Module 3 - The Endoplasmic Reticulum

Question 1

What does the ER consist of?

Answer 1

ER is made up of a network of membranes called cisternae. The cisternae of the ER are connected to the outer nuclear envelope.

The 2 sections of ER are:

1. The rough ER (RER) and the ribosomes attached to it. RER is the site for protein translation and some modification.

The Rough ER is rough because of the ribosomes attached to it. The ribosomes are enzyme made or rRNA and composed of 2 subunits and are the major enzyme responsible for protein production and translation.

2. The smooth ER (SER)
   •synthesis and processing of lipids, phospholipids, and steroids
   •location of carbohydrate metabolism
   •location where glucose-6-phosphate can be converted to glucose
   •in muscle cells, the SER regulates calcium ion concentration, which is important for muscle contraction

Question 2

How is the nucleus connected to the ER?

Answer 2

The nucleus is connected to the ER cisterna by the outer layer of the nuclear envelope. Some of the nuclear pores connect the nuclear envelope with the ER membranes so molecules can pass through these structures freely

Question 3

Define the following:

• Proteins to be Transported
• Transport Vesicle
• Golgi Apparatus

Answer 3

• Proteins that have been made in the E R shuttle to the Golgi for further modification.
• These are used to carry proteins that still need to be modified between the E R and the Golgi apparatus.
• This organelle is involved in protein modification and transport.

Question 4

What are the 2 faces of the Golgi Apparatus?

What are the Cisternae of the GA?

Answer 4

Cis face of the Golgi apparatus
This is the side of the Golgi apparatus that faces the ER.

Trans face of the Golgi apparatus
This is the side of the Golgi apparatus that faces away from the ER

These are flattened disks of membrane. The Golgi has different enzymes and functions in the different cisternae.

Question 5

What are the benefits are to using RNA instead of DNA in cellular processes outside of the nucleus?

Answer 5

The main points to take away are that the combination of DNA, RNA and protein offer a “division of labour” of sorts (much like the many organelles in a cell). This allows the integrity of the genetic material as DNA being protected in the nucleus, so it is segregated from other cellular processes, with RNA being able to leave and make protein. This also allows an increasing complexity in cellular processes, since you can have many more genes preserved in a cell and being translated to a variety of proteins at the same time. The structure of DNA also lends itself better to the role of genetic code- it is more stable than RNA due to features in its structure (deoxyribose vs ribose, double stranded vs single stranded). Finally, the structures of the 20 amino acids allow more variety and flexibility in the potential of different chemistry and physical shapes than only using RNA-based enzymes and structures.

Question 6

What are the 3 types of RNA?

Answer 6

Messenger RNA

mRNA is RNA that will be translated into protein. Unlike rRNA and tRNA, it is a coding template for peptides. Any RNA molecules that do not serve as a template for protein are called noncoding.

Ribosomal RNA
These RNAs make up the ribosome complex to translate messenger RNA into protein. There are two subunits that make up a ribosome that are different sizes. In humans, the large ribosomal subunit is ~5,000 nucleotides, and the small ribosomal subunit is ~1,900 nucleotides. These are key parts of the machinery that makes proteins.

Transfer RNA

TRNAs serve as linker molecules that link specific building blocks of proteins (amino acids) to the mRNA that is coding the peptide during translation. TRNAs are tiny compared to most mRNA, measuring in at 73-93 nucleotides long.

Question 7

What are some other noncoding RNAs?

Answer 7

Short interfering R N A (siRNA) will bind to messenger R N A and cause it to be degraded. This effectively turns off the gene.

Question 8

Where does transcription occur?

Answer 8

Nucleus

Question 9

What is the role of RNA polymerase?

Answer 9

The actual synthesis of RNA from DNA is facilitated by an enzyme, termed RNA polymerase. Eukaryotes have 3 types, each of which makes a different kind of RNA. RNA polymerase II (pol II) synthesizes mRNA. RNA polymerase I is responsible for catalyzing most of the rRNA required for a functional ribosome. RNA polymerase III synthesizes transfer RNA, as well as some other RNA molecules.

Question 10

What is the role of transcription factors?

Answer 10

Transcription factor is a protein that binds to specific DNA sequences, and by doing so controls the rate of transcription from DNA to messenger RNA. Transcription factors perform this function alone or with other proteins in a complex. Transcription factors can promote (as an activator) or block (as a repressor) the transcription of genes by altering the ability of RNA polymerase to start transcription.

