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a. Epigenetic control
- control of gene expression by altering the chromatin structure (relaxed or compact)
- compact DNA is inaccessible for transcription
- compaction of the chromatin is influenced by modifications to histones and the DNA
- the overall pattern of chromatin modification in a cell or an organism is called epigenome
- ex: paramutation; effect of maternal diet on baby's development; genetic imprinting

b. Transcriptional control
- transcriptional activators bind to enhancers and increase transcription by stimulating / stabilizing the assembly of the basal transcription apparatus
- insulators block the action of enhancers

c. RNA processing
- capping, splicing, poly(A) addition, alternative splicing, RNA editing

d. RNA stability
- degradation of the 5'cap, poly(A) tail, the 5' UTR, the RNA-coding region, and the 3' UTR affect stability of mRNA

e. RNAi
- uses short double-stranded RNAs known as miRNA and siRNA as a guide to suppress gene expression
- only eukaryotes
- RNA cleavage; blocking translation; chromatin condensation

f. Translation control and polypeptide processing
- translatoin initiation proteins bind to the 5' UTR and facilitate the binding of ribosomes
- the translation of some RNAs is affected by the binding of proteins to sequences in the 3' UTR
- some mRNAs regulate translation by forming secondary structures

g. Protein localization
- protein marked by Ubiquitin
- proteasome recognize, choose protein, and recycle amino acids

h. Protein turnover

In eukaryotic cells, transcription takes place in the _____________. In bacteria, transcription takes place in the _____________.

(A) Cytosol, Nucleus
(B) Nucleus, Cytosol
(C) Endoplasmic Reticulum, Nucleus
(D) Nucleus, Endoplasmic Reticulum

(B) Nucleus, Cytosol

In eukaryotic cells, transcription takes place in the Nucleus. In bacteria, transcription takes place in the Cytosol.

During the process of transcription, the RNA goes through some extra steps such as adding a cap, adding a tail, and the splicing of introns. In which type of cell does this extra processing occur?

(A) Prokaryote
(B) Eukaryote
(C) Both Prokaryote and Eukaryote
(D) Neither

(B) Eukaryote

Extra processing of the RNA such as adding a cap, adding a tail, and the splicing of introns take place only in eukaryotic cells.

Describe the process of Alternative Splicing. Does it happen in Prokaryotes, Eukaryotes, or Both?

Alternative Splicing occurs in Eukaryotes, and is when exons (as well as introns) could be removed from the RNA during processing to form mRNA. This allows multiple proteins to be formed from the same sequence of DNA.

What enzyme is responsible for constructing mRNA using DNA as a template?

(A) DNA Polymerase
(B) RNA Polymerase
(C) DNA Transcriptase
(D) RNA Transcriptase

(B) RNA Polymerase

RNA polymerase is responsible for constructing mRNA using DNA as a template.

What is the primary difference between the promoters found in the DNA of eukaryotic versus prokaryotic cells?

Promoters in eukaryotic DNA are longer and more abundant than those in prokaryotic cells.

Which of the following is the common name for the Eukaryotic Promoter?

(A) TATA Box
(B) Shine Delgarno Sequence
(C) GCCG Box
(D) GCGCCG Prinbow Box

(A) TATA Box

The TATA Box is the common name for the Eukaryotic Promoter, based off of its sequence.

What is the difference between the template strand and coding strand in the process of transcription?

The template strand is the strand of DNA that the RNA Polymerase reads as it generates mRNA.

The coding strand is not read by RNA Polymerase. Its sequence resembles the newly synthesized strand of mRNA except that the coding strand contains Thymine instead of Uracil.

True or false? The Coding Strand is also called the Sense Strand.

True. The Coding Strand is also called the Sense Strand.

RNA Polymerase reads the template strand in the _______ direction, and RNA is generated in the ________ direction.

