Central dogma of molecular biology

Question 1

DNA Polymerase DNA synthesis Requirements

Answer 1

• 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

Question 2

DNA Polymerase Proofreading

Answer 2

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

Question 3

Helicase

Answer 3

(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

Question 4

Primase

Answer 4

A specialized RNA polymerase that synthesizes short stretches of RNA used as primers for DNA synthesis

Question 5

Replication Origin

Answer 5

Segment in a DNA molecule at which unwinding begins

Question 6

Replication Fork

Answer 6

Y-shaped region in double-stranded DNA at which the two strands are separated and replicated during DNA synthesis

Question 7

Leading Strand

Answer 7

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

Question 8

Lagging Strand

Answer 8

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

Question 9

Okazaki Fragments

Answer 9

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

Question 10

DNA Ligase

Answer 10

An enzyme that joins adjacent Okazaki fragments

Question 11

Gene

Answer 11

A unit of DNA that contains the information to specify synthesis of a single polypeptide chain or functional RNA

Question 12

Transcription

Answer 12

The formation of an RNA copy of the information carried in DNA for one gene

Question 13

Protein-Coding Gene

Answer 13

Gene carrying information used to build protein molecules; RNA copies constitute the mRNA molecules of cells

Question 14

RNA Polymerase

Answer 14

An enzyme that copies one strand of DNA (the template strand) to make the complementary RNA strand using as substrates ribonucleoside triphosphates

Question 15

RNA Polymerization Reaction

Answer 15

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

Question 16

DNA Replication / RNA synthesis Direction

Answer 16

Molecules are synthesizedn in the 5’ -> 3’ direction

Question 17

Transcription Intiation

Answer 17

1. RNA polymerase, with the help of initiation factors, recognizes and binds to a specific sequence of double- stranded DNA called a promoter
2. 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
3. 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

Question 18

Promoter

Answer 18

DNA sequence that determines the site of transcription initiation for an RNA polymerase

Question 19

Transcription Bubble

Answer 19

The 12-14 base-pair region of melted DNA in the active site of the polymerase

Question 20

Transcription Strand Elongation

Answer 20

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

Question 21

Transcription Termination

Answer 21

The final stage in RNA synthesis; the completed RNA molecule is released from the RNA polymerase and the polymerase dissociates from the template DNA

Question 22

Precursor mRNAs

Answer 22

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

Question 23

5’ Cap

Answer 23

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

Question 24

RNA Splicing

Answer 24

A process that results in removal of introns and joint of exons in pre-mRNAs

Question 25

Poly(A) Tail

Answer 25

A string of adenylic acid residues added to a free 3’-hydroxyl group on pre-mRNA

Question 26

Alternative Splicing

Answer 26

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

Question 27

Isoform

Answer 27

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

Question 28

Translation

Answer 28

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

Question 29

Messenger RNA (mRNA)

Answer 29

Carries the genetic information transcribed from DNA in a linear form

Question 30

Codons

Answer 30

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

Question 31

Transfer RNA (tRNA)

Answer 31

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

Question 32

Anticodon

Answer 32

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

Question 33

Ribosomal RNA (rRNA)

Answer 33

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

Question 34

Methionine

Answer 34

Amino acid that begins the synthesis of all polypeptide chains in prokaryotic and eukaryotic cells

Question 35

Reading Frame

Answer 35

The sequence of nucleotide triplets (codons) that runs from a specific translation start codon in an mRNA to a stop codon

Question 36

Open Reading Frame

Answer 36

Region of sequenced DNA that is not interrupted by stop codons in one of the triplet reading frames

Question 37

Synonymous Mutation

Answer 37

A mutation during protein-coding that would be predicted to have no effect on the function of the encoded protein

Question 38

Nonsense Mutation

Answer 38

A mutation during protein-coding that would terminate the protein sequence early and would likely cause a complete loss of function

Question 39

Frameshift Mutation

Answer 39

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

Question 40

Aminoacyl-tRNA

Answer 40

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

Question 41

Aminoacyl-tRNA Synthesases

Answer 41

Enzyme responsible for adding the correct amino acid to a given tRNA by the recognition of particular features of the tRNA structure