M,Bio, 01.1 and 01.2

Questions and Answers

What is the primary function of DNA in an organism?

To provide genetic instructions used for development, functioning, growth, and reproduction.

What is the difference between the sugar molecules found in DNA and RNA?

DNA contains deoxyribose, while RNA contains ribose.

What is the role of messenger RNA in the central dogma?

To carry instructions from DNA to control the synthesis of proteins.

What is the primary function of enzymes in molecular biology?

To accelerate chemical reactions by lowering the activation energy required. Signup and view all the answers

What is the key difference between semi-conservative and conservative DNA replication?

In semi-conservative replication, the original DNA strands serve as templates, whereas in conservative replication, the original DNA molecule remains intact. Signup and view all the answers

Which type of DNA replication involves the breakdown of the original DNA molecule into fragments?

Dispersive replication. Signup and view all the answers

Which enzyme is responsible for joining nucleic acid molecules together?

Ligase. Signup and view all the answers

What is the primary difference between DNA replication and PCR?

DNA replication is a natural biological process, while PCR (Polymerase Chain Reaction) is an in vitro technique used to amplify specific DNA sequences. Signup and view all the answers

What is the function of helicase enzymes in the replication process?

To break hydrogen bonds between complementary strands, separating the process, causing the A-T rich region to separate. Signup and view all the answers

What is the purpose of single-stranded binding proteins (SSBs) in the replication process?

To bind to separated DNA strands within the bubble, preventing re-annealing and protecting from nuclease. Signup and view all the answers

What is the difference between the leading and lagging strands in terms of DNA synthesis?

Leading strand synthesis is continuous and occurs in the 5' to 3' direction, while lagging strand synthesis is discontinuous and occurs in short Okazaki fragments in the opposing direction. Signup and view all the answers

Why is an RNA primer necessary for DNA synthesis?

Because DNA polymerase cannot initiate synthesis of a new strand, it can only add nucleotides to an existing 3' hydroxyl OH group, which the RNA primer provides. Signup and view all the answers

What is the function of topoisomerase I and II in the replication process?

Topoisomerase I cuts DNA on one strand to release tension, while topoisomerase II (DNA gyrase) cuts double-stranded DNA and rejoins to relieve tension. Signup and view all the answers

What is the role of primase in the replication process?

To synthesize a short RNA primer complementary to the DNA template strand, providing a starting point for DNA polymerase. Signup and view all the answers

What is the result of the replication fork moving?

The replication fork continues to unwind, and new DNA synthesis occurs. Signup and view all the answers

What is the importance of RNA primers in lagging strand synthesis?

Each Okazaki fragment needs a separate RNA primer to initiate DNA synthesis, allowing for discontinuous synthesis. Signup and view all the answers

What is the purpose of the replication bubble?

To create a small region where the DNA strands are separated, allowing for the replication process to occur. Signup and view all the answers

What is the role of DNA ligase in the replication process?

To seal the nicks in the DNA backbone, creating a continuous strand. Signup and view all the answers

What type of activity do DNA polymerase I in prokaryotes and RNase H with flap endonuclease 1 (FEN1) in eukaryotes exhibit to remove RNA primers?

5' to 3' exonuclease activity Signup and view all the answers

What is the process by which exonuclease activity degrades RNA primers?

Cleaving phosphodiester bonds at RNA-DNA junctions Signup and view all the answers

Which enzyme is responsible for filling the gap left by the removal of RNA primers in prokaryotes?

DNA polymerase I Signup and view all the answers

What is the role of DNA polymerase δ in eukaryotes during the removal of RNA primers?

Extending the newly synthesized DNA strand by adding DNA nucleotides to the 3' end Signup and view all the answers

What is the primary function of DNA ligase during the removal of RNA primers?

Sealing the nicks between newly synthesized and existing strands Signup and view all the answers

What type of bond is formed between the 3' OH end of one nucleotide and the 5' phosphate end during the sealing of nicks?

Phosphor diester bond Signup and view all the answers

Study Notes

Molecular Biology and Bioinformatics Study Guide

DNA (Deoxyribonucleic Acid)

Has genetic instructions used for development, functioning, growth, and reproduction
Double helix structure with two strands coiling around each other
Consists of:
- Phosphate group: sugar - deoxyribose
- Nitrogenous bases: adenine, thymine, cytosine, and guanine (no uracil)

RNA (Ribonucleic Acid)

Single-stranded molecule
Roles:
- Coding, regulation, and expression of genes
- Messenger carrying instructions from DNA to control protein synthesis
Consists of:
- Phosphate group: sugar - ribose
- Nitrogenous bases: adenine, uracil, cytosine, and guanine

Gene

Specific sequence of nucleotides in DNA/RNA that codes for proteins and units of heredity
Carries instructions for protein synthesis

Enzymes

Proteins that act as catalysts to accelerate chemical reactions
Lower activation energy needed for a reaction to occur, increasing the reaction rate
Types:
- Nucleases: cut, shorten, or degrade
- Ligases: join nucleic acids together
- Polymerases: make copies
- Modifying enzymes: remove or add chemical groups
- Topoisomerases: introduce or remove supercoils from covalently closed-circular DNA

DNA Replication

Three Types of Replication

Conservative: original double-stranded DNA remains intact, and a new double-stranded DNA molecule is synthesized
Semi-conservative: two strands of the original DNA serve as templates for synthesizing new complementary strands
Dispersive: original DNA molecule is broken down into fragments, each acting as a template for new synthesis

Stages of DNA Replication

Stage 1 - Separating the Strands

Initiation at oriC sequence in the genome
Binding of DnaA to origin of replication site
Recruitment of helicase enzymes to break hydrogen bonds between complementary strands
Formation of replication fork and bubble
Single-stranded binding proteins (SSBs) bind to separated DNA strands, preventing re-annealing and protecting from nuclease
Topoisomerase I and II relieve tension in DNA

Stage 2 - Synthesis of New DNA

Primer synthesis by primase
DNA synthesis on leading and lagging strands
- Leading strand synthesis: continuous 5' to 3' synthesis by DNA polymerase III
- Lagging strand synthesis: discontinuous in short Okazaki fragments by DNA polymerase III
- Directional synthesis: leading strand in the same direction as fork movement, lagging strand in the opposite direction
Why RNA primers are needed:
- DNA polymerase cannot initiate synthesis without a primer
- RNA primer provides a starting point for DNA synthesis
- Binding of RNA primer to template strand
- Synthesis of RNA primer by RNA polymerase
- Replacement of RNA primer with DNA nucleotides

Stage 3 - Removing the RNA Primer and Sealing the Lagging Strands

Removal of RNA primers:
- Exonuclease activity by DNA polymerase I in prokaryotes or RNase H and flap endonuclease 1 (FEN1) in eukaryotes
Replacement with DNA:
- Gap filling by DNA polymerase I in prokaryotes or DNA polymerase δ in eukaryotes
Sealing nicks:
- DNA ligase catalyzes the formation of phosphodiester bonds between nucleotides

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Description

This study guide covers the basics of molecular biology, focusing on the structure and functions of DNA and RNA, including their roles in genetic instruction, development, and gene expression.