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BIOMETRICS

BIOMETRICS. Module Code: CA641 Week 11- Basic Definitions . Image: http :// whitni13.blogspot.ie/2013/03/dna-structure.html. Outline. A molecular biology primer The Cell The DNA The Central Dogma of molecular biology Genetic diseases example

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BIOMETRICS

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  1. BIOMETRICS Module Code: CA641 Week 11- Basic Definitions Image: http://whitni13.blogspot.ie/2013/03/dna-structure.html

  2. Outline • A molecular biology primer • The Cell • The DNA • The Central Dogma of molecular biology • Genetic diseases example Acknowledgement: this presentation was created following Prof. LiviuCiortuz, “Computer Science” Faculty, “Al. I. Cuza” University, Iasi, Romania: http://profs.info.uaic.ro/~ciortuz/

  3. A Molecular Biology Primer- The Cell • The cellis the basic structural and functional unit of all known living organisms. • Instead of having brains, cells make decisions trough complex networks of chemical networks called pathways: • synthesize new materials • break other materials down for spare parts • signal to eat, replicate or die • Two different types of cells/organisms: Prokariotesand Eukariotes. Image: http://www.clipart.dk.co.uk/371/az/Human_body/Cell

  4. Life depends on 3 critical molecules • Nucleobases: cytosine (C), guanine (G), adenine (A), thymine (T)/ uracil (U) • DNA : made of A, C, G, T • Hold information on how a cell a cell works • RNA :made of A, C, G, U • provide templates to synthesize amino-acids into proteins • transfer short pieces of information to different parts of the cell • Protein : made of (20) amino acids (AA) • form enzymes that send signals to other cells and regulate gene activity • form body’s major components (e.g. hair, skin, etc.)

  5. DNA Structure Discovered in 1952 – by James Watson (biologist), and Francis Crick, (physicist, PhD std.) - Nobel Prize Image:http://www.biologycorner.com/bio1/DNA.html

  6. Some basic terminology • Chromosome : an organized structure of DNA in cell • in humans, 23 pairs • Locus: specific position on a chromosome (where a base pair is present) • Genetic map: orderedset of lociplus the information they contain • Chromatin: mass of genetic material that condenses to form chromosomes Image: http://www.accessexcellence.org/RC/VL/GG/human.php

  7. Basic terminology contd.’ • Genome: all genetic material • Gene: substring of DNA that encodes for a specific protein, length measured in base-pairs • contains introns(non-coding) and exons(coding) • Alleles: some nucleotides may differ in different individuals • Example: 18bp TACAagTACAaattGATT ATGTtcATGTttaaCTAA Image: http://en.wikipedia.org/wiki/Gene

  8. DNA Replication Image: The double helix of DNA unwinds and each side serves as a pattern to make a new molecule. Image courtesy U.S. Department of Energy Human Genome Program

  9. The Central Dogma of Molecular Biology DNA -> RNA -> Protein

  10. From DNA to RNA (transcription) • RNA • made of A , C, G, U. A-U, C-G • obtained from DNA sequence • Example: Step1: Nuclear RNA • TACAagTACAaattGATT -> AUGUucAUGUuuaaCUAA Step2: mRNA(transcript) - discard introns -> AUGUAUGUCUAA • Some other types of RNA exist, that do not code for proteins, but have other roles (sRNA, microRNA)

  11. From mRNA to proteins (translation) • Protein : - 20 possible aminoacids (AA) • AAs are obtained by ‘reading’ the mRNA • Each codon(triplet of DNA nucleotides) corresponds to one of the 20 amino acids: • E.g. UUG -> L (Leucine) • Stopcodons: UAA, UAG, UGA • Startcodon: AUG • Example: • mRNA : AUG|UAU|GUC|UAA=> aminoacids: START(M-Methionine), Y(Tyrosine), V (Valine), STOP • Note: a change from UAU to UAA would transform Y into STOP, yielding the wrong protein (SNPs –single nucleotide polymorphism, alleles)

  12. Genetic code The redundancy in the table — one amino acid may be encoded by several different codons — is a kind of defence against mutations... Image: http://biology.kenyon.edu/courses/biol114/Chap05/Chapter05.html