(A) 5' to 3', 5' to 3'
(B) 5' to 3', 3' to 5'
(C) 3' to 5', 3' to 5'
(D) 3' to 5', 5' to 3'

(D) 3' to 5', 5' to 3'

RNA Polymerase reads the template strand in the 3' to 5' direction, and RNA is generated in the 5' to 3' direction.

Which of the following nitrogenous bases is NOT found in mRNA?

(A) A
(B) T
(C) C
(D) G

(B) T

You will not find the base Thymine in RNA. Instead, Adenine will pair with Uracil (A-U). The base pair Cytosine-Guanine (C-G) remains the same.

What would be the mRNA strand from the template strand:
3'-TACTAG-5'?

(A) 5'-AUGAUC-3'
(B) 5'-ATGATC-3'
(C) 5'-GAUCAU-3'
(D) 5'-GACTAT-3'

(A) 5'-AUGAUC-3'

The template strand 3'-TACTAG-5' will have an mRNA strand of 5'-AUGAUC-3'.

Which of the following are mechanisms that may allow an RNA polymerase to know when to stop transcription?

I. RNA polymerase recognizes a known sequence of DNA called a terminator that signals the RNA polymerase to stop transcription.
II. mRNA forms a hairpin on itself that impairs the polymerase from moving forward.
III. RNA Polymerase receives a signal from telomerase that the DNA template is ending, causing transcription to end.

(A) I Only
(B) I and II Only
(C) II and III Only
(D) I and III Only

(B) I and II Only

The following are mechanisms that allows an RNA polymerase to know when to stop transcription

1. RNA polymerase recognizes a known sequence of DNA called a terminator that signals the RNA polymerase to stop transcription.

2. mRNA forms a hairpin on itself that impairs the polymerase from moving forward.

Which of the following is a difference between the mRNA from Prokaryotic cells versus Eukaryotic cells?

I. In Prokaryotic cells, the RNA polymerase directly makes the mRNA without any extra processing.
II. In Eukaryotic cells, mRNA contains exons, which are later removed with further processing.
III. In Prokaryotic cells, mRNA undergoes translation and transcription simultaneously.

(A) I Only
(B) I and II Only
(C) I and III Only
(D) I, II, and III

(C) I and III Only

The following are differences between the mRNA from Prokaryotic cells versus Eukaryotic cells:

- In Prokaryotic cells, the RNA polymerase directly makes the mRNA without any extra processing.

- In Eukaryotic cells, mRNA contains INTRONS, which are later removed with further processing.

- In Prokaryotic cells, mRNA undergoes translation and transcription simultaneously.

Fill in the blanks: In Eukaryotes, mRNA is ______________, so each mRNA molecule can only be translated into one protein. In _____________, each mRNA molecule can be translated into different proteins, making this mRNA _________________.

(A) Monoprotomic, Archaea, Polyprotomic
(B) Monoprotomic, Prokaryotes, Polyprotomic
(C) Monocistronic, Prokaryotes, Polycistronic
(D) None of the above.

(C) Monocistronic, Prokaryotes, Polycistronic

In Eukaryotes, mRNA is Monocistronic, so each mRNA molecule can only be translated into one protein. In Prokaryotes, each mRNA molecule can be translated into different proteins, making this mRNA Polycistronic.

Introns are removed via a process known as __________________.

(A) Dicing
(B) Splicing
(C) Cutting
(D) Crossing

(B) Splicing

Introns are removed via a process known as splicing.

What is the difference between introns vs. exons in terms of expression?

Introns are noncoding regions while exons are coding regions. This means that introns will not be expressed and exons will encode all of the expressed proteins.

Which of the following is not a modification made to pre-mRNA before it becomes mature mRNA?

(A) The addition of 5' cap
(B) The addition of the poly-A tail
(C) The splicing of introns
(D) The removal of telomeric mRNA

(D) The removal of telomeric mRNA

After RNA polymerase makes pre-mRNA, the pre-mRNA goes through some modifications such as:

- the addition of a 5' cap

- the addition of the poly-A tail

- the splicing of introns

What is the role of polyadenylate polymerase?

