The Nucleus

Question 1

What is the primary function of the nucleus?

Answer 1

To protect the cell’s DNA - which contains all the information necessary for a cell to survive

Question 2

How does the nucleus protect the DNA?

Answer 2

• Regulates what molecules can access the DNA
• Separates the DNA from other cell compartments
• Keeps it organized - DNA is fragile and easily damaged, and any problems with DNA will lead to major poblems in the cell and body

Question 3

What 4 components of the nucleus work together to protect the DNA?

Answer 3

• The Nuclear Envelope
• The Nucleolus
• The Nucleoplasm and Nuclear Matrix
• The Chromosomes and Chromatin

Question 4

Descrive the Nuclear Envelope.

Answer 4

The nuclear envelope controls what molecules have access to the nucleus, and separates the DNA from other cell compartments. It is a double membrane structure that encloses the nuclear material. The outer membrane of the nuclear envelope is connected to the ER, which is important for making proteins.

Question 5

Describe Chromosomes and Chromatin.

Answer 5

Strands of DNA are organized and stored in chromatin that make up chromosomes within the nucleus.

Chromatin - complex of DNA and proteins forming highly organized fibers

Chromosomes - highly condensed chromatin found in the nucleus only during cell division

Question 6

Describe the Nucleoplasm and Nuclear Matrix.

Answer 6

The nucleoplasm is a 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.

Question 7

Describe the Nucleolus.

Answer 7

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

Question 8

Describe the Nuclear Pore.

Answer 8

The nuclear envelope contains pores which regular molecular traffic in and out of the nucleus. Small molecules like water and oxygen can pass through the membrane freely. Nuclear pore complexes in the nuclear membrane regulate the movement of large molecules into and out of the nucleus.

Question 9

Briefly describe how DNA organized within a cell.

Answer 9

All of your genes are stored in long strands of DNA that complex with proteins to form highly organized fibers called chromatin. Chromatin condenses into chromosomes.

Segments of this DNA sequence contain genetic information called genes. You inherited your genes from a combination of your parents’ genes. Your specific set of genes are what largely define your personal traits.

DNA is a linear molecule made up a sequence of smaller molecules called nucleotides.

Question 10

Briefly describe genes.

Answer 10

Every cell in the body contains the complete genome including every gene. However, specific cells have different genes turned on and off to function properly.

Question 11

Describe the structure of nucleotides.

Answer 11

Each nucleotide is made up of 3 components:

1. A nitrogenous base:
   - There are two categories of bases in DNA: purines (adenine and guanine) and pyrimidines (cytosine and thymine or uracil in RNA)
2. A pentose sugar (ribose)
   - Each sugar has a 5’ and 3’ end
   - The 5’ end is where the phosphate is attached in a single nucleotide
3. Phosphates
   - Attached to the 5’ carbon of one sugar and the 3’ carbon of another by phosphodiester bond

Question 12

Describe how phosphodiester bonds are formed in single strand DNA.

Answer 12

1. The incoming nucleotide is added to the 3’ sugar of the existing chain of DNA. 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 by product
3. A phosphodiester bond is formed between the new nucleotide and the existing strand of DNA

Question 13

Describe how DNA base pairs link.

Answer 13

Adenine pairs with Thyamine
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, becase they run in opposite directions

Question 14

Describe how DNA forms a double stranded helix.

Answer 14

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, the bases stack themselves in the center while the sugar-phosphate backdone remains outside. In order for the bases to come into contact with as little water as possible, this “ladder” of double-stranded DNA twists to become a spiral staircase.

Question 15

How is DNA organized within genes?

Answer 15

Genes
Genes contain information to make a protein, and this is refered to as coding DNA. In eukaryotes these genes are located on chromosomes and are separated by large spaces of DNA called noncoding DNA. These do not correspond to protein production.

Coding
Exons are the sections of a gene that contain the information that is used to make a protein, called coding sequences, or coding DNA. Introns are sections of DNA that are not used to make a protein, called noncoding sequences, or non-coding DNA. There are also sections termed regulatory sequences which control when a gene is turned on or used. The important thing to take away is that ost of a gene is not actually used to make a protein - only a small amount is.

