Polymers {nucleic acid}| can have nucleotides connected by phosphodiester bonds. Nucleic acids are 10% of body dry weight.
structure
Phosphodiester-bond phosphate groups link pentose fifth carbon to next-pentose third carbon, called 5' to 3' linkage. Nucleotide nitrogenous bases are perpendicular to phosphodiester bond chain. Nucleotide ribose rings are parallel to phosphodiester bond chain. Phosphodiester bonds have no rotation. Nucleic acids have no branches.
information
Molecules encode genetic information in base sequences and replicate using strands as templates. DNA bases are adenine A, guanine G, cytosine C, and thymine T. DNA codes instructions for replication, transcription, and translation, to initiate and grow tissues and organs during development, to react to cell environment during development and in life, and to cycle over hours, days, months, and years.
Repressors typically form at constant rate {constitutive synthesis}.
If A hydrogen-bonds to T by conventional Watson-Crick pairing, another T can hydrogen-bond to A {Hoogsteen pairing}. If G hydrogen-bonds to C by conventional Watson-Crick pairing, another C can hydrogen-bond to G.
Bacteriophage, plasmids, and chromosomes have mobile genetic elements {replicon}.
Mutations {nonsense mutation} can make stop codons from non-stop codons.
Pyrimidine can substitute for pyrimidine, or purine can substitute for purine {transition, nucleotide}.
Pyrimidine can substitute for purine, or vice versa {transversion}.
DNA has two linear polynucleotide strands hydrogen-bonded together to form twisted ladder shape {double helix}|.
hydrogen bonds
Nitrogenous bases adenine and thymine in DNA or uracil in RNA can link by two hydrogen bonds, on aromatic-ring side away from pentose and phosphate, if aromatic-ring planes are parallel, with one inverted. Nitrogenous bases cytosine and guanine can link by three hydrogen bonds, on aromatic-ring side away from pentose and phosphate, if aromatic-ring planes are parallel, with one inverted.
ladder
Strands are pentose sugars and phosphodiester bonds and make ladder sides. Strand bonds have opposite direction. Nitrogenous-base and hydrogen-bond-link planar aromatic rings are ladder rungs. Because tetrahedral chemical bonds form at angle, ladder twists and is helical.
Ribose sugar (RNA) or deoxyribose sugar (DNA), phosphate group, and nitrogenous-base adenine, guanine, cytosine, and thymine in DNA or uracil in RNA can link to other bases with phosphodiester bonds to make sequences {base sequence} {DNA sequence}.
Two adjacent nucleic-acid polymers {anti-parallel strands} can have opposite bond direction.
Hydrogen bonding between adenine and thymine in DNA or uracil in RNA, or between guanine and cytosine {base pairing}, links two DNA strands or DNA and RNA strands.
Hydrogen bonds can form between adenines and thymines in DNA or uracils in RNA, and between cytosines and guanines {complementary bases}.
polymer chain {strand, DNA}.
Topoisomerase and gyrase affect DNA coiling and can add to or subtract from helix angle {supercoiling}. Circular DNA has negative supercoiling.
Molecules {effector} can help RNA polymerase bind to DNA or help DNA strands separate.
Histone H1 connects DNA beads {nucleosome}. Nucleosomes have 200 bases, two H2A histones, two H2B histones, two H3 histones, two H4 histones, and other regulatory proteins.
Proteins {catabolite activator protein} (CAP) can bind to cAMP to form cAMP-CAP complexes, which bind to promoter for gene that breaks down lactose and galactose. If glucose is low, cAMP builds up.
Enzymes {modification enzyme} can methylate DNA at special sites.
Enzymes {topoisomerase} {gyrase} can affect DNA coiling and can add to or subtract from helix angle for supercoiling.
Cells can copy DNA double helices {replication, DNA}| {DNA replication}.
separation
Replication protein uses ATP to separate DNA nucleotide chains, by breaking hydrogen bonds between nitrogenous bases, so DNA unwinds. Replication protein starts at one DNA location and separates chains in both directions simultaneously. Single-strand binding protein keeps DNA strands apart.
pairing
RNA primer binds to operon first part and provides starting molecule to which DNA polymerase can add paired deoxyribonucleotides. Free deoxyribonucleotides hydrogen-bond with DNA-strand deoxyribonucleotides: A and T, or C and G.
linking
DNA polymerase links deoxyribonucleotides by phosphodiester bonds between pentoses, at rate 10 nucleotides per second. Pyrophosphate leaves. Copying error rate is only 10^-9. Exonuclease checks new strand at new deoxyribonucleotide pairs to see if deoxyribonucleotides paired correctly. Exonuclease removes wrongly paired nucleotides. Second exonuclease checks if double helix is correct and unwinds DNA if DNA double helix is not correct.
ligating
DNA ligase joins DNA strand ends. Both new strands link from ribose fifth carbon to next-ribose third carbon. One strand is continuous. One strand has Okazeki fragments. DNA ligase connects Okazeki fragments.
result
Replication makes two double helices, each with one strand of old double helix and one new strand {semiconservative replication, DNA}.
