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Basic Sciences Biochemistry DNA & RNA

4 questions

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A nucleotide is made up of a nitrogenous base, 5-carbon sugar, and one or more phosphate groups. A nucleoside is just a nitrogenous base and 5-carbon sugar, no phosphate groups.

less  The deoxyribonucleic acid (DNA) 5-carbon sugar is 2-deoxy-ribose and

the DNApyrimidines are cytosine and thymine; DNA does not use uracil. The ribonucleic acid (RNA) 5-carbon sugar is ribose and the RNA pyrimidines are cytosine and uracil; RNAdoes not use thymine.

 Guanine has a ketone. Thymine has a methyl. Deamination of cytosine makes uracil.

 The nitrogenous pyrimidines (1 cyclic ring, see image) are Cytosine, Thymine, andUracil. Mnemonic: CUT the PY (pie).

 The nitrogenous purine bases (2 cyclic rings, see image) are Adenine and Guanine. Mnemonic: Pur e A s G old.

When dsDNA is formed, adenine pairs with thymine, and guanine pairs with cytosine. less  G-C pair has 3 H-OH bonds

 A-T pair has 2 H-OH bonds

 The adenine-thymine (A-T) bond consists of 2 hydrogen bonds; the guanine- cytosine (G-C) bond consists of 3 hydrogen bonds. A higher content of G-C bond increases the melting point of DNA.

De novo synthesis of both purines and pyrimidines involves PRPP (Phosphoribosyl pyrophosphate)

Purine synthesis: requires glycine, aspartate, and glutamine

less  PRPP + glutamine + aspartate + glycine = IMP

 IMP is converted into the ribonucleotides AMP or GMP. These can be converted to ADPand GDP by adenylate and guanylate kinases, respectively.  Nucleoside diphosphate kinase, which has broad specificity,

convert ADP and GDP to ATPand GTP.

Pyrimidine synthesis: orotic acid (aka orotate) + PRPP = OMP

 OMP → UMP → UDP. UMP + glutamine → CDP (ribonucleotides). dTDP is made from dUMP.

Last step of nucleotide synthesis: ribonucleotides (ADP, GDP, UDP, CDP) are converted toDNA (deoxyribonucleotides) by ribonucleotide reductase

Clinical Correlate: Inability to convert orotic acid to UMP → orotic aciduria.

less  Autosomal recessive defect in UMP synthase (a bifunctional enzyme,

including orotic acid phosphoribosyltransferase and orotidine-5’-phosphate decarboxylase).

 Presents with megaloblastic anemia that is not responsive to iron, folate or vitamin B12supplementation. If not corrected, causes developmental/intellectual impairment.

Treated with lifelong uridine supplementation.

Transcription

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Basic Sciences Biochemistry DNA & RNA

5 questions

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Called "transcription" because both DNA and RNA are nucleic acids, as opposed to translation, in which the genetic code in nucleic acids is translated into amino acids

3 types of RNA: ribosomal RNA, messenger RNA, and transfer RNA

less  rRNA is still transcribed from DNA, but isn’t translated – instead, it plays

several key roles in ribosomes, including recognition and positioning of tRNA and mRNA.

It also catalyzes peptidyl transferase activity of 60S subunit.  rRNA comprises 80% of eukaryotic RNA

 mRNA is the transcript of DNA

 tRNA has 1 amino acid bound to its 3’ end; matches amino acids with mRNA codons during translation

Start codon: AUG (or rarely GUG) AUG inAUGurates protein synthesis

less  In eukaryotes, AUG → Met. In prokaryotes, AUG → formylMet (fMet)

Stop codons: UGA, UAA, UAG UGA=U Go Away

UAA=U Are Away UAG=U Are Gone

less  Also known as nonsense codons since mutations into these codons cause

chain termination

Transcription is controlled via 4 cis-acting elements: promoters, enhancers, silencers/operators, and response elements

less  Promoters are where RNA polymerase and transcription factors (TFs) bind to

initiate transcription (often located 25 to 50 bases upstream of the gene, and often contains A-T rich sequences of TATA or CAAT boxes)

 Enhancers also bind TFs, and can significantly ↑ the rate of transcription (can be located upstream, downstream, or a distance from the gene)

 Silencers repress transcription when repressors, a subset of TFs, bind to them (known as operators in prokaryotes)

 Response elements bind specific TFs (e.g. heat shock response element, estrogen response element) and modulate transcription

Eukaryotic RNA polymerases I, II, and III

less  RNAP I transcribes rRNA (most abundant)

 RNAP II transcribes mRNA

α-amanitin (deadly toxin found in certain mushrooms): inhibits RNAP II → liver damage when ingested

 RNAP III transcribes tRNA (shortest RNA)

 "Rampant, Massive, Tiny": RNAP I transcribes the most abundant

type rRNA, RNAP II transcribes the longest type mRNA, RNAP III transcribes the shortest type tRNA

Prokaryotic RNAP is made of 5 subunits and can synthesize all the 3 kinds of RNA RNA polymerases do not require primers

less  Prokaryotic RNAP binds directly to promoters

 Eukaryotic RNAP’s require TFs (pre-initiation complex) to direct transcription

tRNA

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Basic Sciences Biochemistry DNA & RNA

4 questions

Short, between 75 and 90 nucleotides

Secondary structure: cloverleaf. Tertiary structure: "L" shaped.

less  The "bottom" of the cloverleaf houses the anti-codon, which pairs with mRNA

codons when brought together in a ribosome

The 3’ end has a CCA sequence that is recognized by aminoacyl-tRNA synthetase, the enzyme responsible for "charging" the tRNA with an amino acid

less  In the 3D image, the CCA is shown in orange

Aminoacylation (aka "charging") covalently bonds an amino acid to the 3’ end of the tRNA

less  There is 1 aminoacyl-tRNA synthetase per amino acid, so each aminoacyl-

tRNA synthetase recognizes multiple tRNAs

(Remember the genetic code is degenerate so there are several different tRNAs that recognize codes for the same amino acid)

 Aminoacylation also gives a phosphate group (hence "charged") that later provides energy for peptide bond formation; aminoacylation converts ATP → AMP (2 phosphate bonds)

Aminoacyl-tRNA synthetases proofread before & after charging; if the wrong amino acid is on the tRNA, the covalent bond is hydrolyzed

Wobble hypothesis: Prokaryotes typically express 40-50 tRNAs, but there are 61 codons → the 3rd position isn’t as critical to pairing between the 3’ codon of mRNA and the 5’ anticodon of tRNA and is allowed some "wobble"

Purine Salvage