Module 2 - The Nucleus

Question 1

What 3 things does the nucleus accomplish to protect the DNA?

Answer 1

• Regulate what molecules can access the DNA
• Separate the DNA from other cell compartments
• Keep it organized-DNA is fragile and easily damaged, so any problems with DNA will lead to major problems in the cell and body.

Question 2

What are the 4 key components of the nucleus?

Answer 2

The Nuclear Envelope - controls what molecules have access to the nucleus, and separates the DNA from other cell compartments. The outer membrane is connected to the ER. It has a double membrane structure

Nuclear pores - regulate molecular traffic in and out of the nucleus. Small molecules like water and oxygen (O2) can pass through the membrane freely. Nuclear Pore Complexes (NPCs) in the nuclear membrane regulate the movement of large molecules (e.g. proteins) into and out of the nucleus

The Nucleolus - nucleolus creates ribosomal RNAs and assembles them into the ribosomal subunits used by the cell to translate proteins. Nucleolus is the site of high amounts of rRNA gene transcription, and the DNA that encodes these genes is organized here

The Nucleoplasm and Nuclear Matrix - viscous, water-based fluid that is enclosed in the nuclear membrane. It contains dissolved molecules and ions that are essential for the function of the nucleus. The main functions of the nucleoplasm are to maintain shape and structure of the nucleus, and serve as a suspension substance for the nuclear contents. The nuclear matrix is a network of filaments within the nucleoplasm that helps to organize the DNA in chromosomes into compartments.

The Chromosomes and Chromatin - highly condensed chromatin found in the nucleus only during cell division
Chromatin is a complex of D N A and proteins forming highly organized fibers

Question 3

What is primary function of Nucleus?

Answer 3

To protect the cell’s DNA and control the molecules that can access it

Question 4

What is DNA?

Answer 4

Deoxyribonucleic acid - the genetic code that is unique to each individuals and most important to cell function

Question 5

Describe the 4 stages of DNA organization

Answer 5

• Nucleotides (a base, five carbon sugar (ribose), phosphate group)
• Genes - segments of DNA sequences
• Chromatin - all of your genes are stored in long strands of DNA that complex with proteins to form highly organized fibers called chromatin.
• Chromosome - chromatin condenses into chromosomes

Question 6

What are nitrogenous bases?

Answer 6

There are two categories of bases in DNA (and RNA):

Purines - have 2 rings in its structure. The two purines in DNA are adenine and guanine.

Pyrimidines -has only 1 ring in its structure. The two pyrimidines in DNA are cytosine and thymine.
Thymine is a pyrimidine that exists only in DNA, and uracil is a pyrimidine that exists only in RNA

Question 7

What is Ribose and Deoxyribose?

Answer 7

5 Carbon sugars (monosaccharides). Each sugar will have a 5’ and 3’ end. The 5’ end of the sugar is the end where the phosphate is attached in a single nucleotide.

Question 8

What are the phosphate group?

Answer 8

Part of the sugar phosphate backbone. Phosphates are attached to the 5’ carbon of one sugar and the 3’ carbon of another by a phosphodiester bond.

Phosphodiester is a covalent bond formed by a phosphate group to the 5’ carbon of one sugar and the 3’ carbon of another sugar

Question 9

How does DNA form into a strand?

Answer 9

Three step process:

1. The incoming nucleotide is added to the 3’ sugar of the existing chain of D N A. The phosphate of the incoming nucleotide binds to the oxygen on the 3’ sugar.
2. A diphosphate (two phosphate groups together) is formed as a byproduct.
3. A phosphodiester bond is formed between the new nucleotide and the existing strand of D N A

Question 10

How do DNA base pairs form connecting two strands of DNA together?

Answer 10

The purines in one DNA strand will always base-pair with the pyrimidines in the opposing DNA strand. This means that hydrogen bonds between opposite bases on each strand form cross-linkages

• ADENINE pairs with THYMINE
• GUANINE pairs with CYTOSINE

This bonding leads to the formation of a double-stranded DNA molecule. Each strand of the DNA is called antiparallel to the other, because they run in opposite directions.

Question 11

Why is DNA a double stranded helix?

Answer 11

The nitrogenous bases of each nucleotide are hydrophobic while the sugar-phosphate backbone is hydrophilic.As a result, when placed in an environment with lots of water (i.e. a cell), the bases stack themselves in the center while the sugar-phosphate backbone remains outside. In order for the bases to come into contact with as little water as possible, this “ladder” of double-stranded D N A twists to become a spiral staircase -a double-stranded helix

Question 12

What are exons and introns?

Answer 12

Exons are the sections of a gene that contain the information that is used to make a protein, called coding sequences, or coding D N A. Introns are sections of D N A that are not used to make a protein, called noncoding sequences, or non-coding D N A. There are also sections termed regulatory sequences which control when a gene is turned on, or used.

Question 13

What is RNA? How does it differ from DNA?

Answer 13

RNA is a nucleic acid that is similar to DNA. The main role of RNA in eukaryotic cells is to transport genetic information that tells the cell what kinds of proteins to make.

1. R N A, the pyrimidine uracil is used instead of thymine.
2. The nucleotides in R N A contain ribose rather than deoxyribose.a.Recall that ribose has an extra oxygen on the 2’ carbon compared to deoxyribose
3. RNA is single stranded -it does not form a double-stranded helix and therefore it is less stable than D N A

Question 14

What are the 3 main types of RNA?