Replication protein uses ATP to separate DNA nucleotide chains, by breaking hydrogen bonds between nitrogenous bases {replication fork}, and so unwinds DNA.
Enzymes {replication protein} can use ATP to separate DNA nucleotide chains, by breaking hydrogen bonds between nitrogenous bases, and so unwind DNA.
Enzyme {single-strand binding protein} keeps DNA strands apart.
RNA primer binds to operon first part and provides a starting molecule for enzymes {DNA polymerase} that synthesize DNA from existing nucleic acid. It adds paired deoxyribonucleotides to DNA template strand and links them to make new strand.
Enzymes {DNA ligase} can join DNA strand ends and can rejoin broken DNA.
One strand forms in 1000-nucleotide segments {Okazeki fragment}. DNA ligase connects Okazeki fragments.
DNA, enzymes, and energy can make RNA {transcription, DNA}| {DNA transcription}.
process: strand separation
RNA polymerase binds to DNA double helix locations {promoter, DNA}. RNA polymerase separates DNA strands for one complete double-helix turn, little more than three nucleotides. RNA polymerase separates two deoxyribonucleotide chains by breaking hydrogen bonds, starting at one double-helix point and going in one direction only. Transcription uses DNA strand lying in third carbon to fifth carbon direction. Direction that chains separate is opposite to chain phosphodiester-bond direction.
process: polymerase
Eukaryotic 5.8S, 18S, and 28S rRNA use RNA polymerase I. Eukaryotic mRNA and snRNA use RNA polymerase II. Eukaryotic 5S rRNA and tRNA use RNA polymerase III. RNA types have different promoters. RNA polymerase does not need primer.
process: matching
Free ribonucleotides in solution hydrogen-bond to matching chain deoxyribonucleotides. Adenine and thymine hydrogen-bond. Adenine and uracil hydrogen-bond. Guanine and cytosine hydrogen-bond. Error rate is 10^-4 to 10^-5.
process: linking
Using phosphodiester bonds, RNA polymerase links ribonucleotides to make RNA sequence. Phosphodiester bonds invert compared to original-DNA-strand phosphodiester bonds. Nucleotides link at rate 50 nucleotides per second.
process: termination
RNA transcription terminates just after poly-uracil region, using RNA chain-terminating proteins. Using rho protein, region near tRNA end curves around to hydrogen bond with itself using paired A and U or C and G ribonucleotides to make a hairpin loop.
process: separation
RNA polymerase leaves DNA, and RNA separates from DNA. Double helix reforms.
product
Transcription makes one rRNA, tRNA, or mRNA strand. In higher animals, mRNA intron regions can make protein, and exons do not. Introns can be separate or overlap.
blocking
Actinomycin can block transcription by sliding between and separating guanines and cytosines. Mushroom poisons block RNA polymerase from making histone protein.
DNA
DNA operons have gene for repressor, promoter where RNA polymerase binds, operator where repressor can bind and inducer can remove repressor, and one or more genes, typically in that order. RNA or protein binding at regulatory regions controls RNA amount.
DNA: repressor
Repressor prevents RNA polymerase from binding at promoter, because operator is next to promoter. Bacteriophage lambda has repressor-gene {cro gene} repressor. Cro and other repressors typically are dimers that have alpha-helix binding in DNA-helix major groove. Repressors can affect several transcriptions {trans-acting control}.
DNA: promoter
Promoters affect downstream transcription {cis-acting control}. Catabolite activator protein binds to cAMP to make cAMP-CAP complexes, which bind to promoter for lactose and galactose breakdown genes. If glucose is low, cAMP builds up.
Enzymes {RNA polymerase} can bind to DNA double-helix promoters.
Three nucleotides {termination sequence} end transcription.
Special enzymes {nuclease} can modify free-floating RNA. Nuclease adds methyl groups to nucleotides. Nucleases make other modified bases, such as inosine. In eukaryotes, nuclease adds adenines to mRNA 3' end to stabilize RNA and protect 3' end. In eukaryotes, nuclease adds nucleotides to mRNA to protect 5' end.
Endonuclease can split long RNA into functional pieces. For example, nuclease divides chain that contains all rRNA types into different ribosomal RNAs. Photolyase restores UV-induced dimers, using light.