Polyadenylate polymerase is the enzyme responsible for catalyzing the construction of the poly-A tail.

True or False? The poly-A tail may assist in the termination of transcription.

True. The poly-A tail may assist in the termination of transcription.

What is the function of the spliceosome?

The spliceosome is responsible for splicing introns out and ligating exons together in making mature mRNA.

What is the spliceosome composed of?

(A) snRNA and snoRNA
(B) snRNA and snRNP
(C) snoRNA and snRNP
(D) snRNA and miRNA

(B) snRNA and snRNP

A spliceosome is a complex protein composed of small nuclear RNA (snRNA) and small nuclear ribonucleic proteins (snRNP) and it is responsible for post-transcriptional splicing of introns in mRNA.

The spliceosome splices introns through:

(A) Two sequential transesterification reactions followed by a ligation reaction.
(B) Two sequential ligation reactions followed by a transesterification reaction.
(C) One transesterification reaction followed by two sequential ligation reactions.
(D) One ligation reaction followed by a two sequential transesterification reactions.

(A) Two sequential transesterification reactions followed by a ligation reaction.

The spliceosome splices introns through two sequential transesterification reactions and a ligation.

True or False? A single strand of mRNA is always transcribed and translated simultaneously.

False. A single strand of mRNA is transcribed and translated simultaneously in prokaryotic cells since both processes occur in the cytoplasm. In eukaryotic cells, however, mRNA is transcribed in the nucleus, processed, and then transported to the cytoplasm to be translated by the ribosome.

After post-transcriptional modifications are complete, where will the mature mRNA go next?

(A) Cytosol
(B) Golgi
(C) Nucleolus
(D) Lysosome

(A) Cytosol

After a eukaryotic cell makes a mature mRNA, the mRNA would exit the nucleus and go to the cytosol where the ribosomes are located. It will then undergo translation.

What are the primary components of a ribosome?

I. tRNA
II. rRNA
III. Proteins

(A) I and II Only
(B) I and III Only
(C) II and III Only
(D) I, II, and III

(C) II and III Only

A ribosome is composed of proteins and ribosomal RNA (rRNA).

Compare the functions of ribosomal RNA (rRNA) and messenger RNA (mRNA).

Ribosomal RNA (rRNA) provides both a functional and structural role within the ribosome, a key participant in protein translation.

True or false? Many rRNA actually form Ribozymes, which are like enzymes that are not made out of proteins.

True. Many rRNA actually form Ribozymes, which are like enzymes that are not made out of proteins.

What is the function of the ribosome?

Ribosomes read an mRNA template to produce a polypeptide.

Ribosomes read the mRNA template from the ___ end to the ___ end.

(A) 3', 5'
(B) 3', 3'
(C) 5', 3'
(D) 5', 5'

(C) 5', 3'

Ribosomes read the mRNA template from the 5' end to the 3' end.

What is the difference between a codon vs. an anti-codon?

A codon is composed of three nucleotides found on the mRNA that code for an amino acid.

An anticodon is part of transfer RNA (tRNA) that complements the mRNA, positioning the tRNA and its attached amino acid for addition to the polypeptide. tRNA are specific for each amino acid.

What is the start codon's function and structure?

The start codon (AUG) is where the ribosome initially attaches to start translating the messenger RNA. This AUG sequence encodes for the amino acid Methionine.

What are the stop codons' function and structures?

The stop codons (UAA, UGA, UAG) signal the ribosome to stop translating. They do not encode for any amino acids.

Think "U Are Annoying", "U Go Away", and "U Are Gone".

The t-RNA with the anticodon of UAC will initially bind at which site within the ribosome?

(A) A-site
(B) E-site
(C) P-site
(D) S-site

(C) P-site

UAC is the anticodon for AUG, which is the start codon. This tRNA molecule carries methionine into the P site to start the translation process.

In Prokaryotes, where does the small Ribosomal Subunit first bind for translation?