Answer 14

• Ribosomal R N A (rRNA)–rRNA and ribosomal proteins make up ribosomes, which are in charge of translating RNA into protein.
• Messenger RNA (mRNA)–mRNA carries instructions to making proteins in the cell
• Transfer RNA (tRNA)-During translation, tRNA brings amino acids to ribosomes in order to build up a protein. R

Question 15

What are proteins important for?

Answer 15

Proteins are critical for proper cell function as they are involved in most cell functions. Improper protein synthesis can contribute to cellular dysfunction and disease state

Question 16

How is DNA tightly packaged?

Answer 16

Level 1 - Double Helix Strand. 2m long stretched out. 2nm in diameter.

Level 2 - Nucleosomes - DNA is wrapped twice around proteins called histones, which shortens the DNA 7-fold. The nucleosomes are linked by linker DNA and form the beads on a strong structure. In a nucleosome roughly ~200 base pairs (bp) of D N A are wrapped around a core of eight histones

Level 3 -Chromatin fibre - string of nucleosomes is coiled into a spiraling fiber, forming a helical structure with a diameter of ~30 nm.This shortens the DNA 42-fold

Level 4 - Chromatin looped domains - The 30 nm chromatin fiber is formed into loops with an average length of 300 nm.
- This shortens the D N A 750-fold.

Level 5 - Heterochromatin - the looped domains are further compressed and folded into lengths of ~700 nm. - Heterochromatin is hyper-condensed DNA. It is present in inactive regions of chromosomes (interphase, part of the cell cycle), and the entire chromosomes will be in this form in cells undergoing mitosis or meiosis (cell division).

Question 17

Define Euchromatin and Heterochromatic

Answer 17

Levels 1-4 of DNA packaging are called euchromatin.
DNA in euchromatin is active, meaning that it can be easily accessed by proteins responsible for:
- Replicating the chromosomes
- Reading a strand of DNA to make RNA

Level 5 of DNA organization is called heterochromatin.At this level, DNA is condensed beyond loop domains and is rendered essentially inactive.

Question 18

What is the central Dogma? What are the three parts of the Central Dogma?

Answer 18

The Central Dogma of molecular biology is a set of principles that explain how D N A contains the instructions for building R N A and proteins, which are essential for the structure and function of the cell and body.

1) Replication - copying of the parent DNA strand before the cell divides so each cell has a copy of the DNA. Main enzyme = DNA Polymerase
2) Transcription - A section of DNA is transcribed to RNA so the RNA can be transported outside of the nucleus. for protein production. Main enzyme = RNA polymerase
3) Translation - The RNA is read and “translated” to produce proteins that perform a specific function in the cell. Main enzyme = ribosome.

Question 19

List and describe the 4 major steps of DNA replication:

Answer 19

1. Unwinding the DNA -
   DNA replication occurs at Origin of Replication (Orc). A group of proteins binds to the Orc to begin replication, the most important being DNA Helicase. DNA Helicase unwinds DNA into two single strands, forming a structure that is called the replication fork.

Note that this step requires energy, as indicated by the ATP to ADP +P step.

2. RNA primers prep the DNA
   DNA Polymerase can only copy a strand of DNA if it has a short piece of RNA bound to it. Therefore, before the cell can copy DNA it must add a primer that is made up of RNA (RNA primer). It does this by using the enzyme primase.
3. Elongation by the DNA polymerase

leading strand runs in the3’ to 5’ direction
lagging strand that runs in the opposite 5’ to 3’ direction

DNA polymerase can only add nucleotides to the 3’ end of a DNA strand, and therefore can only move along the parent strand (or ”template strand”) of DNA in the 3’ to 5’ direction, creating a new strand that is in the 5’ to 3’ orientation.

For the other strand of DNA (the lagging strand) replication is more complex. This is because the lagging strand is in a 5’ to 3’ direction, so DNA polymerase can’t move along it to begin synthesis of a new strand until it is able to ‘read’ the strand in the 3’ to 5’ orientation. To mitigate potential damage to the lagging strand while it is not yet being replicated, single stranded binding proteins (SSBPs) bind to the single stranded DNA.

the lagging strand loops out and many RNA primers are synthesized on a 3’ carbon on the DNA. The DNA polymerase then synthesizes DNA in patches along these primers. These short patches, or fragments, are termed Okazaki fragments.

The lagging strand is synthesized in many discontinuous chunks.

4. Termination

Once all the RNA primers are removed but there is no upstream piece of RNA for DNA polymerase to start synthesis of DNA to replace them.

The enzyme telomerase carries a short piece of RNA within the enzyme that helps create an extension to the parent DNA strand. The RNA serves as a template. Telomerase uses an RNA primer to build multiple short pieces of DNA onto the 3’ end of a the new DNA strand.

Ligase catalyzes the phosphodiester backbones

Question 20

Summary of DNA Replication

Answer 20

1. DNA helicase unwinds the DNA
2. RNA Primase adds a primer to both strands. For the lagging strand in segments.
3. DNA Polymerase synthesizes the leading strand. Another DNA Polymerase synthesizes the lagging strand in Okazaki fragments
4. Telomerase replaces RNA primers with DNA. Also extends the leading strand and DNA polymerase copies leading strand.
5. DNA Ligase joins the DNA strands by allowing phosphodiester bonds to form.

Question 21

What are two types of DNA repair?

Answer 21

1.REPAIR DURING DNA REPLICATION

DNA polymerase has a proofreading function and can check that it is not making mistakes.

2.REPAIR THROUGHOUT THE CELL CYCLE

DNA repair proteins are continually scanning DNA for errors and making repairs. Some check immediately after replication, fixing the newly synthesized strand of DNA, whereas others check at different points throughout the cell cycle