DNA Structure and Function PDF

## DNA poly deoxy ribonucleotide covalently linked by 3'5' phosphodiester bonds It is found in: - Eukaryotic cells: in nucleus and mitochondria and chloroplast of plants - Prokaryotic cells: single chromosomal DNA and non-chromosomal DNA "plasmid" It may be: - Double Strand Linear as in Nucle...

## DNA poly deoxy ribonucleotide covalently linked by 3'5' phosphodiester bonds It is found in: - Eukaryotic cells: in nucleus and mitochondria and chloroplast of plants - Prokaryotic cells: single chromosomal DNA and non-chromosomal DNA "plasmid" It may be: - Double Strand Linear as in Nuclear DNA. - Double Strand Circular as in mtDNA, Bacterial chromosomal DNA, Plasmids & Some Viruses - Single strand Circular or linear in some small viruses ### Structure of DNA 1. **Primary**: linear sequence of nucleotides The DNA exists as a double helix, with a pair of nucleotides bound together by complimentary base pair interactions (hydrogen bonds) The backbone of DNA is made up of **sugar phosphate units**. The nitrogenous base is attached to the sugar and is available for bonding. The back bone of DNA is made of **sugar-phosphate units** 2. **Secondary**: interactions between bases by hydrogen bonds to form DNA double helix. - DNA has a repeating structure. - **Antiparallel** 2 chains are held together by the hydrogen bonding between bases "2 bonds bet A&T, 3 bonds bet C&G) **Hydrophobic interactions = base stacking**: interactions between adjacent base pairs. This adds stability to the double helix once the strands have been brought together by base pairing Each turn of DNA is made up of **10.4 nucleotide pairs** One turn of helix measure around **3.4 nm**. Each base pair is **0.34 nm** apart (distance between adjacent nucleotide pairs). **Major & minor grooves**: Because of coiling of 2 strands around each other **Base pairing** : According to Chargaff's rules, concentration of adenine (A) is equal to thymine (T) and the concentration of cytidine (C) is equal to guanine (G) **Complimentary**: one purine is connected to one pyrimidine The bases can pair only if 2 polynucleotide chains that contain them are **anti-parallel**. ### Types & forms of DNA: #### Conformation of DNA: depends on: - The base composition of DNA - Physical conditions (salt, temp). - ß form is the **dominant form of DNA** under physiological condition of the cell - (low salt conc). It is the conformation described by Watson and Crick. - **Z-DNA**: produced experimentally & contains single groove. - **A DNA & Z DNA**: in high salt conc or in presence of alcohol #### Denaturation (Melting): Is separation of 2 strands of DNA and can be done by: - Enzymes as **helicase**. - Increasing temperature (A-T base-pairs will be less thermally stable than those rich in G-C base) - Addition of alkalis (decreasing salt conc that leads to break down of hydrogen bonds). **Melting temperature (TM)**: the temperatures that can denaturate 50% of the DNA molecule. **Annealing (renaturation)**: reforming of DNA double helix again if thermally melted DNA is cooled. **Hybridization**: rejoin between DNA strand and other **DNA, RNA or probe.** ## Genes (arrangement of DNA) A gene is a functional and physical unit of heredity passed from parent to offspring. It is a segment of DNA and codes for a single protein. **Genes in eukaryotes consist of**: - **Coding regions**: called **exons** - **Non-coding regions**: called **introns** - **Regulatory sequences**: (determine when & where protein is made (and how much is made) **Genome**: the entire DNA contained in organism or cell (23 pairs: 22 autosomes and 1 sex chromosomes) - A small amount of DNA is also present in the mitochondria **Chromosomes** are pieces of linear DNA and contain many genes. Gene → Nucleosome → chromosome→ genome - In non-dividing cells, chromosomes are too fine & tangled. It is called **chromatin**. - During mitosis, become more condensed and become visible. It is called **chromatid** ### Chromatin or chromatid: Complex of DNA and protein - Histones and non-histone proteins are present. - Non-histone proteins include proteins involved in transcription, replication and DNA repair. - Histones are proteins that are closely associated with DNA molecules. - Histones are responsible for **structure of chromatin** & in **regulation of gene expression** - Histones contain high percentage of positively charged amino acids (lysine) so interact with negatively phosphate groups in DNA helix to **form nucleosomes** - Histones are present in all organisms except bacteria and some algae. #### Types: - **H1 (or H5)**: **linker histones**. 