(A) Shine-Dalgarno Sequence
(B) TATA box
(C) TATAAT
(D) Inititator sequence

(A) Shine-Dalgarno Sequence

The Shine Dalgarno-sequence is in the 5' untranslated region of the RNA, and is where the small Ribosomal Subunit first binds.

At which site on the ribosome will an incoming tRNA (other than the tRNA with the anticodon of UAC) bind?

(A) A-site
(B) E-site
(C) P-site
(D) S-site

(A) A-site

The A-site on the ribosome is where the tRNA initially enters carrying an amino acid. The name "A-site" comes from the word "amino acid."

Which site on the ribosome holds the growing polypeptide chain?

(A) A-site
(B) E-site
(C) P-site
(D) S-site

(C) P-site

The P-site on the ribosome is where the polypeptide chain is forming. The name "P-site" comes from the word "polypeptide."

From which site on the ribosome does the empty tRNA exit?

(A) A-site
(B) E-site
(C) P-site
(D) S-site

(B) E-site

The E-site on the ribosome is where the empty tRNA exits. That name "E-site" comes from the word "exit."

True or false? After the ribosome releases the newly-formed proteins, another class of proteins called Chaperones help this protein be transported.

False. After the ribosome releases the newly-formed proteins, another class of proteins called Chaperones help this protein fold properly.

As the tRNA in the P-site shifts to the E-site, which of the following is true?

I. The ribosome shifts towards the 5' end of the mRNA.
II. The tRNA in the A-site shifts to the P-site.
III. The amino acid from the A-site moves to bind to the polypeptide chain in the P-site.

(A) I Only
(B) II Only
(C) I and II Only
(D) I, II, and III

(B) II Only

As the tRNA in the P-site shifts to the E-site...

- The ribosome shifts towards the 3' (NOT 5') end of the mRNA.
- The tRNA in the A-site shifts to the P-site.
- The polypeptide chain in the P-site moves to bind to the amino acid in the A-site.

True or false? There are multiple Hairpin Loops typically seen in tRNA.

There are multiple Hairpin Loops typically seen in tRNA.

Which of the following terms can be used to describe a tRNA molecule that is bound to an amino acid?

I. Charged
II. Paired
III. Activated

(A) II only
(B) I and III only
(C) II and III only
(D) I, II and III

(B) I and III only

A tRNA molecule that is bound to an amino acid is typically described as Charged or Activated.

The bond between an amino acid and a tRNA is a high-energy bond. How many molecules of ATP are required by the Aminoacyl-tRNA Synthase enzyme (the enzyme that forms this bond) to form this bond?

(A) 0
(B) 1
(C) 2
(D) 3

(C) 2

2 molecules of ATP are required for each bond formed between an amino acid and tRNA (catalyzed by Aminoacyl tRNA Synthase).

What site does the ribosome recognize and initially bind to in eukaryotic vs. prokaryotic cells?

The ribosome recognizes and binds to the 5' cap of eukaryotic mRNA.

The ribosome recognizes and binds to the Shine-Delgarno Sequence of prokaryotic mRNA.

True or False? The Shine-Delgarno Sequence acts as a both a 5' cap and a start codon.

False. The Ribosome recognizes and binds to the Shine-Delgarno Sequence and then moves down the mRNA strand until it reaches the start codon (AUG) where it will start translation. Furthermore, the Shine-Delgarno-Sequence doesn't provide protection to the mRNA strand like the 5' cap does.

True or False? Prokaryotic mRNA does not contain any non-coding regions.

False. From the 5' to 3' end, prokaryotic mRNA contains non-coding mRNA, the Shine-Delgarno Sequence, non-coding mRNA, the start codon, coding mRNA, the stop codon, and then more non-coding mRNA

Eukaryotes contain a 5' cap and a poly-A tail to protect their mRNA. Compare the composition of these two structures.

The 5' cap is a methylated guanosine tripohosphate while the poly-A tail is a string of hundreds of adenine nucleotides.