Question 11

Describe the three stages of transcription

Answer 11

1. Initiation

Binding of transcription factors to the Transcription Start Point. Upstream of the start point is a region of the gene termed the promoter. The promoter region closest to the transcription start point is the core promoter, since it is essential for transcription. Transcription factors bind to the core promoter at a sequence called the TATA box. Once the transcription factors are bound to the TATA box, RNA polymerase II can bind to the promoter.

Binding of all of these transcription factors facilitates transcription by 3 mechanisms:

1. Guiding RNA polymerase II to the correct DNA strand
2. Unwinding the double stranded DNA enough for RNA polymerase II to access the gene being transcribed
3. Activating the enzyme function of RNA polymerase II by adding two phosphate groups to it (a process called phosphorylation)
4. Elongation

The moving of the transcription complex (made up of R N A polymerase and the transcription factors) forward is the second stage of transcription. RNA polymerase extends the RNA molecule 5’ to 3’ while reading the DNA template strand. The entire region of unwound DNA, called the transcription bubble, is covered by the RNA polymerase. This protects the unwound single-stranded DNA from damage.

3. Termination

Termination step is the least understood in eukaryotes, since eukaryotes do not have defined methods to stop transcription. Research has indicated that there are proteins that can bind to RNA polymerase II to induce termination. Transcription normally ends when the RNA is literally cut from the RNA polymerase by a separate enzyme.

Question 12

What is post transcriptional RNA processing?

Answer 12

In order to keep the newly created RNA long enough in the cell to produce the appropriate proteins some modifications are made after synthesis.

1. The first modification is the addition of the 5’ methylguanosine cap on the mRNA. The cap is consisted of a guanosine triphosphate (GTP) and is added to the 5’ end of the mRNA via an unusual 5’ to 5’ triphopshate linkage. The GTP has a methyl group added to the 7 position immediately after capping.

The reason for this cap is to protect mRNA from premature degradation.

2. Then the 3’ Polyadenylation step occurs
   - adds around 200 adenosine to the 3’ end of the mRNA immediately after it is cut from the R N A polymerase II.

This creates a structure called a poly (A) tail.The poly (A) tail is essential for binding proteins that are necessary to transport the m R N A out of the nucleus and to start translation.

3. RNA Splicing
   Genes are organized into exons and introns. All the introns need to be removed

Transport to the cytoplasm occurs after post -transcriptional modifications.

Question 13

How does RNA exit the nucleus?

Answer 13

A complex of proteins binds to the messenger R N A to assist in its transport out of the nucleus through the nuclear pore complex.

Question 14

What is translation?

Answer 14

Translation is the third and final step in the Central Dogma processes. It involves taking the mRNA transcript of a gene and converting it to a functional protein.

Question 15

How do 4 DNA bases give us the language for 20 different amino acids?

Answer 15

• It does so by using sequences of three R N A nucleotides, each of which corresponds to a specific amino acid or stop signal during protein synthesis.
• One sequence of 3 nucleotides that codes for an amino acid is called a codon.

3 bases = 4x4x4= 64 possible different codons. Enough for 20 amino acids and a stop codon. But this also means that there are multiple codons for some amino acids.

Question 16

What are protein factors?

Answer 16

Initiation factors bind to the mRNA, including the methyl-guanosine cap on the 5’ end of the m R N A. These help the small ribosomal subunit identify the initiation site.

Elongation factors (EFs) are proteins that assist in elongation. Some EFs form complexes to deliver the tRNAs and the GTP energy source to the ribosome.

Question 17

Describe the role of ribosomes

Answer 17

The ribosome is composed of a large and small subunit, both made of ribosomal RNA (rRNA). The small subunit is responsible for binding to the mRNA, while the large subunit has four important sites where the peptide is built.
•A site: where tR N As first attach to the ribosome.
•P site: where newly arrived amino acid is removed from its t R N A and added to the growing peptide by a peptide bond.
•E site: where the spent t R N A is ejected from the ribosome.
•Finally, there is the polypeptide exit tunnel, where the peptide is guided and is ultimately released.

Question 18

Describe the role of tRNA

Answer 18

Each tRNA will recognize a codon and be attached to its accompanying amino acid.

• The job of the t R N A is to deliver the correct amino acid to the growing peptide.
• It does this by containing a complimentary sequence to the codon, termed the anticodon.
• T R N As are also bonded to an amino acid.

The bond holding the amino acid to the t R N A provides the energy to make the new peptide bond on the growing amino acid chain.

Question 19

What are the 3 steps of translation?

Answer 19

1. Initiation - First, the small ribosome subunit attaches to the mRNA molecule near the methyl-guanosine cap at the 5’ end where initiation factors are bound.

