MIDTERM: NUCLEIC ACIDS Flashcards by Sunwoo's Berry

Molecular repositories for genetic information & are jointly referred to as the “ molecules of heredity”

NUCLEIC ACIDS

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2 TYPES OF NUCLEIC ACIDS

~ DEOXYRIBONUCLEIC ACID (DNA)
~ RIBONUCLEIC ACID (RNA)

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Serves as the genetic material in all living organism as well as in most viruses

DEOXYRIBONUCLEIC ACID (DNA)

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Involves in protein synthesis and sometimes in the transmission of genetic information

RIBONUCLEIC ACID (RNA)

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DISCOVERY OF NUCLEIC ACIDS
- Isolated nuclei from pus cell and found that they contained “nuclein”

FRIEDRICH MIESCHER - 1869

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DISCOVERY OF NUCLEIC ACIDS
- Discovered purine and pyrimidines

EMIL FISCHER - 1800s

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DISCOVERY OF NUCLEIC ACIDS
- Recognizes that nucleins are associated with histones (where DNA coils in irregular pattern)

GEHEIMRAT ALBRECHT KOSSEL - 1894

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DISCOVERY OF NUCLEIC ACIDS
- Introduced the term nucleic term

RICHARD ALTMANN - 1899

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DISCOVERY OF NUCLEIC ACIDS
- Recognize the 5-carbon ribose sugar and later discover deoxyribose in nucleic acids

P.A. LEVENE - 1909

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DISCOVERY OF NUCLEIC ACIDS
- Demonstrated a color test known as Feulgen test for the DNA

ROBERT FEULGEN - 1914

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DISCOVERY OF NUCLEIC ACIDS
- Stressed that there are 2 types of nucleic acids

P.A. LEVENE - 1929

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DISCOVERY OF NUCLEIC ACIDS
- Discovered that several species contain equal amounts of the bases : A = T ; & G = C (chargaff’s rule)

ERWIN CHARGAFF - 1950s

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DISCOVERY OF NUCLEIC ACIDS
- Bombarded DNA with X-rays then deduced the overall structure of the molecule

MAURICE WILKINS & ROSALIND FRANKLIN - 1950s

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DISCOVERY OF NUCLEIC ACIDS
- Suggested a triple helix structure of DNA

LINUS PAULING - 1953

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DISCOVERY OF NUCLEIC ACIDS
- Constructed double-helical model for DNA & published their findings in APRIL 25, 1953 issue of nature magazine
- Received nobel prize

JAMES WATSON & FRANCIS CRICK

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A double - stranded molecule with a long chain of nucleotides

NUCLEIC ACID : STRUCTURE DNA STRUCTURE

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 Single building block of DNA
 Deoxyribose sugar , phosphate group & nitrogenous base

NUCLEOTIDES

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 Information - containing parts of DNA
 DNA sequences are measured in numbers of base pairs

NITROGENOUS BASES

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NITROGENOUS BASES
- Purines

ADENINE (A )& GUANINE (G)

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NITROGENOUS BASES
- Pyrimidines

CYTOSINE (C) & THYMINE (T)

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Formed when the nucleotides are joined into long chains when strong attachments called phosphodiester bonds from between the deoxyribose sugars & the phosphate

SUGAR - PHOSPHATE BACKBONE

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Opposing orientation of the 2 nucleotide chains in a DNA

ANTIPARALLELISM

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DNA CONFIGURATION IN THE NUCLEUS
- DNA molecules are extremely LONG
 DNA of smallest chromosome : ________ long if stretched out , but is package into a chromosome (2 um long)

14 mm

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Process by which the long , linear DNA molecules are tightly compacted & organized into a more condensed structured within the
cell

DNA PACKAGING

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Single - stranded molecule in most of its biological roles and has a shorter chain of nucleotides

RNA STRUCTURE

Ribose sugar , phosphate group , and nitrogenous base

NUCLEOTIDE

DNA or RNA? - usually double stranded - THYMINE as base - DEOXYRIBOSE as sugar - Maintains protein - encoding information - CANNOT function as an enzyme - PERSISTS

DNA

DNA or RNA? - usually single - stranded - URACIL as base - RIBOSE as sugar - carries protein - encoding information and control how information is used - CAN function as an enzyme - TRANSIENT

