Central dogma of molecular biology Flashcards
DNA replication: DNA makes RNA makes protein (transcription, translation, mRNA, tRNA, genetic code) E-Book sections: 5.2; 5.4, 5.5
DNA Polymerase DNA synthesis Requirements
- A single-stranded DNA template
- A DNA primer base paired with the template, and with a free hydroxyl group at the 3’ end of the primer to accept a new nucleotide
- A source of deoxyribonucleoside 5’-triphosphate (dNTPs) precursors
DNA Polymerase Proofreading
When an incorrect base is incorporated during DNA synthesis, base pairing between the 3’ nucleotide of the nascent strand and the template strand does not occur; the polymerase pauses and then transfers the 3’ end of the growing chain to its exonuclease site, where the incorrect misfired base is removed; the 3’ end is transferred back to the polymerase site, where the region is copied correctly
Helicase
(1) Any enzyme that moves along a DNA duplex using the energy released by ATP hydrolysis to separate (unwind) the two strands; required for DNA replication. (2) Activity of certain initiation factors that can unwind the secondary structures in mRNA during initiation of translation
Primase
A specialized RNA polymerase that synthesizes short stretches of RNA used as primers for DNA synthesis
Replication Origin
Segment in a DNA molecule at which unwinding begins
Replication Fork
Y-shaped region in double-stranded DNA at which the two strands are separated and replicated during DNA synthesis
Leading Strand
One of the two daughter DNA strands formed at the replication fork by continuous synthesis in the 5’ -> 3’ direction; the direction of leading-strand synthesis is the same as movement of the replication fork
Lagging Strand
One of the two daughter DNA strands formed at the replication fork as short, discontinuous segments (Okazaki fragments), which are synthesized in the 5’ -> 3’ direction and later joined
Okazaki Fragments
Short (<1000 bases), single-stranded DNA fragments that are formed during synthesis of the lagging strand in DNA replication and are rapidly joined by DNA ligase to form a continuous DNA strand
DNA Ligase
An enzyme that joins adjacent Okazaki fragments
Gene
A unit of DNA that contains the information to specify synthesis of a single polypeptide chain or functional RNA
Transcription
The formation of an RNA copy of the information carried in DNA for one gene
Protein-Coding Gene
Gene carrying information used to build protein molecules; RNA copies constitute the mRNA molecules of cells
RNA Polymerase
An enzyme that copies one strand of DNA (the template strand) to make the complementary RNA strand using as substrates ribonucleoside triphosphates
RNA Polymerization Reaction
Nucleophilic attack by the 3’ oxygen in the growing RNA chain on the a phosphate of the next nucleotide precursor to be added -> formation of a phosphodiester bond and the release of pyrophosphate
DNA Replication / RNA synthesis Direction
Molecules are synthesizedn in the 5’ -> 3’ direction
Transcription Intiation
- RNA polymerase, with the help of initiation factors, recognizes and binds to a specific sequence of double- stranded DNA called a promoter
- RNA Polymerase and the initiation actors separate the DNA strands to make the bases in the template strand available for base pairing with the bases of the rNTPs that the RNA polymerase will polymerize
- Approximately 12-14 base pairs of DNA around the transcription site are separated, allowing the template strand to enter the active site of the enzyme- where catalysis of phosphoddiester bond formation between rNTPs that are complementary to the template strand take place
Promoter
DNA sequence that determines the site of transcription initiation for an RNA polymerase
Transcription Bubble
The 12-14 base-pair region of melted DNA in the active site of the polymerase
Transcription Strand Elongation
RNA polymerase moves along the template DNA, opening the double-stranded DNA in front of its direction of movement and guiding the strands back together so that they reassociate at the upstream end of the transcription bubble
Transcription Termination
The final stage in RNA synthesis; the completed RNA molecule is released from the RNA polymerase and the polymerase dissociates from the template DNA
Precursor mRNAs
The primary RNA product formed by transcription of a gene; Splicing of introns and modifications to the
5’ and 3′ ends of the pre-mRNA are necessary to form a mature mRNA that can be transported out of the nucleus and translated on ribosomes
5’ Cap
A 7-methylguanylate that is connected to the terminal nucleotide of the RNA by an unusual 5’,5’ triphosphate linkage; protects an mRNA from enzymatic degradation and assists in its export to the cytoplasm
RNA Splicing
A process that results in removal of introns and joint of exons in pre-mRNAs
Poly(A) Tail
A string of adenylic acid residues added to a free 3’-hydroxyl group on pre-mRNA
Alternative Splicing
Process by which the exons of one pre-mRNA are spliced together in different combinations, generating two or more different, mature mRNAs from a single pre-mRNA
Isoform
One of several forms of the same protein whose amino acid sequences differ slightly and whose general activities are similar; may be encoded by different genes or by a single gene whose primary transcript undergoes alternative splicing
Translation
The process by which the nucleotide sequence of an mRNA is used as a template to join the amino acids of a polypeptide chain in the correct order
Messenger RNA (mRNA)
Carries the genetic information transcribed from DNA in a linear form
Codons
Sequence of three nucleotides in DNA or mRNA that specifies a particular amino acid during protein synthesis; of the 64 possible codons, three are stop codons, which do not specify amino acids and cause termination of synthesis
Transfer RNA (tRNA)
The key to deciphering the codons in mRNA and serves as an adaptor to link three bases of RNA sequence to a particular amino acid; each type of amino acid has its own subset of tRNAs, which are covalently bound to that amino acid and carry it to the growing end of a polypeptide chain when the next codon in the mRNA calls for it
Anticodon
Sequence of three nucleotides in a tRNA that s complementary to a codon in an mRNA; base pairing between a codon and anticodon aligns the tRNA carrying the corresponding amino acid for addition to the growing polypeptide chain during protein synthesis
Ribosomal RNA (rRNA)
Associates with a set of proteins to form ribosomes, which form the scaffold for stepwise alignment of the codons in mRNA with the anticodons in tRNA; the ribosome also catalyzes the sequential formation of peptide bonds between amino acids carried by tRNAs for the assembly of a polypeptide chain
Methionine
Amino acid that begins the synthesis of all polypeptide chains in prokaryotic and eukaryotic cells
Reading Frame
The sequence of nucleotide triplets (codons) that runs from a specific translation start codon in an mRNA to a stop codon
Open Reading Frame
Region of sequenced DNA that is not interrupted by stop codons in one of the triplet reading frames
Synonymous Mutation
A mutation during protein-coding that would be predicted to have no effect on the function of the encoded protein
Nonsense Mutation
A mutation during protein-coding that would terminate the protein sequence early and would likely cause a complete loss of function
Frameshift Mutation
An addition or subtraction of one or two bases during protein-coding that will shift the reading frame, which would lead to a scrambled amino sequence with an early termination of the protein
Aminoacyl-tRNA
Activated form of an amino acid, used in protein synthesis, consisting of an amino acid linked via a high-energy ester bond to the 3’-hydroxyl group of a tRNA molecule
Aminoacyl-tRNA Synthesases
Enzyme responsible for adding the correct amino acid to a given tRNA by the recognition of particular features of the tRNA structure