It then crawls forward until the correct A U G sequence is found (start codon). The initiator t R N A then binds to it, and the large ribosomal subunit encloses the m R N A, with the initiator tRNA in the P-position.

2. Elongation is a multiple step cycle in translation, and moves forward as a continuous loop. •Each cycle adds one amino acid to the growing chain of amino acids, called a peptide.
3. Termination -
   The growing peptide chain ends when the stop codon is reached (U AA, UAG, U G A). They are not connected to a tRNA molecule unlike the other codons. Rather, they attract release factors, which also fit into the A site of the ribosomes. It substitutes water for the amino acid to attach to the peptide in the P site, and leads to the production of a carboxylic acid and releases the peptide.

Finally, a ribosome release factor occupies the A site. This then leads to the release of the large and small ribosome subunits from the m R N A, and these can be recycled for more translation.

Question 20

What are the 4 major types of mutations?

Answer 20

Point Mutation - Single nucleotide is changed. Has three outcomes :
•Silent mutation: The mutation does not cause the amino acid to change.
•Missense mutation: the mutation does cause the amino acid to change.
•Nonsense mutation: the mutation replaces an amino acid codon with a stop codon, ending translation, and preventing the production of the rest of the amino acid. This is very detrimental, specially near the start of a sequence.

Insertion - An extra base pair is added to DNA. This shifts the 3-base pair reading frame down by one, which can alter every amino acid produced. A similar reading frame-shift effect is seen with two base pairs, but three will add a new amino acid.

Deletion - A base pair is removed from the D N A sequence. Like insertion, this alters the reading frame if not in multiples of three

Large Scale Deletion, Insertion, Recombination - his can involve entire chromosomes or just parts of chromosomes. These changes are often lethal.

Question 21

List and describe the categories of the amino acids based on their R groups?

Answer 21

1. Hydrophobic amino acids are also called non polar. They can be aliphatic, which indicates the R chain is a straight carbon chain, or aromatic, which indicates a circular carbon R chain with double bonds. These amino acids are normally found in the core of the protein, or interacting with other hydrophobic molecules like fats or lipids in a membrane
2. The aromatic amino acids have ring structures with double bonds that have distinct properties associated with this chemical structure. These are very large, and the gain or loss of these amino acids can cause deformities in the protein structure.
3. The polar hydrophilic side chains can form hydrogen bonds that stabilize proteins. These are more common on the outside of a protein.
4. These amino acids carry a positive or negative charge, and are therefore hydrophilic. They are found on the outside of proteins where they can interact with water

You will see that similarly charged amino acids cluster around each other in the genetic code. If

Question 22

What are amino acids linked together by?

Answer 22

Amino acids are linked together through the peptide bond.
•The carboxylic acid group of one amino acid and the amino group of the second amino acid undergo a dehydration step. This linkage is the peptide bond. •Peptide bonds occur only between these two groups, and not the R groups of the amino acids. The amino acids can rotate around these bonds.
•In a long chain of amino acids held together by peptide bonds, there will be two distinct ends: one with the amino group free, and one with the carboxylic acid group free.
•These are called the amino terminus and the carboxy terminus

Question 23

What are the 4 types of protein structures?

Answer 23

1. The primary protein structure is the linear peptide sequence. This is simply the linear amino acid sequence. These can be written using the three letter amino acid codes or single letter amino acid codes as short hand.
2. Secondary protein structure are the regions of organization in the peptide sequence. Some examples of common secondary structures are: Alpha helix:this is a tight coil that forms hydrogen bonds with the backbones of every fourth amino acid. Beta sheets: planes are formed between rows of amino acids with hydrogen bonds between the backbones.
3. Tertiary (3°) structure is the 3D structure of the complete protein. This is defined by the secondary structures and domains of the protein. For a protein to properly fold, other proteins (molecular chaperones) are necessary to achieve the correct shape.
4. Quaternary structure is when multiple proteins are assembled into a complex.The individual proteins are called subunits if they cannot have a function outside the complex.

Question 24

What is a domain?

Answer 24

Domain is the basic building block of a protein structure. Certain protein domains have some clearly defined function associated with them, like an enzyme.

Question 25

What are the 2 major type of protein shape modifications the cells can make?

Answer 25

• Covalent modifications are relatively long lasting. Disulfide bonds, and the addition of sugar structures are examples. Adding phosphate groups, methyl groups, or acetyl groups are all methods of changing protein shape. These will activate or inactivate proteins, or change how they can interact with other proteins in the cell.
• Non- covalent modifications are relatively short lived. This can include proteins interacting with each other in binding sites, or small molecules like calcium or magnesium binding transiently.