module 10 Flashcards
what are the physiological roles of nucleotides?
-energy currency (ATP)
-signaling molecules (cAMP)
-enzyme co-factors (NAD, FAD)
-building blocks of nucleic acids
what are the physiological roles of nucleic acids?
-genetic information (DNA, RNA)
-all stages of protein synthesis (DNA, mRNA, tRNA, rRNA)
what are the structural features of nucleotides?
all share three components:
-ribose sugar (ribose or deoxyribose)
-nitrogenous base (purine or pyrimidine)
-phosphate(s)
what is ribose and deoxyribose?
-all nucleotides contain a ribose backbone
-ribose within nucleotides is in a cyclized form (b-D-ribofuranose)
-for DNA, 2’ carbon of the ribose is in the deoxy form
-RNA contain ribose; DNA contains deoxyribose
what are nitrogenous bases?
-two families; purines (two ring system) and pyrimidines (single ring)
-nitrogenous bases are planar and relatively non-polar
what are the five standard nitrogenous bases?
-adenine, guanine and cytosine are in both RNA and DNA
-the fourth base differs; DNA has thymine and RNA has uracil
how to nitrogenous bases link to ribose?
-through N-glycosidic bonds
-all bases link to C1 of the sugar
-in purines, N bond is to N9 of base
-in pyrimidines, N bond is to N1 of base
what is nucleotides vs nucleosides?
-nucleotides and nucleosides differ in whether they are phosphorylated at the C5 position
-nucleotides have 1-3 phosphorylates on the 5’ position: one(NMP), two (NDP), three (NTP)
-nucleotides are phosphorylated nucleosides
what is an alternative method for naming nucleotides?
-to specify the number and position of the phosphoryl groups
-for ex: adenosine 5’-triphosphate (ATP) rather than adenylate
what is the nomenclature of nucleotides and nucleosides?
- which nitrogenous base is present (base name)
- whether the sugar is ribose or deoxyribose (deoxy prefix)
- whether there are phosphoryl group (suffix of osine from nucleosides, ylate for nucleotides)
what are the two physiological roles of nucleotides?
-energy transfer
-signal transduction
what is energy transfer of nucleotides?
-anhydride linkages in ATP are high energy bonds
-the energy released from hydrolysis of these bonds drives many biochemical reactions
what is signal transduction of nucleotides?
-cyclic AMP, formed from ATP in a reaction catalyzed by adenylyl cyclase
-common intracellular messenger produced in response to hormones
what bonds join nucleotides in nucleic acids?
-nucleotides form linear nucleic strands through 3’-5’ phosphodiester linkages
-these are identical in DNA and RNA
-identical, independent of the nucleotides being joined
-the strand of sugar linked by phosphodiester bridges is called the backbone of nucleic acid
what is the sequence information within nucleic acids?
-it is the sequence of bases that uniquely characterizes a nucleic acid
-nucleic acid strands have a direction and their sequence are presented 5’->3’
-sequence of bases is a form of linear information (blueprint)
what is the structure of ribonucleic acid (RNA)? how does it differ from DNA?
differs from DNA in that:
-RNA contains ribose rather than deoxyribose
-RNA contains uracil rather than thymine
-RNA is single-stranded but can adopt complex 3-dimentional structures
what is rRNA?
ribosomal RNA
-an integral part of ribosome
-80% of RNA in cells
what is tRNA?
transfer RNA
-carry activated amino acids to ribosome for protein synthesis (small molecules 73-95 nucleotides long)
what is mRNA?
messenger RNA
-code for proteins
-contains triplet codons that specify the amino acid sequence of a protein
what is miRNA?
micro RNA
-are short oligonucleotides (22-24 nts in length)
-function in transcriptional and post-translational regulation of gene expression
what is the difference in stability between RNA and DNA?
-the 2’ hydroxyl group of RNA increases its susceptibility to base hydrolysis at the phosphodiester linkage (breaks down easier)
-the greater stability of DNA is consistent with its role as a long term information storage molecule
who discovered the double helix?
-james watson and francis crick postulated the double helix structure of DNA in 1953
-this model explained all the known experimental data and predicted the mechanism for storing and replication the genetic information
who actually discovered the double helix?
-rosalind franklin and maurice wilkins obtained the X-ray diffraction data that showed that DNA is a helix
-their efforts set the stage for watson and crick
what is the basic of double helix?
-two helical DNA strands coiled around a common axis forming a right-handed double helix
-strands run in opposite directions and complimentary to eachother
-sugar-phosphate backbones are on the outside of the helix, nitrogenous bases are on the inside
-base pairs are perpendicular to helix axis
-Watson-crick base pairing matches a purine with a pyrimidine to give a constant helix diameter
what is the base pairing in the double helix?
-adenine (A) base pairs with thymine (T)
-guanine (G) base pairs with cytosine (C)
-the specificity of Watson-Crick base pairing is largely determined by the hydrogen bonding groups of the nitrogenous bases
-the A-T and G-C hydrogen bonded pairs are planar and have the same dimensions
what is chargaff’s rule?
A+G=T+C
-number of purines equals the number of pyrimidines in duplex DNA
what are the weak forces that stabilize the double helix?
-hydrophobic effects
-stacking interactions
-hydrogen bonds
-charge-charge interactions
what are the hydrophobic effects and stacking interactions in the double helix?
-hydrophobic effects; burying the purine and pyrimidine rings in the interior of the helix
-stacking interactions: stacked base pairs form van der waals contacts
what are the hydrogen bonds and charge-charge interactions in the double helix?