220 AAs - **H2A** - **H2B** - **H3** - **H4** - **Core histones**: associate with **DNA** to form nucleosomes (150) ### Nucleosomes: packing of chromatin - Each nucleosome consists of 146 base pair DNA & 8 histone. Two copies of each of core histones - The DNA is wrapped around the histone core →2 turns per nucleosomes. - DNA extends as a thread from nucleosome to nucleosome. - A **50 base pair DNA** connects two nucleosomes (linker DNA). - Without histones the unwound DNA in chromosomes would be very long. For example, Each human cell has about **1.8 meters of DNA**, but when wound on histones it is about **0.09 mm** - Histones contain a few lysine. - Under normal cellular conditions, the R group of lysine is positively charged, which can interact with the negatively charged phosphates in DNA. - The positive R group of lysine may be neutralized by acetylation, reducing the binding force between histones and DNA during gene expression #### Histone acetylation : acetylases vs deacetylase - Histone acetylation plays an important role in the regulation of gene expression. - Acetylation neutralizes the positive charges on the histones by changing amines to amides and decreases the ability of histones to bind to DNA. - The decreased binding allows chromatin expansion, and permits transcription (transcriptionally active). - Hyper acetylated chromatins transcriptionally active (increase gene expression). - Cancer Cells are Rich in Histone Decetylases (increase replication). ## RNA (ribonucleic acid) 1. **tRNA (transfer RNA)**: 10-15% - There are > 20 different tRNA molecules (75 to 95 nucleotides) - All tRNA's from all organisms have a similar structure, indeed a human tRNA can function in yeast cells. - It consists of 4 arms and 3 loops. - It is carrier of amino acids to the site of protein synthesis. - There is at least one t-RNA molecule to each of 20 amino acids required for protein synthesis. - Eukaryotic tRNA are less stable than prokaryotic tRNA 2. **mRNA**: 1-5%. They are single-stranded linear molecules. - Eukaryotic mRNA is more stable than prokaryotic mRNA. - Eukaryotic mRNA molecules are: - Capped at **5' end** to protect mRNA from nuclease attack. The cap is **methylated GTP**. - At **3' end** it contains **poly A tail** to protects mRNA from nuclease attack - In prokaryotes **5' end** of mRNA contains a sequence sequence rich in A and G is known as **Shine-Dalgarno sequence** that helps attachment of mRNA with ribosome during protein synthesis. - Functions: - mRNA is direct carrier of genetic information from nucleus to cytoplasm. - Genetic information is present in mRNA in the form of genetic code. - Sometimes it may contain information for the formation of more than one protein. 3. **rRNA**: 80% - Ribosomal RNA is a component of the ribosomes (the protein synthetic factories in the cell). - Ribosome provide site for protein synthesis; it consists of 2 subunits: - Large and small one that consists of RNA and proteins - Contain three RNA binding sites that are: - The A site - The P site - The E site 4. **snRNA**: small nuclear RNA - Associated to SNRNP (snurps) - Important for: - Removal of introns (splicing). - Maintenance of telomeres or chromosomal ends ## MCQ on Nucleotides, DNA & RNA 1. DNA is made up of phosphate group, an organic base, and a) Protein b) Sugar c) Fat d) None of the above 2. The sugar obtained by ATP hydrolysis is a) Glucose b) Ribose c) Arabinose d) Ribulose 3. The correct statement describes the Z-form of DNA is: a) Compacted than B-form b) Left handed manner c) The predominant one d) Bearing 11 base pairs in each turn 4. All the following bases present in DNA Except: a) Adenine B) Guanine c) Uracil D) Cytosine 5. Which one of the following is nucleotide? a) Adenosine b) Thymidine c) Cytidylate d) Cytidine 6. Concerning the B-form of DNA strand, the false statement is: a) Adenine pairs with thymine b) Each strand has an opposite polarity c) Each double helix contain 10 base pairs d) The two strands are coiled in a left handed manner 7. Which of the following not contain phosphate group? a) Cytidylate b) Guanylate c) Uridine d) Adenylate 8. Which of the following is methyl uracil? a) Cytosine b) Thymine c) Adenine d) Inosine 9. Not involved in DNA structure: a) Uracil b) Cytosine c) Thymine d) Inosine 10. In DNA, cytosine is paired with: a) Uracil b) Guanine c) Adenine d) Inosine 11. Ribose is the component of all the following