DNA Replication Review Quiz

DNA Replication Review

• DNA replication is the process of creating two identical DNA molecules from a single original DNA molecule.
• The two strands of the DNA double helix separate, and each strand serves as a template for the synthesis of a new, complementary strand.

DNA Synthesis Review

• Leading strand is synthesized continuously in the 5' to 3' direction.
• Lagging strand is synthesized discontinuously, forming Okazaki fragments, which are then joined together.
• DNA polymerase III is the primary enzyme responsible for synthesizing new DNA strands.
• Primase is needed to synthesize RNA primers for the lagging strand.
• DNA polymerase I replaces RNA primers with DNA.

DNA Synthesis Stages

• Initiation: DNA unwinds at the replication fork.
• Elongation: New nucleotides are added to the 3' end of the growing DNA strand, complementary to the template strand. Leading strand grows continuously; lagging strand grows in fragments.
• Termination: Replication ends when the entire DNA molecule has been copied.

DNA Synthesis Summary

• DNA replication is semi-conservative, meaning each new DNA molecule consists of one original strand and one new strand.
• New DNA strands are synthesized in the 5' to 3' direction.
• Enzymes like DNA polymerase III, Primase, and DNA polymerase I play key roles in the process.

Gene Expression: Outline

• Part 1. Overview gene expression: Introduction to gene expression concepts
• Part 2. Transcription: The process of converting DNA to mRNA
  • Involves RNA, specifically mRNA, tRNA, rRNA, and snRNA
  • Focuses on steps of transcription and pre-mRNA modifications.
• Part 3. Translation: The process of converting mRNA to a protein
  • Involves the genetic code, tRNA and the steps of translation
• Part 4. Mutations: Changes in DNA sequence

Central Dogma of Biology

• DNA replication, transcription, and translation
• Transcription converts DNA to mRNA
• Translation converts mRNA to protein

Heritable Defects and Enzymes

• DNA holds genetic information, expressed as proteins.
• Archibald Garrod (1902) proposed that genes dictate phenotype via enzymes.
• Alkaptonuria is a hereditary disease caused by a missing enzyme that breaks down homogentistic acid. This builds up and oxidizes, turning black.

"One Gene - One Enzyme" Refined

• Not all proteins are enzymes, but their synthesis depends on genes.
• Proteins are often composed of several polypeptide subunits, each having its own gene.
• Hemoglobin is an example, consisting of four polypeptide subunits.

Gene Expression Overview

• Gene expression is the process of transcription and translation.
• A DNA strand is the template to synthesize a complementary mRNA strand (mRNA, tRNA, rRNA, snRNA).
• mRNA contains the code for making amino acid sequences of a polypeptide.
• Translation happens at ribosomes.

RNA Terminology

• mRNA (messenger RNA): Carries the genetic code for protein synthesis.
• tRNA (transfer RNA): Transports amino acids to ribosomes during protein synthesis.
• rRNA (ribosomal RNA): Forms part of the ribosome, where protein synthesis occurs.
• snRNA (small nuclear RNA): Involved in eukaryotic RNA processing.

Transcription: Key Features

• Transcription is the process of converting DNA messages into a complementary RNA copy (mRNA).
• Only one DNA strand is transcribed (template strand).
• RNA polymerase adds ribonucleotides to the 3’ end of the growing mRNA chain, using the template DNA strand.
• Synthesis proceeds in the 5' to 3' direction.

Transcription Overview

• DNA is separated for transcription, exposing a single DNA strand.
• RNA polymerase synthesizes a complementary mRNA copy.
• mRNA synthesis occurs in the 5' to 3' direction, using the 3' to 5' template strand.

Transcription Gene Structure

• Gene = promoter + transcription unit
• Less than 2% of human DNA codes for genes; the rest is noncoding.
• Transcription initiation, elongation, and termination are the three stages of transcription.
• Transcription begins at the promoter region (e.g., the TATA box).

Initiation - Finding the Genes

• Genes are identified by promoters: specific nucleotide sequences (e.g., TATA box).
• Transcription factors bind to the promoter, luring RNA polymerase.
• Eukaryotes have three RNA polymerases (I, II, III); bacteria have one.

Initiation (Continued)

• DNA is unwound, exposing the template strand.
• RNA polymerase starts RNA synthesis at the transcription start site.
• RNA nucleotides bind to the template strand in a complementary fashion.

