BIOL 101 1 DNA - Human Genetics and Molecular Biology PDF

Human Genetics and Molecular Biology 01/10/2024 Dr. Ayat sayed 1  DNA Site In chromosome inside the nucleus...

Human Genetics and Molecular Biology 01/10/2024 Dr. Ayat sayed 1  DNA Site In chromosome inside the nucleus Eukaryotes In chromosome inside Site mitochondria In Chromosomes non chromosomal DNA Prokaryotes (Plasmids) In the cytoplasm 01/10/2024 Dr. Ayat sayed 2  DNA Function Store genetic information transmit it to next generation (Through replication) Control protein synthesis inside each cells to be able to perform its physiologic functions (Through transcription and translation) 01/10/2024 Dr. Ayat sayed 3  DNA & NUCLEOTIDE STRUCTURE DNA is a polymer of deoxynucleotides linked together by phosphodiester bonds Each nucleotide consists of 3 components: a nitrogenous base (purine or pyrimidine ) a 5-carbon sugar (deoxy-pentose) Phosphate. 01/10/2024 Dr. Ayat sayed 4  DNA & NUCLEOTIDE STRUCTURE Purines are heterocyclic 2 ring structure. The purines commonly found in nucleic acids are adenine (A) and guanine (G) Both adenine (A) and guanine (G) are found in DNA and RNA. Other purine metabolites, not usually found in nucleic acids, include xanthine, hypoxanthine, and uric acid. Pyrimidines One ring structure. Cytosine (C) is present in both DNA and RNA. Thymine (T) is usually found only in DNA, whereas uracil (U) is found only in RNA. 01/10/2024 Dr. Ayat sayed 5  DNA & NUCLEOTIDE STRUCTURE Pentose sugar If the pentose is deoxyribose, the nucleic acid is DNA (deoxyribonucleic acid). If the pentose is ribose, the nucleic acid is RNA (ribonucleic acid). Phosphate One or more phosphate groups is attached to the 5′ carbon of the pentose sugar Nucleosides and Nucleotides Nucleosides are formed by covalently linking a base to the number 1 carbon of a sugar by N- glycosidic bond. Nucleotides are formed when 1 or more phosphate groups is attached to the 5′ carbon of a nucleoside by phospho-ester bond. Nucleoside di- and triphosphates are high- energy compounds like ATP and GTP 10/1/2024 Dr. Ayat sayed 7  DNA STRUCTURE Primary Secondary Tertiary Structure Structure Structure The sequence of bases Double stranded Chromatin in the nucleic acid chain DNA gives the primary structure of DNA. 01/10/2024 Dr. Ayat sayed 8  Primary structure of DNA The sequence of bases in the nucleic acid chain gives the primary structure of DNA. DNA is formed of polymers of nucleotides (dNTPs)( d.AMP , d.GMP , d.TMP , d.CMP) The nucleotides are covalently bounded by 3`,5`phosphodiester bond. Polarity: the strand has 2 ends , one end (5`end) with free phosphate and the other (3`end)with free (OH). The base sequence of a nucleic acid strand is written by convention, in the 5′→3′ 5′-TCAG-3′ or TCAG 01/10/2024 Dr. Ayat sayed 9  Secondary structure of DNA Double stranded linear Two DNA strands are annealed to each other according to the base paining complementary. Base complementary (Chargaff ’s rules) means that A always pairs with T (2 hydrogen bonds), G always pairs with C (3 hydrogen bonds). So that the amount of A equals the amount of T, the amount of G equals the amount of C. Thus, total purines equals total pyrimidines. The 2 strands are antiparallel (opposite in direction) One strand is 5′→3′, and the other is 3′→5′ 01/10/2024 Dr. Ayat sayed 10 Watson and Crick double helix model The 2 DNA strands wind around each other forming right handed double helix (B form). The hydrophilic sugar-phosphate backbone of each chain is outside of the chain The hydrophobic bases are stacked inside of the helix. Each turn is 10.5 base in length and 2 nm width On its exterior surface, the double helix of DNA contains two grooves The major grooves act as a binding sites for regulatory proteins Minor groove is for histone binding 01/10/2024 Dr. Ayat sayed 11  Compare between A,B,Z forms of DNA. clip_image034 01/10/2024 Dr. Ayat sayed 12  Different forms of DNA Parameters A -DNA B-DNA Z-DNA Direction of helical Right Right Left rotation Residues per turn of 11 10 12 base pairs helix Major groove narrow and deep wide and deep Flat Comments Rare, the dehydrated most prevalent within cells biologic