Why doesn't prokaryotic mRNA need the 5' cap and poly-A tail?

The prokaryotic mRNA does not have the 5' cap and poly-A tail because transcription and translation both happen simultaneously in the cytosol; thus, the mRNA does not need to "travel."

For eukaryotic mRNA, on the other hand, it needs to exit the nucleus and travel to the ribosome, and the 5' cap and poly-A tail are added on as extra protection.

During translation in _____________ cells, the first amino acid in the polypeptide chain is formylmethionine. During translation in _________________ cells, the first amino acid in the polypeptide chain is methionine.

(A) Eukaryotic, Eukaryotic
(B) Eukaryotic, Prokaryotic
(C) Prokaryotic, Prokaryotic
(D) Prokaryotic, Eukaryotic

(D) Prokaryotic, Eukaryotic

During translation in Prokaryotic cells, the first amino acid in the polypeptide chain is formylmethionine. During translation in Eukaryotic cells, the first amino acid in the polypeptide chain is methionine.

What role does formylmethionine play in the human body?

Formylmethionine acts as an alarm system in the human body and can trigger an immune response. It basically tells your body that there is a foreign bacteria invader.

Compare Missense, Nonsense and Frameshift Mutations.

Missesne mutations replace one amino acid for another.
Nonsense mutations will add a premature stop codon, and can also be called a Truncation Mutation.
Frameshift mutations alter the number of nucleotides in the sequence, and will affect the amino acid sequence for all following codons.

True or false? Because the genetic code is Degenerate and the third nucleotide could be changed and not alter the amino acid coded for, there are also Silent or Degenerate Mutations that do not affect the protein.

True. Because the genetic code is Degenerate and the third nucleotide could be changed and not alter the amino acid coded for, there are also Silent or Degenerate Mutations that do not affect the protein.

What is the central dogma of molecular biology?

In what direction is the DNA template strand being read during transcription? What direction is mRNA being synthesized?

DNA is read 3 to 5
mRNA is made 5 to 3

What the following types of RNA to their function

(A) mRNA
(B) tRNA
(C) rRNA
(D) snRNA

I. brings amino acids by recognizing the codon on the mRNA using the anticodon
II. contains information that is translated into protein
III. aids in the splicing by forming the spliceosome
IV. makes of the enzymatically active ribosome

(A) mRNA --> II
(B) tRNA --> I
(C) rRNA --> IV
(D) snRNA --> III

Define monocistronic and polycistronic. Do prokaryotic or eukaryotic generate these types of mRNA?

monocistronic: mRNA creates 1 protein --> eukaryotic mRNA

polycistronic: mRNA can result in different proteins --> prokaryotic mRNA

What enzyme is responsible for the activation/charged tRNA?

(A) aminoacyl-tRNA synthetase
(B) ribozymes
(C) A and B
(D) None of the above

(A) aminoacyl-tRNA synthetase

this enzyme is responsible for attaching the correct amino acid onto the 3 prime end of the tRNA

Draw the structure of a tRNA. Label the 5 and 3 prime end and the where the anticodon is found

the 3 prime end is the location where the amino acid attachment site

Why is the aminoacyl tRNA bond a high energy bond? What purpose does this serve?

the aminoacyl tRNA bond is a high energy bond because the aminoacyl-tRNA synthetase hydrolyses ATP to AMP to generate the high energy ester bond. This is useful because the energy of that bond can be used to catalyze the formation of a peptide bond during translation

Why is the genetic code considered to be degenerate?

its degenerate because more than one codon can specify a single amino acid

Describe the wobble position in the genetic code and its purpose

In the genetic code, we know that more than one codon can specify a single amino acid. The first 2 bases are usually the same but the third base in the codon is variable --> this third base is called the wobble position

It is believed the wobble portion is designed to protect against mutations

T/F mutations in the wobble poisition are considered to be frameshift mutations

F

mutations in the wobble position are POINT mutations. Specifically it is a silent mutation because it has no effect on protein synthesis

Match the following mutations to their correct description

(A) Nonsense mutations
(B) Missense Mutations
(C) Frameshift mutations
(D) Silent mutations

I. mutation that produces a codon that codes for a different amino acid
II. mutation in which nucleotides are added or deleted causing a shift in the reading frame
III. mutation where the codon encodes for a premature stop codon
IV. a point mutation where it has no effect on protein synthesis

(A) Nonsense mutations --> III
(B) Missense Mutations --> I
(C) Frameshift mutations --> II
(D) Silent mutations --> IV

What do missense, nonsense and silent mutations have in common?