Elongation

• RNA polymerase continues moving along the DNA strand.
• It synthesizes mRNA by adding complementary RNA nucleotides.
• The DNA strands rejoin behind the polymerase
• The growing mRNA transcript is extended until the terminator is reached.

Termination

• RNA polymerase releases from the template.
• The pre-mRNA transcript is released.
• The DNA rewinds and more transcripts are made

At Home Exercise

• Understanding of “Central Dogma,” similarities/differences between DNA replication, transcription, and translation.
• Similarities/differences between DNA polymerase and RNA polymerase.

mRNA Modifications

• Nuclear enzymes modify pre-mRNA in eukaryotes before it goes to the cytoplasm.
• 5' cap: modified guanine added for ribosome attachment.
• Poly(A) tail: to prevent breakdown and aid in transport.
• RNA splicing: removing introns and joining exons to produce a continuous coding sequence.

Genetic Code

• Genetic code is a series of codons (triplets of nucleotides).
• Each codon codes for a specific amino acid (or stop).
• The genetic code is unambiguous, meaning each codon codes for only one amino acid.
• The code is redundant.

Universality of the Code

• Most organisms use the same genetic code (with some exceptions in mitochondria).
• This allows for the easy transfer of genes between species.

In-Class Questions

• Discussing the number of codons, amino acids, and start/stop codons.
• Listing the amino acids with unique codons
• Identifying mRNA and DNA codon sequences

Ribosomes

• Protein and ribosomal RNA (rRNA) complexes.
• Ribosomes have three sites (A, P, E) for tRNA interactions.
• Antibiotics affect ribosome function; different antibiotics target different prokaryotic ribosomes.

Translation

• The process by which mRNA is read, and amino acids are brought together to form a polypeptide chain.
• Ribosomes move along the mRNA, reading codons.
• tRNA brings amino acids to the ribosome and attaches them to the growing polypeptide chain.
• Termination occurs when a stop codon is reached causing the release of the complete polypeptide.

Translation Review

• 5' and 3' ends, and N-terminus and C-terminus.
• Enzyme that transfers amino acids to tRNA (aminoacyl-tRNA synthetase).
• Type of bonds that hold together amino acids in a polypeptide (peptide bonds).

Polyribosomes

• Multiple ribosomes translating a single mRNA simultaneously, thus increasing the rate of protein synthesis

Differences Between Prokaryotic and Eukaryotic Gene Expression

• Location of transcription(prokaryotes:in cytoplasm; eukaryotes:in nucleus)
• mRNA processing(prokaryotes:doesn't have mRNA processing, no 5' cap or 3'poly(A) tail; eukaryotes:have mRNA processing, 5' cap and 3' poly(A) tail and introns removed)
• mRNA structure(prokaryotic mRNA:polycistronic mRNA; eukaryotic mRNA:monocistronic mRNA)
• Transcription/translation(prokaryotes:transcription and translation occur in the same compartment and simultaneously-eukaryotes:transcription occurs in the nucleus while translation occurs in the cytoplasm)

Protein Targeting

• Eukaryotes create some proteins with a "signal peptide" that directs it to the endoplasmic reticulum (ER).
• All ribosomes start out as "free ribosomes."

Mutations

• Changes in genetic material.
• May be transmitted to future generations (Germ-line).
• Point Mutation: chemical change in one base pair.
• Missense Mutation: one amino acid changed in the polypeptide.
  • Nonsense Mutation: changes into one of the stop codons, terminating polypeptide synthesis prematurely.
• Frameshift Mutation: inserting or deleting one or two bases causes a "frame shift".
• Mutagens (chemical or physical) interact with DNA to cause mutations.

Summary - Types of Mutations

• Point mutations (base substitutions):
  • Silent: no change to amino acid.
  • Missense: one amino acid change.
  • Nonsense: premature stop codon.
• Frameshift mutations (insertions/deletions): disrupt the reading frame, causing major changes in the resulting polypeptide.

In-Class Questions

• Various questions on understanding concepts and processes of gene expression and mutations.

Review - Transcription

• Enzyme adding ribonucleotides: RNA polymerase.
• Transcription initiation region: promoter.
• Direction of mRNA synthesis: 5' to 3'.
• Three Post-Transcriptional Modifications: 5' cap, 3' poly(A), RNA splicing.
• Location of codons:mRNA.

Additional note

• Various examples and diagrams are included to illustrate the concepts.

Test your knowledge on the key processes of DNA replication and synthesis. This quiz covers the roles of various enzymes and the differences between leading and lagging strands. Challenge yourself and reinforce your understanding of molecular biology!