RNA

A process by which DNA make a copy of itself during cell division

DNA REPLICATION

it is the summary of process of storing and expressing genetic information

CENTRAL DOGMA

process of transferring information from DNA to RNA is called _________

TRANSCRIPTION

process of converting genetic information contained in RNA into a proteins is called ______

TRANSLATION

A ________ must carry out 2 jobs: duplicate itself and control the development of the rest of the cell in a specific way - Francis Crick

GENETIC MATERIAL

DISCOVERY OF THE GENETIC MATERIAL - Isolated the genetic material formWBC nuclei : he noted it had an acidic nature containing N (NITROGEN) &P (PHOSPHORUS) , & called it nuclein

1869: Friedrich Miesche

- 1st to link inherited disease & protein  People who had certain inborn errors of metabolism did not have certain enzymes

1902: Archibald Garrod

 Investigated virulence in Diplococcus (now known as Streptococcus pneumoniae)  2 strains - rough type (AVIRULENT/did not develop) & smooth type (VIRULENT/developed) - what happen is that the polysaccharide coat/capsule it shielded the bacteria from the immune system of mouse  Transforming principle

1928: Frederick Griffith

one bacterial type into another

TRANSFORMING PRINCIPLE

 Identified the transforming material as DNA by preparing boiled virulent bacterial cell lysates & sequentially treated them with enzymes  Conclusion : transforming principle in Griffith's experiment was DNA

1944 : Oswald T. Avery , Colin Macleod , &M.J. MacCarty

 Confirmed that the DNA of the bacteriophage was the carrier of its genetic determination

1953: Alfred Hershey & Martha Chase

Why must DNA be replicated?

DNA must be replicated so that information it holds can be MAINTAINED AS PASSED TO FUTURE CELL GENERATIONS

MODES OF DNA REPLICATION  Replicated DNA would consists of 1 OLD and 1 NEW strand A. SEMICONSERVATIVE REPLICATION B. CONSERVATIVE REPLICATION C. DISPERSIVE REPLICATION

SEMICONSERVATIVE REPLICATION

MODES OF DNA REPLICATION  2 NEWLY CREATED STRANDS are bought together & the parental strands reassociate A. SEMICONSERVATIVE REPLICATION B. CONSERVATIVE REPLICATION C. DISPERSIVE REPLICATION

CONSERVATIVE REPLICATION

MODES OF DNA REPLICATION  Each strand would consist of BOTH OLD and NEW DNA A. SEMICONSERVATIVE REPLICATION B. CONSERVATIVE REPLICATION C. DISPERSIVE REPLICATION

DISPERSIVE REPLICATION

DNA replication occurs during ______

S PHASE

OVERVIEW OF DNA REPLICATION

1. helicase binds to origin and separates strands. 2. binding proteins keep strands apart 3. primase makes a short stretch of RNA on the DNA template 4. DNA polymerase adds DNA nucleotides to the RNA primer 5. DNA polymerase proofreading activity checks and replaces incorrect bases 6. continuous strand synthesis continues in a 5' to 3' direction 7. discontinuous synthesis produces okazaki fragments on the 5' to 3' template 8. enzymes remove RNA primers. Ligase seals sugar-phosphate backbone

Human DNA replicates at a rate of about __________________

50 bases per second

what is the site where the DNA is locally open is called a?

REPLICATION FORK - because it resembles fork

ENZYMES IN DNA REPLICATION - unwinds parental double helix A. HELICASE B. BINDING PROTEINS C. PRIMASE D. DNA POLYMERASE E. LIGASE

HELICASE

ENZYMES IN DNA REPLICATION - stabilize separate strands A. HELICASE B. BINDING PROTEINS C. PRIMASE D. DNA POLYMERASE E. LIGASE

BINDING PROTEINS

ENZYMES IN DNA REPLICATION - makes a shorts stretch of RNA on DNA template - adds short primer to template strand. A. HELICASE B. BINDING PROTEINS C. PRIMASE D. DNA POLYMERASE E. LIGASE

PRIMASE

ENZYMES IN DNA REPLICATION - binds nucleotides to form new strands - adds DNA nucleotides to RNA primers A. HELICASE B. BINDING PROTEINS C. PRIMASE D. DNA POLYMERASE E. LIGASE