Using enzymes {rho protein}, region near tRNA end curves around to hydrogen bond with itself, using paired A and U or C and G ribonucleotides.
Proteins induced from other sites control RNA transcription {transcriptional control}.
E. coli tryptophan operon (trp) has five genes, but, if tryptophan is at high levels, only short transcription {leader, DNA} can happen {attenuation}. Leader makes hairpin that stops transcription. If tryptophan is low, full operon transcribes, because different hairpin has few tryptophans.
mRNA, rRNA, and tRNA together can make protein {translation, RNA}| {RNA translation}.
template
mRNA nucleotide sequence codes for protein. mRNA is 2% of all RNA.
process
AUG or GUG codon, which codes for methionine, always starts mRNA. mRNA attaches to both smaller ribosome rRNA and larger ribosome rRNA. Ribosomes have two slots, one {peptidyl site} for current amino acid and one {aminoacyl site} for amino acid to add. Three mRNA nucleotides are in slots and lie in 5' carbon to 3' carbon direction.
process: tRNA
tRNA has amino acid on one side tip and three nucleotides on other side tip. Nucleotide tip can be complementary to three mRNA nucleotides in one slot. tRNA with complementary tip hydrogen-bonds its three tip nucleotides to the three slot nucleotides and brings one amino acid into ribosome slot. Streptomycin prevents tRNA attachment to first site.
process: peptide bonding
When amino acids are in both slots, ribosomal enzymes and GTP-protein complex join both amino acids by one peptide bond. Amino acid adds to protein chain in one second.
process: shift
Then ATP shifts both amino acids one slot. Messenger RNA also slides over one slot, leaving one slot empty. Diphtheria toxin inhibits translocation enzyme.
process: repeat
Empty slot fills with tRNA, amino acid comes in, and enzymes make peptide bond.
process: termination
The last three mRNA nucleotides are UAG, UAA, or UGA and do not pair with any tRNA tip, so slot stays empty and terminates mRNA coding. Puromycin terminates amino-acid chain early.
process: release
Enzyme releases protein and mRNA from ribosome.
modification
Enzymes can modify free-floating proteins after translation. Enzymes can remove formyl group from methionine. Enzymes can remove amino acids from amino end. Enzymes can form disulfide bonds. Enzymes can add hydroxyl to side chain. Enzymes can add sugar. Enzymes can add phosphate. Enzymes can split protein into functional parts.
Three DNA or RNA nucleotides {codon} can code for amino acids. Up to six codons can code for same amino acid. Codons coding for same amino acid have same first two bases. Coding redundancy can minimize errors. Codons are the same for all species, except for mitochondria. Mitochondrial DNA uses different genetic code for different groups.
Before initiation sites, mRNA has a purine-rich ribosome-binding site {Shine-Dalgarno sequence}, which matches rRNA molecule site. With extra ribosomal proteins, some bind to Shine-Dalgarno site and prevent or slow protein synthesis.
mRNA sites control translation rate and protein synthesis {translational control}.
Genes {suppressor gene} can make tRNA with an anticodon that matches stop codon but adds an amino acid. If DNA mutation makes a stop codon, such tRNAs allow cell to continue reading mRNA. Suppressor genes suppress such mutations.
Bases A, C, G, and T can attach to N-(2-aminoethyl)-glycine {peptide nucleic acid} (PNA). PNAs have no electric charge, are more stable, and bind better to DNA or RNA than oligonucleotides do.
triplex
If PNA is all C or T and so is homopyrimidine, PNA strand can lie in double-stranded-DNA major groove and bind to double-stranded DNA {PNA-DNA triplex}. Two PNA strands can push away a DNA strand, which forms a loop, and make a triple-strand {triplex invasion}. PNA strand can bind to DNA strand, displacing but not removing other DNA strand {duplex invasion}. Two PNA strands can bind to opposite DNA-strand regions, displacing but not removing DNA strands {double duplex invasion}.
DNA {TNA} can have different sugar than ribose.
DNA {xDNA} can be less likely to mutate.
Combining adenosine and three phosphate groups {adenosine triphosphate} (ATP) can carry energy in phosphate bonds. Magnesium or calcium ions attach to phosphate to make ATP have neutral charge. ATP decreases noradrenaline release from adrenergic nerves and acetycholine release from cholinergic nerves.
Combining guanine and three phosphate groups {guanidine triphosphate} (GTP) can carry energy in phosphate bonds. Magnesium or calcium ions attach to phosphate to make ATP have neutral charge.