function is unknown, form of B-form (under at physiological conditions but may be related to gene lower hydration and (low salt and high degree of regulation. in areas rich in G and higher salt content hydration). C 01/10/2024 Dr. Ayat sayed 13  Chromatin is the 3ry structure in which DNA interact with the DNA- binding proteins and packed inside the cells There are 2 classes of DNA-binding proteins involved in maintaining the compact structure of chromatin: a- Histones b- Non-histones 01/10/2024 Dr. Ayat sayed 14  A- HISTONES The major class of DNA-binding proteins 5 types: H1, H2A, H2B, H3, H4. Histones are rich in basic amino acids lysine and arginine, so they are positively charged on the proteins. They form ionic bonds with the negatively charged DNA. Functions of histones: condensation of the DNA into more compact chromosomes. Protect the DNA from digestion by exonucleases. Regulatory role Histones in are not present in prokaryotes 01/10/2024 Dr. Ayat sayed 16  Nucleosome Structure Nucleosome Nucleosome is the basic packaging unit of chromatin results from binding of DNA to histones generates 10 nm structure. Formed of 1-DNA core: 140-150 Base pair (bp) of supercoiled DNA 8 histones (2 molecules of H2A, H2B, H3, H4). 2- Linking region: 20-200 bp of DNA that joins one nucleosome core to the next 1 molecule of histone (H1) which protects the linker DNA from digestion by nucleases. 01/10/2024 Dr. Ayat sayed 18  Chromatin Structure ▪ A series of nucleosomes is sometimes called “beads on a string” or a 10nm chromatin fiber. ▪ This fiber is then coiled again forming the 30 nm fiber. ▪ The later is organized into loops to form 300 nm fiber. ▪ Further condensation occurs to eventually form the 700 nm chromatid ▪ Finally, the 1400 nm chromosome is formed. ▪ Each eukaryotic chromosome contains one linear molecule of double-stranded DNA.  Chromatin The DNA in the nucleus exists in two forms: Heterochromatin : more compact, stain dense Gene poor (AT rich) transcriptionally less active the genes are silenced by methylation, Seen in interphase and mitotic chromosomes It is not sensitive to digestion by DNAase (nuclease) Euchromatin : less compact structure, Stain light More sensitive to Less sensitive to transcriptionally more active, nucleases nucleases Gene rich ( CG rich) Generally corresponds to the nucleosomes (10-nm fibers) loosely associated with each other or (looped 300-nm fibers). It is sensitive to digestion by DNAase (nuclease) 01/10/2024 Dr. Ayat sayed 20  Types of DNA Double stranded linear: Eukaryotic nuclear chromosome. Double stranded circular: Mitochondrial, bacterial chromosome, plasmid, viral and chloroplast. Single stranded circular DNA: (small viruses) 01/10/2024 Dr. Ayat sayed 21  Mitochondrial DNA It is a circular double stranded DNA of about 16 kb length It codes for few number of genes as enzymes involved in energy production and electron transport chain. 5-10 times mutation rate than nuclear DNA It is maternally inherited because the ovum contains hundreds or thousands of mitochonderia compared to the sperm.  Explain Denaturation/Renaturation of DNA 01/10/2024 Dr. Ayat sayed 23 Definition: Double-stranded DNA can be denatured (separated) by conditions that disrupt hydrogen bonding, resulting in “melting” of the double strand into two single strands The covalent 3-5 phosphodiester bonds are not broken in this process so the sugar phosphate backbone is maintained. Desaturating factors: Heat, alkaline pH, chemicals such as formamide and urea 01/10/2024 Dr. Ayat sayed 24 Melting temperature (TM): Temperature at which 50% of the DNA molecule exist as single strands is called Tm. The TM differ according to base composition of the DNA molecule High TM value in DNA molecule rich in C-G base pair Renaturation (reannealing) Denatured single-stranded DNA can be renatured (annealed) If the denaturing condition is slowly removed 01/10/2024 Dr. Ayat sayed 25  Denaturation and Renaturation of DNA Such renaturation or annealing of complementary DNA strands is an important Step in Polymerase chain reaction 01/10/2024 Dr. Ayat sayed 26  Endo-nuclease and Exo-nuclease enzymes Nucleases are enzymes that hydrolyze nucleic acids Exonucleases remove nucleotides from the 5′ or the 3′ end of a nucleic acid. Endonucleases cut within the nucleic acid and release nucleic acid fragments. 