Biosynthesis of Nucleotides and Gene Expression

What are the atom sources of carbon and nitrogen that contribute to purine ring formation?

The atom sources for purine ring formation include carbon from bicarbonate, aspartate, and formate, and nitrogen from glutamine and aspartate.

What are the atom sources of nitrogen that contribute to pyrimidine ring formation?

The atom sources for pyrimidine ring formation include nitrogen from carbamoyl phosphate and aspartate.

What are the enzymes and major mechanisms that control the biosynthesis of nucleotides?

Key enzymes include ribonucleotide reductase (RNR) for deoxyribonucleotide synthesis, amidotransferases for purine and pyrimidine synthesis, and nucleoside phosphorylase for degradation.

How is deoxyribonucleotide generated?

Deoxyribonucleotides are generated from ribonucleotides through the action of ribonucleotide reductase (RNR), which reduces the ribose sugar.

What are key facts about ribonucleotide reductase (RNR)?

RNR is responsible for converting ribonucleotides to deoxyribonucleotides, is regulated by various mechanisms, and has different forms for different nucleotide substrates.

What is the difference between the salvage pathway and the degradation pathway of nucleotides?

The salvage pathway recycles nucleosides back to nucleotides using enzymes like transferases and uridine phosphorylase, while the degradation pathway breaks down nucleotides to eliminate excess nitrogen, producing uric acid or ammonia.

How is one-carbon metabolism used in nucleotide biosynthesis?

One-carbon metabolism provides carbon units for purine and pyrimidine ring formation, primarily through the donation of formate during the synthesis pathways.

What are the differences between CPSI and CPSII?

CPSI is involved in the urea cycle and requires N-acetylglutamate as an activator, while CPSII is involved in pyrimidine biosynthesis and is regulated by ATP and UTP.

What is the role of phosphoribosyl amine in nucleotide biosynthesis?

Phosphoribosyl amine is a key intermediate in the de novo synthesis of purines, leading to the formation of inosine monophosphate (IMP).

What is the significance of PRPP in nucleotide metabolism?

PRPP (phosphoribosyl pyrophosphate) is a crucial precursor in both purine and pyrimidine nucleotide biosynthesis, serving as a ribose sugar donor.

What is the function of nucleoside phosphorylase in nucleotide degradation?

Nucleoside phosphorylase breaks glycosidic bonds in nucleosides, releasing nitrogen and producing free bases for further degradation.

What is the role of xanthine oxidase in nucleotide degradation?

Xanthine oxidase is involved in the degradation of purines, converting hypoxanthine to xanthine and then to uric acid, which is excreted in urine.

What are the three types of RNA polymerases and their functions?

RNA polymerase I synthesizes rRNA, RNA polymerase II synthesizes mRNA, and RNA polymerase III synthesizes tRNA and other small RNAs.

What is the TATA box and its significance in transcription?

The TATA box is a consensus sequence in the promoter region of genes that helps initiate transcription by RNA polymerase II.

What is the central dogma of molecular biology?

The central dogma describes the flow of genetic information from DNA to RNA to protein.

What are the stages of protein synthesis?

The stages of protein synthesis include tRNA activation, initiation, elongation, and termination.

What is the difference between constitutive genes and inducible genes?

Constitutive genes are expressed continuously, while inducible genes are expressed only in response to specific signals or conditions.

What is a consensus sequence?

A consensus sequence is a nucleotide sequence that represents the most common nucleotides found at each position in a set of related sequences.

What is the significance of RNA in gene expression?

RNA plays critical roles in gene expression, with mRNA being translated into proteins, while rRNA and tRNA assist in the translation process.

How long do most human mRNAs exist before being cleared?

Most human mRNAs exist for 1 to 10 hours before being degraded by cellular nucleases.

What is the role of second messengers in signal transduction?

Second messengers relay signals received by receptors on the cell surface to target molecules inside the cell, amplifying the signal.

What is a protein binding site represented by a consensus sequence?

A short sequence of nucleotides found several times in the genome, thought to play the same role in different locations.