Genes to Proteins
From the coding sequences in a gene, a protein will ultimately be made.

Question 16

How do you think an understanding of hydrogen bonds influenced the discovery of DNA structure?

Answer 16

Understanding how the bases could pair together to maximize hydrogen bonds gave Watson and Crick an idea about how wide the structure of DNA could be.

Question 17

What is the main role of RNA in eukaryotic cells?

Answer 17

To carry information that tells the cell what kind of proteins to make.

Question 18

How does RNA differ from DNA?

Answer 18

1. In RNA, the pyrimidine uracil is used instead of thymine
2. The nucleotides in RNA contain ribose rather than deoxyribose
   - 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 therefor is less stable than DNA

Question 19

What are the types of RNA?

Answer 19

Messenger RNA (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
- Ribosomes are a complex made up of rRNA and ribosomal proteins and is in charge of producing proteins in the cell 

Ribosomal RNA (rRNA): make up ribosomes, which are in charge of translating RNA into protein

Question 20

Outline the 5 levels of DNA Packaging.

Answer 20

1. DNA double helix formation
2. Nucleosomes “Beads on a String”
   - DNA is wrapped twice around proteins called histones, which shortens the DNA 7 fold
   - The DNA wrapped histones are called nucleosomes
   - Individual nucleosomes are separated by linker DNA to form the “beads on string” structure
   - In a nucleosome, approx. 200 base pairs of DNA are wrapped around a core of eight histones (in an oxtameric arrangement)
   - Histone H1 pins the DNA to the core particle
3. 30nm Chromatin Fiber
   - The string of nucleosomes is coiled into a spiralling fiber, forming a helical structure with a diameter of 30nm
   - This shortens the DNA 42 fold
4. Chromatin Looped Domain
   - The 30nm chromatin fiber is formed into loops with an average length of 300nm
   - This shortens the DNA 750 fold
5. Heterochromatin
   - The looped domains are further compressed and folded into lengths of approx. 700nm
   - The heterochromatin is hyper condensed DNA - it is present is inactive regions of chromosomes and the entire chromosomes will be in this form in cells undergoing cell division

Question 21

Describe the difference between Euchromatin and Heterochromatin.

Answer 21

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 and 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 22

What is the Central Dogma of molecular biology?

Answer 22

A set of principles that explain how DNA contains the instructuions for building RNA and proteins, which are essential for the structure and function of the cell and body.

Question 23

What are the 3 components of the Central Dogma?

Answer 23

Replication: DNA is copied before a cell divides so that both the original cell and the new cell each have complete copies of DNA. The major enzyme involved in this process is DNA polymerase.

Transcription: information from a section of DNA is copied into RNA to transport this information out of the nucleus for protein production. The major enzyme involved in this process is RNA polymerase.

Translation: the RNA is read and translated to produce proteins that perform a specific function in the cell. The major enzyme involved in this process is the ribosome.

Question 24

Briefly purpose of DNA replication and its semi conservative nature.

Answer 24

Every cell contains a complete copy of DNA. Therefore, DNA must be copied in preparation for cell division, so the new cell will have a copy of the genome.

DNA replication is semi conservative, meaning that when DNA is replicated, one strand of the partent DNA is used as a template for the daughter DNA. The end result is that in every cell, one strand of the DNA is the original parent strand and the other is newly synthesized (the parent DNA is “semi” conserved).

DNA is most vulnerable to damage during replication becase the conds between the two strands are broken. There are many proteins that try to make this process less risky for the cell.

Question 25

What are the 4 steps in DNA replication?