except: a) FAD b) NAD c) DNA d) Co A-SH 12. In protein biosynthesis, the amino acids are carried by: a) t RNA b)m RNA c)r RNA 13. The drug that inhibits xanthine oxidase is: a) Colchine b) Aspirin c) Probencid d) Allopurinol 14. All of the following statements regarding nucleosomes are true except: a) They are beaded structures. b) The beads are linked by DNA chain. c) The DNA has a packing ratio of about 7 in the nucleosome. d) The primary structure of histones is a characteristic of the cell type and species 15. All of the following about tRNA is true except that: a) They have extensive intrachain hydrogen bonding b) they contain number of bases that have been modified post- transcriptionally c) They contain an anticodon triplet of bases at 5' end of molecule that is complementary to the triplet codon on mRNA 16. In nucleic acids, the phosphate group is attached to the.... Carbon of the sugar: a) 5 b) 4 c) 3 d) 1 17. In nucleic acids, the bases are always attached to the...... Carbon of the sugar: a) 5 b) 4 c) 3 d) 1 18. If one side of DNA molecules contains the following sequence of nucleotides, AGTCCG, the complementary sequence on the other side would be: a) GCCTGA C) TCAGGA b) AGTCCG d) CTGAAT 19. Which biomolecules has both catalytic activity and ability to store genetic information? a) DNA b) RNA c) ATP d) Protein 20. Not involved in RNA structure: a) Adenine b) Thymine c) Cytosine d) Guanine 21. Uric acid is the end product of: a) Guanine b) Uracil c) Cytosine d) Thymine 22. Uric acid is: a) 2,6 dioxypurine c) 8-aminopurine b) 2,6,8 aminopurine d)6 aminopurine 23. A purine base is: a) Guanine b) Hypoxanthine c) Adenine 24. The sugar present in the structure of thymidylic acid is: a) Deoxyribose b) Ribose c) Ribulose d) All of the above d) Thymine 25. The nitrogenous base present in GMP is: a) Guanine b) Guanosine c) GDP d) GTP 26. Removal of phosphate group from guanylic acid will produce: a) cGMP b) GTP c) Guanosine d) Glutathione 27. Addition of phosphate group to adenylic acid will produce: A) GDP b) ADP c) adenosine d) AMP 28. Adenine is: a) 6-amino purine b) 2,4-dioxy-pyrimidine c) 6-oxypurine d) 5-amino pyrimidine 29. In nucleosides, the sugar is attached with purine by nitrogen: a) Seven b) Nine c) Two d) One 30. Among the B-form of DNA strand, the false statement is: a) Adenine pairs with thymine b) Each strand has an opposite polarity c) Each double helix contain 12 base pairs d) The two strands are coiled in a right handed manner 31. 7-Methylguanosine at 5' end present in: a) rRNA b) mRNA c) tRNA d) SnRNA 32. What is the best event describes the introns? a) They are retained upon processing of ribosomal RNA b) They are excised upon processing of ribosomal RNA c) They are space sequences d) They are added to mRNA during splicing reaction 33. Nucleic acid is formed of nucleotide that linked together with: a) Phosphodiester bond b) Hydrogen bond c) Peptide bond d) Disulfide 34. The enzyme responsible for formation of cAMP is: a) Adenine deaminase c) Arginase b) Phosphodiesterase d) Adenylate cyclase 35. Replacement of adenine by guanine in the structure of adenylic acid produces: a) Guanosine b) GMP c) GTP d) cGMP 36. The substrate of adenylate cyclase is: a) AMP b) ATP c) ADP d) GTP 37. The 2 strands of DNA are a. identical b. Complementary c. Homogenous d. Heterogonous 38. If the cytosine content of double stranded DNA is 20% of the total bases, the thymine content would be: a.20% b.30% c. 40% d. 50% 39. Which of the following is left handed DNA? a) B-DNA b) Z-DNA c) A-DNA d) C-DNA 40. The function of tRNA is to: a) Provide a site for polypeptide synthesis b) Transport amino acids to the ribosome c) Travel to the ribosome to direct the assembly of polypeptides d) Transcribe DNA 41. Together with protein, rRNA: a) Provide a site for polypeptide synthesis b) Transport amino acids to the ribosome c) Travel to the ribosome to direct the assembly of polypeptides d) Transcribe DNA 42. Regarding the base pairing of DNA: a) Adenine is paired with thymine b) Guanine is paired with thymine c) Adenine is paired with uracil d) Guanine is paired with adenine 43. Mitochondrial DNA is: a) Double strand circular b) Double strand linear c) Single strand circular d) single strand circular 44. Nuclear DNA is: a) Single strand circular b) Single strand circular c) Double strand circular d) Double strand linear 45. Uric acid in animals turns to............ by.......... a. Ammonia - uricase b. Allantoins- uricase c. Urea-urease d. xanthine- xanthine oxidase