01/10/2024 Dr. Ayat sayed 27 01/10/2024 Dr. Ayat sayed 28 What is the structure indicated below? A. Purine B. Purine nucleoside C. Purine nucleotide D. Pyrimidine nucleoside 01/10/2024 Dr. Ayat sayed 29  The width of the double helix in B-form DNA in nm is (A) 1 (B) 2 (C) 3 (D) 4 01/10/2024 Dr. Ayat sayed 30 DNA does not contain (A) Thymine (B) Adenine (C) Uracil (D) Deoxyribose 01/10/2024 Dr. Ayat sayed 31 IN DNA G-C pairs by (A) 1 Hydrogen bond (B) 2 Hydrogen bonds (C) 3 Hydrogen bonds (D) 4 Hydrogen bonds 01/10/2024 Dr. Ayat sayed 32 IN DNA A-T pairs by (A) 1 Hydrogen bond (B) 2 Hydrogen bonds (C) 3 Hydrogen bonds (D) 4 Hydrogen bonds 01/10/2024 Dr. Ayat sayed 33 The width (helical diameter) of the double helix in B-form DNA is (A) 1 nm (B) 2 nm (C) 3 nm (D) 4 nm 01/10/2024 Dr. Ayat sayed 34 The number of base pair in a single turn of B-form DNA molecule is (A) 4 (B) 8 (C) 10 (D) 12 01/10/2024 Dr. Ayat sayed 35 Left handed double helix is present in (A) Z-DNA (B) A-DNA (C) B-DNA (D) None of these 01/10/2024 Dr. Ayat sayed 36 In a DNA molecule the thymine concentration is 30%, the guanosine concentration will be (A) 10% (B) 20% (C) 30% (D) 40% 01/10/2024 Dr. Ayat sayed 37 IN a DNA molecule, the guanosine content is 40%, the adenine content will be (A) 10% (B) 20% (C) 30% (D) 40% 01/10/2024 Dr. Ayat sayed 38 In double stranded DNA molecule (A) Guanine content does not equal cytosine content (B) Adenine content does not equal thymine content (C) Adenine content equals uracil content (D) Guanine content equals cytosine content 01/10/2024 Dr. Ayat sayed 39 In a DNA molecule the thymine concentration is 30%, the guanosine concentration will be A. 10% B. 20% C. 30% D. 40% 01/10/2024 Dr. Ayat sayed 40 Exercise: Using Chargaff’s Rules In dsDNA (ds = double-stranded) % A = % T (% U) %G=%C % purines = % pyrimidines A sample of DNA has 30% T; what is the % G? 30% T + 30% A = 60% therefore, % C + % G must total 40% 20% C and 20% G Ans: 20% G 01/10/2024 Dr. Ayat sayed 41  A medical student working in a molecular biology laboratory is asked by her mentor to determine the base composition of an unlabeled nucleic acid sample left behind by a former research technologist. The results of her analysis show 10% adenine, 40% cytosine, 30% thymine and 20% guanine. What is the most likely source of the nucleic acid in this sample? A. Bacterial chromosome B. Bacterial plasmid C. Mitochondrial chromosome D. Nuclear chromosome E. Viral genome 01/10/2024 Dr. Ayat sayed 42 Answer: E. A base compositional analysis that deviates from Chargaff ’s rules (%A = %T, %C = %G) is indicative of single-stranded, not double stranded nucleic acid molecule. All options listed except E are examples of circular (choices A, B and C) or linear (choice D) DNA double helices. Only a few viruses (e.g. parvovirus) have single-stranded DNA 01/10/2024 Dr. Ayat sayed 43  How many types of histone molecules are found in nature? a) 3 b) 4 c) 5 d) 6 01/10/2024 Dr. Ayat sayed 44 Mutations in mitochondrial DNA results in all of the following except : A. Defects in enzymes of Respiratory chain I and IV B. Maternal pattern of diseases C. Paternal pattern of diseases D. Non-Mendelian inheritance for diseases 01/10/2024 Dr. Ayat sayed 45 Endonuclease activation and chromatin fragmentation are characteristic features of eukaryotic cell death by apoptosis. Which of the following chromosome structures would most likely be degraded first in an apoptotic cell? B. 10-nm fibre C. 30-nm fibre D. Chromaride E. Heterochromatin 01/10/2024 Dr. Ayat sayed 46 Answer: B. The more “opened” the DNA, the more sensitive it is to enzyme attack. The 10-nm fiber, without the H1, is the most open structure listed. The endonuclease would attack the region of unprotected DNA between the nucleosomes. 01/10/2024 Dr. Ayat sayed 47 Melting temperature of DNA is increased by its (A) A and T content (B) G and C content (C) Sugar content (D) Phosphate content 01/10/2024 Dr. Ayat sayed 48 01/10/2024 Dr. Ayat sayed 49