DNA POLYMERASE

ENZYMES IN DNA REPLICATION - joins Okazaki fragments and seals other nicks in sugar - phosphate backbone A. HELICASE B. BINDING PROTEINS C. PRIMASE D. DNA POLYMERASE E. LIGASE

LIGASE

 Laboratory technique used to produce multiple copies of a specific DNA sequence  DNA replication conducted outside cells

DNA AMPLIFICATION

 1st best known DNA amplification technique  Uses DNA polymerase to rapidly replicate a specific DNA sequence in a test tube

POLYMERASE CHAIN REACTION (PCR)

PCR PROCESS

1. Selects target sequence in virus genome PREPARATION 2. PRIMERS 3. FREE NUCLEOTIDES / HEAT - RESISTED POLYMERASE/ TAQ POLYMERASE TEMPERATURE SHIFT (DENATURATION 94 C - separate double helix to unbound) 5. TARGET SEQUENCE UP 6. HEAT SEPARATES Strands PRIMING (50 C- 65 C ~ creating of new DNA) 7. PRIMERS HYBRIDIZE DUE TO BASE COMPLEMENTARY EXTENSION (72C) 8. DNA FILLS IN/ EXTEND 9. REPEAT PROCESS MANY TIMES (amplification - process is repeated to produce many copies and to detect the pathogen)

- isolation from bacteria - _______ is extracted from Thermus aquaticus & vent polymerase from Thermococcus sorais

TAQ POLYMERASE

USES /APPLICATION OF PCR - identify GENETIC MARKERS associated with disease , detection of mutation , ID of pathogens , & screening of genetic disorders a. Genetic testing & diagnostics b. Forensics c. Disease diagnostics d. Biomedical research e. Environmental monitoring f. Paternity relationship testing g. Ancient DNA studies

a. Genetic testing & diagnostics

USES /APPLICATION OF PCR - ID of SUSUPECTS/ VICTIMS and provide evidence for criminal investigations a. Genetic testing & diagnostics b. Forensics c. Disease diagnostics d. Biomedical research e. Environmental monitoring f. Paternity relationship testing g. Ancient DNA studies

Forensics

USES /APPLICATION OF PCR - infectious diseases caused by microorganism a. Genetic testing & diagnostics b. Forensics c. Disease diagnostics d. Biomedical research e. Environmental monitoring f. Paternity relationship testing g. Ancient DNA studies

Disease diagnostics

USES /APPLICATION OF PCR - STUDY OF GENE expression of patterns , genetic variations , DNA sequencing , etc. a. Genetic testing & diagnostics b. Forensics c. Disease diagnostics d. Biomedical research e. Environmental monitoring f. Paternity relationship testing g. Ancient DNA studies

Biomedical research

USES /APPLICATION OF PCR - detection & ID of microorganism in soil, water , & air samples a. Genetic testing & diagnostics b. Forensics c. Disease diagnostics d. Biomedical research e. Environmental monitoring f. Paternity relationship testing g. Ancient DNA studies

Environmental monitoring

USES /APPLICATION OF PCR - establish biological relationship a. Genetic testing & diagnostics b. Forensics c. Disease diagnostics d. Biomedical research e. Environmental monitoring f. Paternity relationship testing g. Ancient DNA studies

Paternity relationship testing

USES /APPLICATION OF PCR - extraction amplification of DNA from ancient specimens a. Genetic testing & diagnostics b. Forensics c. Disease diagnostics d. Biomedical research e. Environmental monitoring f. Paternity relationship testing g. Ancient DNA studies

Ancient DNA studies

determines the order of the 4 chemical building blocks - called bases that make up the DNA molecule

DNA SEQUENCING

Basis for DNA sequencing : Complementary base pairing

 Adenine A <_> Thymine T  Cytosine C <_> Guanine G

Method used for DNA sequencing :  Invented by Frederick Sanger in 1977 a way to determine the base sequence of a small piece of DNA  Generates a series of DNA fragments identical sequence that are complementary to the DNA sequence of interest  AKA CHAIN TERMINATION METHOD: dideoxynucleotides ddNTPs are added, terminating the DNA synthesis  Uses ddNTPs to determine the order of nucleotides in a nucleic acid A. Sanger sequencing B. Next generation sequencing