They are all point mutations

T/F RNA polymerase requires a primer to generate a transcript

F

RNA Polymerase DOES NOT require a primer in order to generate a transcript

The TATA box on the promoter region is also known as the ___ site

(A) -25
(B) -65
(C) 25
(D) 65

(A) -25

the TATA box is also the -25 site

T/F transcription factors aid RNA polymerase onto the TATA box

T

transcription factors help bring RNA Polymerase 2 to the correct spot

Where does transcription begin?

(A) -1 site
(B) +1 site
(C) 0 site
(D) None of the above

(B) +1 site

the +1 site is the first base transcribed from DNA --> RNA

Match the correct RNA polymerase to their function

(A) RNA Pol 1
(B) RNA Pol 2
(C) RNA Pol 3

I. responsible for the synthesis of tRNA and some rRNA
II. responsible for the synthesis of hnRNA
III. responsible for the synthesis of rRNA

(A) RNA Pol 1 --> III
(B) RNA Pol 2 --> II
(C) RNA Pol 3 --> I

What is hnRNA (heterogeneous nuclear RNA)?

hnRNA is pre-mature mRNA it hasn't been modified in any way

The primary transcript formed at the end of transcription is called

(A) mRNA
(B) hnRNA
(C) snRNA
(D) miRNA

(B) hnRNA

at the end of transcription the primary transcript produced is called hnRNA (pre-mature mRNA)

Only after processing has occurred do you generate mRNA

What are the 3 post-transcriptional modifications that must be made in prokaryotic mRNA?

None

Prokaryotic mRNA does not undergo modification because transcription and translation occur simultaneously

What are the 3 post-transcriptional modifications that must be made in eukaryotic mRNA?

1. Splicing (removal of introns and ligatation of axons_

2. addition of a 5 prime methylguanylate triphosphate cap

3. addition of a 3 prime Poly A Tail

What is the purpose of the addition of a 5 prime cap on eukaryotic mRNA?

1. protects mRNA from degradation

2. allows for ribosome recognition

What is the purpose of the addition of a 3 prime Poly A tail on eukaryotic mRNA?

1. protects again degradation
2. aids in the export of mRNA from the nucleus

What molecules are responsible for splicing

I. snRNA
II. snRNPs
III. miRNA
IV. siRNA

(A) I only
(B) IV only
(C) I and II only
(D) I and IV only
(E) I, II and IV only

(C) I and II only

snRNA and snRNPs (snurps) are responsible for carrying out splicing

What functions do both snRNA and snRNPs serve in splicing?

they both recognize the splice sites of introns and remove them

Describe alternative splicing

allows for the generation of multiple proteins from a single transcript. It is also used to regulate gene expression

T/F carrier proteins are responsible for exporting the processed mRNA to the cytoplasm

F

the processed mRNA exits the nucleus through NUCLEAR PORES

T/F Translation requires the use of energy in the form of GTP

T

all the stages involved in translation require GTP to be used as the energy source

The ribosome contains 3 sites. What are they and what do they do?

A site: (aminoacylt t-RNA binding site)

P site: (where the polypeptide chain forms)

E Site: (site where tRNA exits)

T/F the small and large ribosomal subunits bind together to form the initiation complex before the mRNA arrives

F

the small subunit of the ribosome binds to the 5 prime end of mRNA and charged tRNA containing Met binds to the P site --> then the large ribosomal subunit binds to form the initiation complex

What are the 3 stages involved in translation?

