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40 Cards in this Set
- Front
- Back
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physiological role of nucleotides and nucleic acids |
nucleotides: -building blocks of nucleic acids -energy currency (ATP) -signaling molecules (cAMP) -enzyme co-factors (NAD,FAD)
nucleic acids: -genetic information (DNA or RNA) -all stages of protein synthesis (DNA, mRNA, tRNA, rRNA) |
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three characteristics of nucleotides |
a) five carbon pentose sugar (ribose or deoxyribose) b)a nitrogenous base (purine or pyrimidine) c) phosphate (s) |
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five carbon pentose sugars |
ribose (RNA) or deoxyribe (DNA)
-ribose, a five carbon aldehyde, cyclizes into B-D-ribofuranose -B-D-ribofuranose exists in a puckered conformation (C-2' or C-3' is either exo or endo) -the 2' carbon of the ribose ring defines whether nucleic acid isDNA or RNA -positions on the ribose ring denoted with "1" to distinguish them from positions in the nitrogenous base |
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nitrogenous base |
-purines and pyrimidines are heterocyclic (contain carbon and nitrogen) nitrogenous bases -these bases are planar and relatively non-polar -purines and pyrimidines have a specific numbering system to allow easy naming of modified bases -nitrogenous bases link to C1' of the pentose through an N-B-glycosyl bond -purines link through N1, pyrimidines through N9 |
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phosphates |
-nucleotides are phosphorylated nucleosides -a nucleotide is assumed to be phosphorylated at the 5' carbon unless specified otherwise -nucleotides can have 1-3 phosphates on the 5' position |
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nomenclature of nucleosides and nucleotides |
things to look for: 1) what base is present 2) ribose or deoxyribose 3) phosphate or no phosphate
nucleosides-> osine (purine) or idine (pyrimidine) nucleotides-> ylate |
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physiological roles of nucleotides and nucleic acids (energy storage) |
-anhydride linkages in ATP are high energy bonds relative to the ester linkage(130 kj/mole vs 14 kj/mol) -the energy released from hydrolysis of acid anhydride bond used for many biochemical reactions (cellular energy currency) |
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physiological roles of nucleotides (signaling molecules) |
-cyclic AMP, formed from ATP in a reaction catalyzed by adenylyl cyclase, is a common intracellular messenger produced in response to hormones and other chemical signals |
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physiological roles of nucleotides (co-enzyme) |
coenzyme functions in acyl group transfer reactions like those observed in metabolism of lipids |
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differential stability of DNA & RNA |
the 2' hydroxyl group makes RNA susceptible to hydroylisis at the phosphodiester linkage - the greater stability of DNA is consistent with its role was a long term information storage molecule |
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phosphodiester bonds link nucleotides in nucleic acids |
-strands of nucleic acids held together by 3'-5' phosphodiester linkages -common type of linkage in both DNA and RNA -5' end lacks a nucleotide on 5' position; 3' end locks a nucleotide on 3' position -nucleic acid sequences presented 5'-> 3' |
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early clues to the structure of DNA: Chargaff's Rules |
1) base composition of DNA varies from one species to another 2) DNA from different tissues of the same species have the same base composition 3) base composition is stable in a species, does not change with age, nutrition, environment, ect 4) number of 'A' residues equals that of T residues and the number of G resides equals that of C residues Thus, A+ G= T+C
(A)=(T) + (G) = (C) |
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DNA is double stranded |
-two complimentary, anti-parallel strands joined by complementary hydrogen bonding - the sequence of one strand determines the sequence of the other - adenine (A) base pairs with thymine (T) -Guanine (G) base pairs with cytosine (C) |
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discovering the alpha helix |
-in 1953, james watson and francis crick postulated the double helix structure of DNA that explained all the known experimental data and predicted the mechanism for storing and replicating the genetic information
-rosalind franklin and maurice wilkins obtained the x-ray diffraction that showed DNA is a helix and provided the helix periodicity |
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basics of the double helix |
-the two strands are antiparallel and complimentary to one another - DNA has two grooves, a major and a minor group -DNA has a phosphate backbone