What are promoters in gene regulation?

Regions that contain consensus sequences to bind transcription factors (TF) and RNA polymerase.

What is the role of enhancers in transcription?

Enhancers are DNA sequences that promote transcription and consist of distal control elements.

What do activators do in gene regulation?

Activators are proteins that bind to distal control elements and interact with mediator proteins and transcription factors.

How does RNA polymerase II interact with enhancers and promoters?

The protein complex formed regulates the amount of mRNA produced.

What is the significance of the phosphodiester bond in RNA?

It links the 3' carbon atom of one sugar molecule to the 5' carbon atom of another.

What is the 5' cap of mRNA?

A methylated guanine nucleotide linked with triphosphates, important for nuclear export and translation initiation.

Why is capping important for mRNA?

It regulates nuclear export, prevents degradation by exonucleases, and promotes translation.

What is the poly-A tail and its function?

A stretch of adenine bases added to the 3' end of mRNA that stabilizes the RNA molecule and aids in nuclear export.

What is alternative splicing?

A form of transcriptional regulation that enables the production of different mRNA isoforms from a single gene.

What are the steps involved in processing eukaryotic mRNA?

Capping of the 5' end, adding a poly-A tail to the 3' end, splicing to remove introns and join exons, and mRNA decay.

What are the four enzymes involved in mRNA decay?

1. Deadenylase 2. Decapping enzyme 3. 5' exonuclease 4. 3' exonuclease.

What is the role of tRNA in translation?

tRNA brings amino acids to form a growing peptide chain during protein synthesis.

What is the role of splicing in mRNA processing?

Splicing involves the removal of introns and the joining of exons to form a mature mRNA molecule.

What happens during mRNA decay?

It involves the degradation of mRNA when there is enough protein, eliminating defective RNAs.

What is the function of translation initiation factor 4E?

It binds to capped mRNA to facilitate the initiation of translation.

How does the poly-A tail affect mRNA stability?

It makes the RNA molecule more stable and prevents its degradation.

What is the significance of the 5' cap in mRNA?

It is crucial for transport through the nuclear pore and resembles the 3' end of RNA.

What is the role of mediator proteins in transcription?

Mediator proteins interact with activators and transcription factors to regulate gene expression.

What is the relationship between mRNA processing and gene expression?

Processing steps like capping, poly-A tail addition, and splicing are key in regulating gene expression.

What is the importance of removing defective RNAs?

Eliminating defective RNAs is crucial for maintaining proper gene expression and cellular function.

What is the start codon and what amino acid does it encode?

The start codon is AUG, which encodes for methionine.

What are the stop codons in protein translation?

The stop codons are UGA, UAG, and UAA.

How many ribonucleotides make up one codon?

Three ribonucleotides make up one codon.

What is the direction in which mRNA codons are read during translation?

mRNA codons are read from 5' to 3'.

In which direction is protein synthesized during translation?

Protein is synthesized from the N-terminus to the C-terminus.

What is the role of aminoacyl tRNA synthetase in protein translation?

Aminoacyl tRNA synthetase attaches amino acids to their corresponding tRNA molecules using energy from ATP.

What is the first step in the stages of protein synthesis?

The first step is tRNA activation.

What happens during the initiation stage of translation?

The small ribosomal subunit attaches to the 5' end of the mRNA strand and moves along until it finds a start codon.

What occurs during the elongation stage of translation?

tRNA continues to drop off amino acids that form a chain linked by peptide bonds.

What is the function of the P-site and A-site in the ribosome?

The P-site holds the tRNA with the growing polypeptide chain, while the A-site holds the incoming tRNA with the next amino acid.

What happens when the ribosome reaches a stop codon?

The ribosome releases the finished polypeptide.

What are the four ribonucleotides mentioned in the notes?

Adenine, guanosine, uridine, and cytidine.

How do ribonucleotides differ from deoxyribonucleotides?

Ribonucleotides contain ribose sugar, while deoxyribonucleotides contain deoxyribose sugar, which has a hydroxyl group at carbon 2 instead of a hydrogen.