Initiation
Elongation
Termination

Put the following steps that occur in initiation in order

I. large subunit binds
II. formation of initiation complex
III. scan for start codon
IV. charged tRNA brings 1st amino acid to P site
V. small ribosomal subunit binds to 5 prime end of mRNA

V. small ribosomal subunit binds to 5 prime end of mRNA
III. scan for start codon
IV. charged tRNA brings 1st amino acid to P site
I. large subunit binds
II. formation of initiation complex

What are the differences in initiation of translation between prokaryotes and eukaryotes?

Prokaryotes:
- small subunit binds to shine dalgarno sequence
- 1st amino acid is fMet

Eukaryotes:
- small subunit binds to the 5 prime cap
- 1st amino acid is Met

T/F the shine dalgarno sequence is found on eukaryotic mRNA and is recognized by the small subunit of the ribosome

F
shine dalgarno sequence is found on PROKARYOTIC mRNA and is recognized by the small subunit of the ribosome

What are the relative sizes of the large and small ribosomal subunit between prokaryotes and eukaryotes. Which has larger ribosomes?

Prokaryotes: 50S and 30S

Eukaryotes: 60S and 40S

eukaryotic ribosomes are larger

T/F the formation of the initiation complex is assisted by initiation factors

T

Initiation factors aid in the formation of the initiation complex

What is the function of peptide transferase in translation?

(A) forms peptide bonds between adjacent amino acids using tRNAs during the translation process of protein biosynthesis
(B) gives the ribosome enzymatic activity
(C) transfers amino acids to the 3 prime end of the tRNA
(D) A and C

A) forms peptide bonds between adjacent amino acids using tRNAs during the translation process of protein biosynthesis

T/F: Peptidyl transferase requires the hydrolysis of GTP to catalyze the formation of peptide bonds

T
Peptidyl transferase requires the hydrolysis of GTP to catalyze the formation of peptide bonds

Which of the following is released after RNA Polymerase reaches the stop codon? What is its function?

(A) Stop proteins
(B) Release Factors
(C) Nothing is release, the polypeptide chain is automatically cleaved
(D) None of the above

(B) Release Factors

release factors cause water to be added to the chain --> hydrolyzes the polypeptide chain --> polypeptide chain is released

T/F only the initiation and elongation phase of translation require energy input in order to proceed

F

ALL STAGES in protein synthesis requires energy

Which of the following is not considered to be post-translational modification

I. Protein Folding
II. Cleavage
III. Formation of quaternary structure
IV. covalent addition of molecules
V. Addition of water

(A) I only
(B) V only
(C) I and V only
(D) I, III and IV only

(B) V only

All of the following are post-translational modification proteins can undergo

- protein folding with the help of chaperones
- cleavage of protein
- formation of quaternary structure
- covalent addition of molecules (phosphorylation, carboxylation, glycosylation, prenylation)

Why does the polypeptide chain undergo post-translational modifications?

tit must undergo these modifications in order to become a fully functioning protein

Match the following covalent modifications to their proper function?

(A) Phosphorylation
(B) carboxylation
(C) Glycosylation
(D) Prenylation

I. addition of lipid groups
II. addition of ogliosaccharides
III. addition of carboxylic acid
IV. addition of phosphate group

(A) Phosphorylation --> IV
(B) carboxylation -----> III
(C) Glycosylation -----> II
(D) Prenylation -------> I

Explain why insulin needs to under go cleavage

When the polypeptide is generated it is inactive therefore cleavage must occur in order to generate the active from of insulin

What is the function of chaperones?

(A) makes sure the right amino acid binds to tRNA
(B) bring RNA Pol to the proper location
(C) aid in protein folding
(D) All of the above

(C) aid in protein folding

Chaperones ensure the proteins are folded in their proper low energy state

Compare heterochromatin and euchromatin.