Organic molecules {nucleotide}| can have a nitrogenous base and a phosphate group bound to a pentose sugar.
location
Mitochondria have nucleotide synthesis.
types
Nitrogenous base determines nucleotide type: purine or pyrimidine. Molecule can contain ribose sugar (RNA) or deoxyribose sugar (DNA). Nucleotides make RNA, DNA, ATP, NAD, FAD, CoA, and cyclic AMP.
nucleic acid
Nucleotides can link to other bases with phosphodiester bonds. Adenine, guanine, cytosine, and thymine are in DNA. Adenine, guanine, cytosine, and uracil are in RNA.
history
Levene and Bass isolated uridylic acid [1931].
Ribonucleotides make higher nucleotides by adding hydrogen atom using NADPH {deoxyribonucleotide} (DNA). Adenylate makes deoxyadenylate. Guanidylate makes deoxyguanidylate. Cytodylate makes deoxycytodylate. Uridylate makes deoxyuridylate. Deoxyuridylate methylation makes thymidylate. Thymine deoxyribonucleotide is stable and is in DNA, instead of uracil deoxyribonucleotide. Uracil ribonucleotide is in RNA, rather than thymine ribonucleotide, because thymine ribonucleotide easily changes into cytosine, but uracil ribonucleotide does not change.
Nucleotides {ribonucleotide} can have hydroxyl group at pentose-sugar second carbon.
Adenine and guanine {purine}| are double-ring nitrogenous bases synthesized from glycine, aspartate, glutamine, carbon dioxide, or methyl groups. Purine breaks down to urate.
Cytosine, thymine, and uracil {pyrimidine, nucleic acid}| are single-ring nitrogenous bases synthesized from carbamoyl phosphate and aspartate, which make carbamylaspartate, which becomes dihydroorotate, which NAD+ oxidizes to orotic acid, making pyrimidine ring. Orotic-acid nitrogen binds to ribose-ring first carbon by pyrophosphate, to make uridylate. Uridylate transamination can make cytidylate.
Nucleotides {nucleoside} can lose a phosphate group.
Nitrogen-containing molecules {base, nucleic acid} {nitrogenous base} can be purine or pyrimidine: adenine, guanine, cytosine, thymine in DNA, or uracil in RNA.
Rather than uracil, similar nucleotides {thymine} can be in DNA, because cytosine can deaminate to become uracil and so change DNA template too easily. If DNA cytosine deaminates, enzymes remove new uracils and replace with cytosine to repair chain.
Bonding uracil and three phosphate groups {uridine triphosphate} (UTP) can carry energy in phosphate bonds. Magnesium or calcium ions attach to phosphates, so ATPs have neutral charge.
Nucleic acids {ribonucleic acid}| (RNA) can have ribonuceotides. Hydroxyl groups at pentose-sugar second carbons make RNA chains unable to lie anti-parallel to each other for more than several bases, so RNA cannot make double helices. RNA can double back on itself to make hairpin loops, with short double strand at neck.
types
Ribose-nucleotide nucleic acid is for protein translation (mRNA), codon translation (tRNA), protein-synthesis sites (rRNA), and intron excision from RNA (snRNA). Specific 22-nucleotide fragments of RNA have regulatory activity.
genes
E. coli has 50 to 200 RNA genes, as do other organisms. Over 95 percent of eukaryotic RNA encodes rRNA, mRNA, and tRNA, not proteins.
RNA {messenger RNA}| (mRNA) can hold information for making proteins. mRNA is 5% of RNA and has short life. mRNA is ribonucleotide chain copied from gene.
Two or three globular RNAs {ribosomal RNA}| (rRNA) can make ribosomes for protein synthesis. rRNA is 80% of RNA. rRNA has three or four long-lived types. Ribosomes look like snowmen, with two main rRNA globules beside each other. Globular rRNAs have two adjacent binding sites for tRNAs and mRNA. Ribosomes use many proteins.
RNA {transfer RNA}| (tRNA) can transfer amino acids from cytoplasm to ribosomes, to make protein chains. tRNA is 15% of RNA.
structure
tRNA is 75 bases long and has three-leaf-clover shape. tRNA has modified bases in three locations to make tRNA hydrophobic and curve back on itself. Middle-clover-leaf tip has three ribonucleotides, which differ for different amino acids. Clover-stem tip has three ribonucleotides that bind an amino acid. Different tRNAs bind different amino acids. There are more than 40 different tRNAs.
number
Different tRNA amounts differ greatly. Low amounts can limit protein production.
codon
RNA has three-nucleotide codons. tRNA has three tip nucleotides {anticodon}. Anticodon binds to first two codon nucleotides exactly but can bind inexactly to third codon nucleotide {wobble}.
mitochondria
Mitochondria have only 22 tRNAs and use only first two codon bases.
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Date Modified: 2022.0225