-hydrogen bonds; hydrogen bonding between base pairs
-charge-charge interactions; electrostatic repulsion of negatively charge phosphate groups is decrease by cations (ex; Mg2+) and cationic proteins
are G-C stronger or A-T?
-G-C; more stable because it has 3-H bonds
-A-T only has 2
many proteins bind DNA in a ____________
sequence-specific fashion (restriction enzymes, transcription factors)
what are the major and minor groups in double helix?
-two grooves of unequal width (and depth): major and minor
-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
what is DNA fingerprinting?
-treating DNA from different individuals with restriction enzymes will break DNA into pieces
-due to differences in genome sequences, DNA from different people will break down into a different number of fragments and fragments of different sizes
-highly variable regions give restriction fragments that are as unique as fingerprints and can be used to identify individuals in a large population
-restriction fragment length polymorphisms (RFLP)
how are restriction endonucleases used as a defense?
-bacterial defense mechanism against viral invasion
-host cells protect their own DNA by covalent modification of bases at the restriction site (ex: methylation)
what are restriction endonucleases? and restriction enzymes?
-recognize and cleave specific DNA sequences
-restriction enzymes cut at palindrome sequences
-names of restriction enzymes reflects origins
-restriction enzymes can be used as “molecular scissors” for manipulation of DNA
what are complimentary strands in duplex DNA?
-duplex DNA contains two complimentary, anti-parallel strands
-because the strands are complimentary, the sequence of one strand determines the sequence of the other strand
how is DNA a carrier of genetic information?
-the complimentary nature of the strands is important for replication and repair
-as the 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
what is denaturation and annealing of DNA?
-denaturation: complete separation of double-stranded DNA by heat or chemical agents (cooperative process, once starts whole thing)
-annealing: reforming the double-stranded helix from single strands
-melting point (Tm), temperature at which half the DNA has become single stranded
-melting temps reflect the sequence compositions: the higher the GC content, the higher the Tm
what is the synthesis of nucleic acid?
-DNA and RNA polymerases are the primary enzymes for synthesizing nucleic acid
-nucleotide triphosphate are the substrates for synthesis
-all polymerase 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
what is polymerase chain reaction (PCR)?
-takes advantage of the ability for each DNA strand to serve as a template for production of a complimentary strand
-uses heat-stable enzymes to make new DNA
-allows for exponential amplification of short regions of DNA very quickly
-PCR revolutionized molecular biology, diagnostics and forensics
-discovered by Kary Mullis and resulted in a nobel prize
why are is packaging of eukaryotic DNA more ordered?
-the amount of eukaryotic DNA necessitates its packaging into higher order structures
-at first level of DNA packing involves formation of nucleosomes
-nucleosome “beads” are DNA-histone complexes on a “string” of double-stranded DNA
what are histones?
-DNA packaging proteins
-highly conserved and positively charged
-are reversibly modified to regulate their interaction with DNA
what are the five histone proteins?
H1 (not in core), H2A, H2B, H3, H4
-nucleosome composed of two molecules of each H2A, H2B, H3, H4 and 146 base pairs of DNA
-H1 binds the region of linker DNA
what is a gene? what has many chromosomes?
-genes are contained within the chromosomes
-viruses and bacteria have single chromosome
-eukaryotes have multiple chromosomes
what is the basic of genetic information?
-a gene is a segment of DNA containing the information for production of a functional biological product (like a protein)
-size of a gene may be estimated from the size of corresponding protein
3 nucleotides=1 codon=1 amino acid
what is bacterial genome?
-millions of base pairs
-closed, circular genome
-no internal interruptions (introns)
-plasmids
bacteria may have additional genetic info in the form of ___________
PLASMIDS
-non-chromosomal DNA
-many plasmids encode information for resistance to antibiotics
-plasmids may be isolated and manipulated (produce insulin)
how does eukaryotic genome differ in organisms?
-billions of nucleotides divided among numerous chromosomes
-different organisms have different number of chromosomes
-each chromosome has a characteristic set of genes
chromosomes are linear, which presents a problem for replicating the ends of chromosomes
-ends of chromosomes containing repeating sequences called telomeres (dont code for anything)
what is special about eukaryotic genome?
-genes interrupted by non-coding regions: introns
-some organelles may contain additional DNA distinct from that of the nucleus: mitochondria and chloroplasts (used to be independent organisms)
what are introns and exons?
-most eukaryotic genes interrupted by non-coding intervening sequences (introns)
-exons contain protein-coding information
-introns vary in size, number and position
-introns removed from mRNA prior to translation
what is a functional advantage of introns?
-multiple mRNAs of different sequences can be generated from a single gene
what is epigenetics?
-refers to functionally relevant changes to the genome that do not involve c change in the nucleotide sequence
-epigenetic changes can alter patterns of gene expression (and associated phenotypes) without altering the underlying DNA sequence (ex: mice and smell)
what does conventional genetics suggest?
-suggests individuals inherit genetic material which they pass to their offspring; that we are carriers rather than editors of genetic info
-in response to environmental influences, our genetic material can be covalently modified
-such modifications include methylation of cytosine residues
-these modifications of DNA can be heritable (passed to offspring)
what is molecular biology and the modern world?
-comparing genomes from different species, as well as individuals from within a species, can provide insight into phenotypic differences
-for example, genome sequencing of wolves and dog revealed sequence differences resembling william’s syndrome
-genomic approaches enable better prediction, understanding and treatment of disease (personalized medicine)
genetic manipulation also allows for creation of __________________
novel organisms with desirable traits
-GMO crops
-Low fat pigs
-glow-in-the dark pets