Sanger sequencing

STEPS IN SANGER SEQUENCING

- DNA AMPLIFICATION - DNA DENATURATION - DISPERSION OF PRIMED DNA - ADDITION OF DNA, POLYMERASE, dNTPs AND ddNTPs - ATTACHMENT OF DNA POLYMERASE

Method used for DNA sequencing :  Collectively referred to the most recent set of DNA sequencing technologies  Ability to sequence millions of small pieces at once that can handle much larger DNA molecules much faster A. Sanger sequencing B. Next generation sequencing

Next generation sequencing

FEATURES OF NGS

1. HIGHLY PARALLEL 2. MICRO SCALE 3. LOW - COST 4. FAST 5. SHORTER LENGTH

 NGS sequencing platform  Each nucleotide can be identified by a disruption in current as it passes through the pores at about 1,000 bases per second  Uses grapheme - contain 1- atom - thick sheet carbon

NANOPORE SEQUENCING

USES / APPLICATION OF DNA SEQUENCING - provide comprehensive information about an organism genetic makeup A. Genome Sequencing B. Medical Diagnostics & Personalized Medicine C. Cancer genomics D. Forensics & human ID E. Evolutionary studies & phylogenetics F. Metagenomics microbial ecology G. Pharmacogenomics H. Ancient DNA studies

Genome Sequencing

USES / APPLICATION OF DNA SEQUENCING - diagnosing genetic diseases identifying diseases causing mutations A. Genome Sequencing B. Medical Diagnostics & Personalized Medicine C. Cancer genomics D. Forensics & human ID E. Evolutionary studies & phylogenetics F. Metagenomics microbial ecology G. Pharmacogenomics H. Ancient DNA studies

Medical Diagnostics & Personalized Medicine

USES / APPLICATION OF DNA SEQUENCING - ID of genetic mutations associated with the development & progression of tumors A. Genome Sequencing B. Medical Diagnostics & Personalized Medicine C. Cancer genomics D. Forensics & human ID E. Evolutionary studies & phylogenetics F. Metagenomics microbial ecology G. Pharmacogenomics H. Ancient DNA studies

Cancer genomics

USES / APPLICATION OF DNA SEQUENCING - analysis of DNA from crime scene samples or unidentified human remains establishing relationship A. Genome Sequencing B. Medical Diagnostics & Personalized Medicine C. Cancer genomics D. Forensics & human ID E. Evolutionary studies & phylogenetics F. Metagenomics microbial ecology G. Pharmacogenomics H. Ancient DNA studies

Forensics & human ID

USES / APPLICATION OF DNA SEQUENCING - reconstructing evolutionary relationships between organisms studying their genetic diversity A. Genome Sequencing B. Medical Diagnostics & Personalized Medicine C. Cancer genomics D. Forensics & human ID E. Evolutionary studies & phylogenetics F. Metagenomics microbial ecology G. Pharmacogenomics H. Ancient DNA studies

Evolutionary studies & phylogenetics

USES / APPLICATION OF DNA SEQUENCING - analysis of complex microbial communities present in various environments A. Genome Sequencing B. Medical Diagnostics & Personalized Medicine C. Cancer genomics D. Forensics & human ID E. Evolutionary studies & phylogenetics F. Metagenomics microbial ecology G. Pharmacogenomics H. Ancient DNA studies

Metagenomics microbial ecology

USES / APPLICATION OF DNA SEQUENCING - ID of genetics variations affecting an individual's response to medications A. Genome Sequencing B. Medical Diagnostics & Personalized Medicine C. Cancer genomics D. Forensics & human ID E. Evolutionary studies & phylogenetics F. Metagenomics microbial ecology G. Pharmacogenomics H. Ancient DNA studies

Pharmacogenomics

USES / APPLICATION OF DNA SEQUENCING - providing insights into the genetic history and evolution of extinct species , including human ancestors A. Genome Sequencing B. Medical Diagnostics & Personalized Medicine C. Cancer genomics D. Forensics & human ID E. Evolutionary studies & phylogenetics F. Metagenomics microbial ecology G. Pharmacogenomics H. Ancient DNA studies

Ancient DNA studies