Answer 25

1. Unwinding of DNA
   - Double stranded DNA needs to be separated into single strands to begin replication
   - DNA replication occurs at regions in the DNA called the 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 - where the rest of replication occurs
   - Note that this step requires energy
2. RNA Primers Bind to Unwound DNA
   - Now that the DNA is unwound, the logical next step is to begin copying the freshly exposed single strands of DNA
   - The enzyme that accomplishes this is DNA polymerase
   - It can only copy a stand of DNA if it has a short piece of RNA cound to it
   - Therefore, before the cell can copy DNA it must add a primer that is made up of RNA -it does this by using the enzyme primase
3. Elongation by DNA Polymerases

Leading Strand (3’ to 5’ direction)

• DNA polymerase can only add nucleotides to the 3’ end of a DNA strand and therefore can only move along the parent strand of DNA in the 3’ to 5’ direction, creating a new strand that is in the 5’ to 3’ orientation
• DNA polymerase catalyzes the new phosphodiester bond between an incoming nucleotide and the existing nucleotide on the backbone - it also ensures that the incoming nucleotide is the correct base pair match to the parent strand

Lagging Strand (5’ to 3’ direction)

• 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
• However, they cannot ward off damage indefinitely, and still need to be synthesized as soon as possible

4. Termination of DNA Replication
   - Now that all RNA primers have been removed, there is a new problem: the primers that were at the tip of the leading and lagging strand have been removed, but there is no upstream piece of RNA for DNA polymerase to start synthesis of DNA to replace them
   - If this were to be left as it is, there would be a very small region of parent strand DNA that is left unreplicated; this would be degraded, since single strand DNA is unstable
   - Therefore, after every cycle of DNA replication, there would be a gradual loss of DNA at this end, causing chromosomes to shrink over time, which would be very damaging to a cell
   - -> The solution to this problem in the cell are structures that extend the end of DNA called telomeres
   - -> Telomeres are long, noncoding sections of DNA at the ends of the DNA molecule
   - -> Since they are non functional, they can be degraded over cell cycles without affecting cell function

Question 26

What are Okizaki fragments?

Answer 26

• 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 patches are called Okazaki fragments
• These fragments are why replication is considered semi discontinuous - the leading strand is synthesized in one continuous process, but the lagging strand is synthesized in many discontinous chunks
• An enzyme goes through and replaces the RNA primers in both strands with DNA
• These new fragments of DNA where the RNA primers used to be are not bound to the other fragments
• An enzyme called a ligase goes through the new strand of DNA and catalyzes these bonds
• Once all of the RNA pimers have been replaced with DNA and ligase had joine the backbones of the Okaziki fragments

Question 27

Describe how telomeres work.

Answer 27

1. The enzyme that adds telomeres called telomerase. It is a unique and interesting enzyme, and it is quite different from the other enzymmes involced in DNA replication. It carries a short piece of RNA within the enzyme that binds to the 3’ overhang and extends past the DNA.
2. This RNA is then used as a template and a DNA polymerase adds a corresponding DNA strand to this extension.
3. There is now an extra long 3’ overhand that contains repetitive. non-functional DNA. An RNA primer is added, and DNA polymerase adds DNA like usual until there is not enough of a 3’ lead for the enzyme to proceed.
4. Telomerase repeats this process several thousand times, creating the long ends of the chromosomes.

Question 28

How can DNA be damaged?

Answer 28

DNA replication is not perfect, mistakes occur frequently. It is estimated that approximately 6 errors occur every time the cell replicates. DNA can also be damaged by other factors like ultraviolet light, oxidation or DNA breaks.

Question 29

What happens when DNA is damaged?

Answer 29

When DNA damage occurs, the result is a mutation in the DNA. A mutation is any change in the DNA structure that results in a variant form that can be passed on to subsequent generations.

Mutations are the underlying cause of many illness and disease. However, they are also how a species can evolve and an essential part of life.

Question 30

Explain the advantages to DNA repair.

Answer 30

DNA repair is important becasue DNA contains all of the information that cells inherit from their ancestors. DNA damage, which could include loss of segments of DNA, could remove some of this information, reducing a cell’s abiliy to perform vital functions. Because DNA is so essential, DNA integrity is a top priority for cells. Cells use multiple strategies to protecting DNA from damage repairing damage that occurs, and correcting errors in DNA sequence.

Question 31

What are the 2 types of DNA repair?

Answer 31

1. Repair during DNA replication: DNA polymerase has a proofreading function and can chekc 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