1) Adenine forms hydrogen bonds with thymine and guanine forms hydrogen bonds with cytosine 2) Chargaff Rule: - A+G = T+C. number of purines always equals the number of pyrimidines in DNA 3) the A-T + G-C hydrogen bonded pairs are planar and have the same dimensions
- a double helix has two grooves of unequal width; major groove and minor groove -within each groove base pairs are exposed and are accessible to interactions with other molecules -DNA binding proteins can use these interactions to "read" a specific sequence |
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weak forces stabilize the double helix |
1) hydrophobic effects; burying purine and pyrimidine rings in the double helix interior 2) stacking interactions; stacked base pairs form vander waal contacts 3) hydrogen bonds; hydrogen bonding between base pairs (A-T 2; G-C 3) 4) charge-charge interactions; electrostatic repulsion of negatively phosphate groups is decreased by cations and catonic proteins |
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certain DNA sequences adopt unusual structures |
-palindrome sequences are self-complimentary about a point and have the potential to form harpins and cruciform structures
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DNA as a carrier of genetic information |
- as a nucleotide sequence of one strand determines the sequence of the other, each strand can be used as a template to produce the other -the resulting two DNA duplexes will be identical to each other - each strand grows through the addition of incoming nucleotides to the 3' end |
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synthesis of nucleic acids |
-DNA and RNA polymerase are the primary nucleic acid synthesizing enzymes in nature -nucleotide triphosphate are the substrates for synthesis -all polymerases synthesize nucleic acids in the 5' to 3' direction -incoming residues are added to the 3' end of the growing strand -incoming residues are selected to be complimentary to the template strand |
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denaturation of DNA |
-denaturation= complete unwinding and separation of double stranded DNA by heat or chemical agents -melting point (Tm)- temperature at which 1/2 of the DNA has become single stranded -annealing= reforming the double stranded helix from single strands -melting temperatures reflect sequence composition the higher the GC content, the higher the Tm |
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powerful technologies from simple ideas |
-polymerase chain reaction (PCR) takes advantage of the ability for each DNA strand to serve as a template for production of a complimentary strand -also uses heat-stable enzymes to make new DNA -allows for exponential amplification of short regions of DNA very quickly -revolutionized molecular biology, diagnostics and forensics -discovered by kary mullis and resulted in a nobel prize |
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protein-DNA interactions |
-there are many proteins that bind to the DNA in a sequence specific fashion (restriction enzymes, transcription factors) -proteins primarily bind to DNA through the major groove -proteins bind to specific sequences through H-bonds to bases and through electrostatic interactions with the phosphate backbone -different base pairs offer unique hydrogen bind potential |
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sequences have a hydrogen-bond code |
-the specific hydrogen binding pattern in the major groove gives rise to specific interactions with proteins |
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restriction endonucleases |
-restriction endonucleases are enzymes that recognize and cleave specific DNA sequences -bacterial defense mechanism against viral invasion -names reflect origin (Bam HI is the first restriction enzyme characterized from Bacillus amylolique faciens strain H) -host cells protect their own DNA by covalent modification of bases at the restriction site -restriction enzymes utilized for specific manipulation of DNA -restriction enzymes allows for genetic DNA |
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restriction maps |
-developing restriction maps indicates specific cleavage sites in a DNA molecule -panel of restriction enzymes used -sizing gel separates fragments (smallest move fastest) |
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DNA fingerprinting |
-DNA sequence can not be used to identify individuals in a large population -highly variable regions give restriction fragments that are as unique as fingerprints -called restriction fragment length polymorhphisms( RFLP) |
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packing of eukaryotic DNA |
-are small enough that they do not need to be packaged into higher order structures -however, eukaryotic DNA is much longer, and needs to be packaged into higher order structures. overall compaction is more than 10,000 fold -packaging is important not only for condensing the DNA, but also for regulating the expression of genes |
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eukaryotic DNA is packaged in nucleosomes |