  13. Protein - Example • DNA sequence => mRNA sequence => protein AA sequence =>protein 3D structure => function (algorithms to determine structure...) • Ex: Haemoglobin Subunit Alpha: MVLSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHFDLS HGSAQVKGHG KKVADALTNA VAHVDDMPNA LSALSDLHAH KLRVDPVNFK LLSHCLLVTL AAHLPAEFTP AVHASLDKFL ASVSTVLTSKYR Function: • Expression levels oxygen- transport • mRNA – microarrays, RNA-seq • Protein - quantitative real time polymerase chain reaction (qPCR)

  14. Genetic alterations on DNA A mutation - a change of the nucleotide sequence of the genome of an organism, virus Image: http://kabupatenklaten.com/gene-mutation-base-pair-insertions-or-deletions-causes-mutation-disorders

  15. Genetic alterations on DNA contd.’ • An insertion(insertion mutation) - the addition of one or more nucleotide base pairs into a DNA sequence • A deletion(deletion mutation) - a genetic in which a part of a chromosome or a sequence of DNA is missing Image: http://www.ebpi-kits.com

  16. The Central Dogma of Molecular Biology DNA -> RNA -> Protein

  17. Protein synthesis • http://www.learnerstv.com/animation/biology/Proteinsynthesis.swf

  18. Examples of genetic diseasesThalassemia • Even a mistake of just one position can have a profound effect. • Here is a small but devastating mutation in the gene for haemoglobin, the protein which carries oxygen in the blood. • good gene: AACCAG • mutant gene: AACTAG • People with thalassemia make less haemoglobin and fewer circulating red blood cells than normal, which results in mild or severe anaemia. • Thalassemia can cause significant complications, (e.g. pneumonia, iron overload, bone deformities and cardiovascular illness)

  19. Cri du chat • A rare genetic disorder caused by a deletion (the length of which may vary) on chromosome 5. • Symptoms • Babies: small at birth, may have respiratory problems, heart defects, muscular or skeletal problems, hearing or sight problems, or poor muscle tone • Adults: may have a small head (microcephaly), an unusually round face, a small chin, widely set eyes, folds of skin over their eyes, and a small bridge of the nose. People with cri-du-chat usually have difficulty walking and talking correctly. They may have behaviour problems (such as hyperactivity or aggression), and severe mental retardation.

  20. Cancer • A broad group of various diseases, all involving unregulated cell growth • Inherited mutations: • in the genes BRCA1 and BRCA2=> with a more than 75% risk of breast cancer and ovarian cancer • in MET gene =>…=> hereditary papillary renal cancer. • in APC gene => …colon polyps…=> colon cancer. • in BRAF gene =>…melanomas and nevi, lung cancers, colorectal cancer • in TP53 gene =>… More than 50% of human tumours contain a mutation or deletion of the TP53 gene • …

  21. Alleles • Dominant - exhibited phenotype • Recessive - "hidden" phenotype Note: • This slide and the next 4 slides are taken from http://www.cancer.gov/cancertopics/understandingcancer/cancergenomics/AllPages

  22. Penetrance • Sometimes one person with a dominant allele will expressa trait, yet that same genotype in another person will remain silent. => differences in penetrance. • Classic Mendeliangenetics: if an individual carries a dominant allele, the trait will be expressed (genotype = phenotype). However, if all carriers of a certain dominant allele in a population do not express the trait (same genotypes/different phenotypes), the gene is said to have incomplete penetrance.

  23. Autosomal Dominant Inheritance • Most hereditary cancer syndromes are inherited in autosomal dominant fashion. • Dominant inheritance occurs when only one copy of an allele is required for a particular trait to be expressed (phenotype). In autosomal dominant inheritance, multiple generations express the traits, with no skipped generations (assuming complete penetrance).

  24. Inherited Cancer Syndromes

  25. Cancer Susceptibility • Inherit a predisposition to cancer, not cancer itself • Mutation carriers can inherit their predisposing genotypes, yet they do not develop cancer => a somatic mutationin a second allele is required for cancer to develop • Sporadiccancer cases in families with a hereditary cancer syndrome. => phenocopies(their phenotype is similar to that of the affected mutation carriers, but their genotype is different) • => genetic testing may determine if the cancer is hereditary or sporadicin nature.

  26. What you should know? • What is the “Central Dogma” of molecular biology? • What is the difference between transcription and translationof the DNA? • What is a codon? • How would you define a gene? • What is DNA sequencing? • What is the difference between an intron and an exon? • What are the positive results of DNA mutations?

  27. Contact • Irina Roznovăț iroznovat@computing.dcu.ie • These slides: http://www.computing.dcu.ie/~iroznovat/tutorials/2012_2013/tutorial_CA641.shtml

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