What is required for the synthesis of alanine?

The synthesis of alanine requires aminotransferase.

What is the role of the ribosome in protein translation?

The ribosome helps tRNA bring in the appropriate amino acid.

What is the significance of the N-terminus and C-terminus in protein structure?

The N-terminus has a free amino group, and the C-terminus has a free carboxyl group, which are important for protein synthesis.

What is a peptide bond?

A peptide bond is a covalent bond that links amino acids together in a protein.

What is the process of mRNA translation to protein?

mRNA codons are translated to amino acids, which are linked by peptide bonds to form a polypeptide chain.

What is the function of the large ribosomal subunit during translation?

The large ribosomal subunit joins the small ribosomal subunit at the start codon and facilitates the formation of peptide bonds.

What happens to the first tRNA after it drops off its amino acid?

The first tRNA breaks off and leaves to pick up another amino acid.

What is the overall outcome of translation?

The overall outcome of translation is the formation of a polypeptide chain that folds into a functional protein.

Which alpha-keto acid receives an alpha-amino group to generate alanine?

Pyruvate.

Which molecule is classified as a purine?

Adenine or Guanine.

How is 5-phosphoribosyl-1-pyrophosphate (PRPP) used?

It is a precursor for nucleotide synthesis.

Is methionine produced from one of the 5 starting families of amino acids?

Yes, methionine is produced from the amino acid family derived from aspartate.

Which amino acid is produced from 3-phosphoglycerate?

Serine.

What is the role of G-protein coupled receptors (GPCR)?

They have seven transmembrane domains and are involved in signal transduction.

What is the function of receptor tyrosine kinases?

They have one transmembrane domain and catalyze phosphorylation of tyrosine residues in target proteins.

What happens when GDP is exchanged for GTP in G proteins?

It causes G protein dissociation and activation of downstream signaling pathways.

What are the two examples of receptors that should be known in detail?

G protein-coupled receptors and receptor tyrosine kinases.

What is a second messenger in signal transduction?

cAMP, phospholipid derivatives, or Ca2+ ions.

How does G-protein activity lead to the production of second messengers?

It activates adenylyl cyclases or phospholipase C.

What is the role of calcium ions (Ca2+) in signal transduction?

Ca2+ acts as a second messenger and regulates proteins like calmodulin.

What is calmodulin and how does it function?

Calmodulin is a protein that binds Ca2+ and undergoes a conformational change to interact with other proteins.

What is the significance of phosphatidylinositol 4,5-bisphosphate (PIP2) in signal transduction?

It is cleaved by phospholipase C to produce diacyl glycerol (DAG) and inositol 1,4,5-trisphosphate (IP3), both of which are second messengers.

What are the three tRNA binding sites in the ribosome?

A site (aminoacyl), P site (peptidyl), and E site (exit).

How are amino acids joined together during protein synthesis?

By peptide bonds formed between the carboxyl group of one amino acid and the amino group of another.

What are the two classes of receptors used in signal transduction?

G-protein coupled receptors and catalytic receptors (e.g., receptor tyrosine kinases).

What is the direction of RNA synthesis?

RNA is synthesized in the 5' to 3' direction.

Why is the TATA box significant?

It is a promoter sequence that helps initiate transcription in eukaryotic genes.

What are the roles of enhancers, activators, or repressors in gene regulation?

Enhancers increase transcription, activators promote transcription, and repressors inhibit transcription.

What are four ways mRNA is processed in eukaryotes?

5' capping, polyadenylation, splicing, and editing.

What is mRNA capping and what is its role?

It involves adding a 7-methylguanylate cap to the 5' end, protecting mRNA from degradation and aiding in ribosome binding.

Which ribosomal subunit first binds mRNA?

The small ribosomal subunit (30S in prokaryotes, 40S in eukaryotes).

Which ribosomal subunit catalyzes the addition of amino acids to the peptide chain?

The large ribosomal subunit (50S in prokaryotes, 60S in eukaryotes).