA to mRNA via H-bonds |
| Talk about the initiation phase of translation. | Initiator tRNA charged with mehionine bas pairs with initial AUG start codon of mRNA at P (peptidyl) site of ribosomal small subunit the large subunit then attaches to the small one forming a complete ribosome having A,P and E (exist subunit). COMMON FOR ALL nRNA |
| Talk about the elongation process of translation. | Lengthening of polypeptide chain by one amino acid per elongation cycle. role of small subunit is to decode the codons while role of large one is peptide-bond synthesis. Second charged tRNA with specific anticodon will go to A site, once bonded to the codon, large subunit catalyzes peptide bonds between the two amino acids present at A and P site tRNA by hydrolyzing the bond between aa and tRNA 3'OH. The dipeptide is attached to tRNA at A site which moves to the P site and the initial tRNA moves to E site to exit, then ribosome-dipeptide-tRNAs move in a distance of a codon (3 nucleotides) P site=peptide A site = amino acid |
| Talk about the termination phase of translation. | Signaled by presence of stop codon, whom donot code for an amino acid or tRNA at A site (non sense codons) finished polypeptide is still attached to P site tRNA which is then released from ribosome which dissosciates to subunits |
| What is a gene? | RNA coding sequence |
| What is the transcription unit? | Region from promoter to 3' UTR after last exon |
| How to know the real open reading frame of a strand? | See first codon if AUG and ends with stop codon- remove one nucleotide from 5' till AUG |
| What are the criteria of classification of chromosomes? | According to banding patterns (uniqueness of each chromosome structurally and functionally) lengths, shape, position of centromere, which gives arm ratios=p/p+q (p=length of petit arm and q=length of long arm (letter after p) (Metacentric- p/p+q=1/2 both arms of both strands are equal) (submetacentric- p/p+q<1/2 short p arm and longer q arm) (acrocentric p/p+q<<<1/2 very short p and long q) (telocentric p/p+q=0 No p arm) |
| What is a nucleosome? | DNA rolled around histone octamer (H2A H2B H3 H4 dimers) 1.75 turns making the chromatin by fusing with each other with H1 |
| What are the two types of chromosomes? | Interphase chromosomes (not condensed) / Mitotic chromosomes (condensed especially at metaphase) |
| What is the karyotype? | 46 human chromosomes at mitosis, species specific. |
| Describe human karyotype? | 2n number of 46 chromosomes, diverse in sizes and centromere placements, each is a double structure consisting of 2 chromatids, connected to a common centromere, it is matching up of mitotic chromosomes into pairs. |
| How are chromosomes present in eukaryotes in different mitotic phases? | Chromatin (interphase) condensed chromatin/ chromosome (mitosis) associated with proteins (histones and non-histones) |
| How and why are DNA molecules packed in nucleus? | DNA consists of 1m length nucleic acid chain, but nucleus is 10 microm, they are packed using proteins, when we talk about DNA and protein packing we are talking about chromosomes and chromatins. |
| What are chromatin? | Organized complex of nuclear DNA combined with histones, they enable DNA packing and regulate DNA expression, its basic unit is mucleosome (octamer of histone H2A,H2B,H3..) consisting of dimer of each of those histone proteins., there are two types of proteins that bind to DNA histones and non-histones. |
| How is chromatin classified? | -Euchromatin (relaxed thin fiber- fiber A (d=35-60 A) /Less unstained filaments in interphase/filaments appear dark and dense at metaphase (condensation), genetically active, clear during interphase (decondensed) ) -Heterochromatin (Condensed fiber B (d=200-300 A), Densly stained filaments, Content of proteins is higher than euchromatin, correspond to 80% of DNA) Can be (constitutive of facultative) |
| Talk about constitutive heterochromatin. | Stable, conserved heterochromatic properties during all phases, fiber called fiber A e.g centromeres |
| Talk about facultative heterochromatin. | Regions that appear heterochromatic at specific times, reversible, euchromatin that are condensed and inactive, but can be reversed into euchromatin, condenses and decondenses. throughout cell cycle, cell type, development stage (Barr Body). |
| What is a Barr Body? | Small dense structure corresponding to inactivated X chromosome. |
| Talk about X-inactivation. | Gives a Barr body that is inactive were no transcription occurs, , discovered by Lyon and called sometimes lyonization 15% of the inactive X chromosome remains active. |
| When does Barr body occur? | Level of gene activity by one X is the normal dosage for a human body, so one X for normal females is kept inactive to maintain normal usage. It is random happening separately in every somatic cell, pattern of X is put randomly by the ancestor somatic cell were one paternal or maternal X will become inactive for all daughter cells. |
| What kind of chromatin are Barr body and why? | Facultative heterochromatin Because the inactive kind of X is heterochromatin while the other is euchromatin, and it can be reversed at certain stages of development, so it varies from euchromatin to heterochromatin. |
| Compare between mitosis and meiosis. | Mitosis (one division of somatic cell or precursor of germ cell/ diploid cell to give 2 diploid cells) Meiosis (two divisions one reductional and one equational of germ layer/ diploid cell gives 4 haploid cells called ootids by oogenesis or sperms by spermatogenesis |
| What are the main differences between oogenesis and spermatogenesis? | Spermatogenesis (in testes, enlargement of diploid cell (spermatogonium) to primary spermatocyte undergoing first meiotic division into secondary spermatocyte that undergoes meiosis 2 to sproduce spermatid which differentaites into spermatozoa with equal amounts of cytoplasm/ continuous) Oogenesis (form ova in ovaries ftwo meiotic divisions almost all of cytoplasm of primary Oocyte derived from Oogonium is found in one of the daughter cells the other is called polar body. secondary oocytes give ootids which then become eggs./ not equal cytoplasm/not continuous) |
| How are genetic information in haploid cells present? | Each have a maternal or paternal chromosome however crossing over might occur during P1 which results in reshuffling alleles between paternal and maternal chromosome which creates gene complex. |
| What are the quantities of chromosomes and genetic information in each phase of mitosis and meiosis? | Mitosis (always 2n,2C in telophase-G1 4n in S-G2-P-M-A) Meiosis (2n in in gametocyte n in secondary gametocyte/ 2C in primary gametocyte before Mitosis 4C after mitosis 2c after M1 c after M2) |
| What is a mutation? | Permanent alteration of any part of DNA sequence |
| How are mutations classified? | Spontaneous ( appear for no known reason, result from biological and chemical processes, during enzymatic process.) Non-Spontaneous (Influenced by an external factor, Induced by natural or artificial factor called mutagen) |