histones: the major proteins of chromatin -highly conserved basic (positively charged) proteins
-eukaryotes contain five histone proteins (H1, H2A, H2B, H3 and H4) -positively charged histones bind to negatively charged sugar phosphates ofDNA -histones can be reversibly modified -nucleosome "beads" are DNA-histone complexes on a "string" of double stranded DNA -each nucleosome is composed of: Histones, H2A, H2B, H3, H4 (2 molecules each) to form the core particle Histone H1 (1 molecule) to bind the linear DNA and ~ 200 bp of DNA |
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RNA |
RNA differs from DNA in that: - RNA contains ribose as the pentose sugar rather than deoxyribosse -RNA generally contains uracil rather than thymine -RNA is usually single stranded, however some RNA molecules adopt complex three dimensional structures |
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RNA three dimensional structures |
-stem-loops or hair pins can form from short regions of complementary base pairs stem: based-paired nucleotides loop: non-complimentary nucleotides |
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different kinds of RNA |
rna - an integral part of ribosomes ~ 80% of RNA in cells -transfer RNA (tRNA): carry activated amino acids to ribosomes for proteins synthesis (small molcules) -messenger RNA (mRNA): codes for proteins; contains triplet codons that specify amino acid sequence of a protein |
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new surprises from RNA |
-microRNA (miRNA) are short oligonucleotides that are processed from longer RNA molecules -function in transcriptional and post transcriptional regulation of gene expression -human genome may have up to 1000 microRNAs regulating 60% of human genes miRNA are implicated in a number of important human diseases |
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some basics of genetic information |
-a gene is a segment of DNA containing the information for production of a fanctional biological product -size of a gene may be estimated from the size of the corresponding protein
3 nucleotides= 1 codon = 1 amino acid -genes are contained within the chromosomes -viruses and bacteria have single chromosome -eukaryotes have multiple chromosomes |
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bacterial genome |
-millions of base pairs (1.7 mm length) -closed, circular genome - no internal interruptions (introns) -bacteria may have additional genetic info in the form of plasmids -plasmids are non-chromosomal DNA - many plasmids encode information for resistance to antibiotics -plasmids may be isolated and manipulated |
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eukaryotic genome |
-billios of nucleotides divided among numerous linear chromosomes (each cell has 2 meters of DNA) -different organisms have different numbers of chromosomes -each chromosome has a characteristic set of genes -genome contains highly and moderatly repetetive sequence and unique DNA -genes interrupted by non-coding regions -some organelles may contain additional DNA distinct from that of the nucleus (mitochondria and chloroplasts) |
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introns |
-most eukaryotic genes are interrupted by non-coding intervening sequences (introns) -introns can vary in size, number and position -introns removed from mRNA prior to translation -not in prokaryores |
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complexity of euk. chromosomes |
highly and moderately repetitive sequences - 10% of the genome is composed of millions of repeats of short sequences -20% of the genomes is composed of thousands of repeats of sequences
telomeres: -at each end of linear chromosome to protect DNA during replication |
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Leonard Hayflick |
-working with cells from an aborted fetus, discovered that cells could only grow & divide a set number of times which is believed to be the reason we age and die three important outcomes of his work: -1) insights into longevity -2) a safer, but controversial, way to make vaccines -3) father of biotechnology |
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hayflick's fountain ofyouth |
-that cells grow and divide a set of number of times before dying gives insight into way we age and die -relates to the shortening of chromosomes with each cell divison -the inability to maintain telomere length contributes to accelerated aging |
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hayflick's better way to make vaccines |
-viruses are often weakened by growing them in cells of other animals -there is the danger, however, that these cells may contain diseases that threaten human health -hayflicks fetal cells proved a safe way to grow and weaken viruses (mumps, rubella, chicken pox) -rubella often causes birth defects. as a result, many women who became infected with this diease during pregnancy would abort their babies
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