Heterochromatin: tightly coiled DNA, appears dark under microscope, genes are silenced

Euchromatin: loosely coiled DNA, genes are active

Match the following to the type of chromatin they will generate

(A) Histone Acetylation
(B) Histone deacetylation
(C) DNA methylation

I. Heterochromatin
II. Euchromatin

(A) Histone Acetylation --> II
(B) Histone deacetylation --> I
(C) DNA methylation ---> I

How does the following affect gene expression?

(A) Histone Acetylation
(B) Histone deacetylation
(C) DNA methylation

(A) Histone Acetylation --> increases gene expression --> active genes
(B) Histone deacetylation --> decreases gene expression --> silences genes
(C) DNA methylation --> decreases gene expression --> silences genes

What are the 3 methods to regulate chromatin structure?

1. Histone Acetylation
2. Histone deacetylation
3. DNA methylation

Describe the affects of histone acetylation on gene expression. What enzyme is responsible for this?

Histone acetylene causes the acetylation of histone proteins --> decreases the (+) charge of lysine residues --> weakens interaction of DNA and histones --> opens chromatin --> easily accessible to transcription machinery --> increases gene expression

Describe the affects of histone deacetylation on gene expression. What enzyme is responsible for this?

histone deacetylases remove acetyl groups --> causes closed chromatin conformation --> decreases gene expression --> silenced genes

Describe the affects of DNA methylation on gene expression. What enzyme is responsible for this?

DNA methyl's adds methyl groups to cysteine and adenine bases --> hinders acmes to transcriptional machinery --> decreases gene expression --> silences genes

T/F DNA methylation occurs on thymine and guanine bases

F

DNA methylation occurs on CYSTEINE and ADENINE bases

Which method can be used for gene amplification?

(A) enhancers
(B) gene duplication
(C) A and B
(D) None of the above

(C) A and B

gene amplification can be done though enhancers and gene duplication

Enhancers are transcription regulatory sequences that function by enhancing the activity of

(A) RNA polymerase at a single promoter site
(B)RNA at multiple promoter sites
(C) transcription factors that bind to promoter but not to RNA polymerase
(D) spliceosomes and lariat formation in the ribosome

(A) enhances activity of RNA polymerase at a single promoter site

specific transcription factos bind to specific DNA sequence, such as an enhancer, and to RNA polymerase at a single promoter sequence. They enable RNA polymerase to transcribe the specific gene for that enhancer more efficiently

Describe how gene duplication functions to cause gene amplification

duplicate the relevant genes either in series or parallel so you've generated many genes of interest on to the chromosome

There are 2 types of operons: Inducible system and Repressible system. Whats the difference between them?

Inducible System: system that is normally turned off, but the presence of a specific molecule can make it turn on

Repressible System: system that is normally turned on but the presence of a specific molecule can make it turn off

Compare positive and negative control in operons

Positive control: when the binding of protein to DNA cause an increase in transcription

Negative control: when the binding of protein to DNA causes a decrease in transcription

the lac operon is a ____ _____ system while the trp operon is a ___ ____ system

Fill in the blank:
Repressible, inducible, positive negative

the lac operon is a NEGATIVE INDUCIBLE system while the trp operon is a NEGATIVE REPRESSIBLE system

Gene expression is regulated at the level of:

(A) Replication
(B) Transcription
(C) Translation
(D) Post-translational Modification

B) Transcription

Gene expression is regulated at the level of transcription, meaning that at certain times only certain DNA will be expressed and transcribed into RNA. This way, we only produce the proteins we need at a given time.

Why wouldn't it be a great idea for gene expression to be regulated at the protein or mRNA level?

It would not be a great idea for gene expression to be regulated at the mRNA or protein level because it would be a complete waste of energy! It takes a lot of ATP to put together proteins and mRNA, so it would be inefficient to make a bunch of proteins or mRNA that the cell will never use.

An operon is a group of ___________ under the control of ___________.

(A) exons, several promotors
(B) exons, a single promotor
(C) genes, several promotors
(D) genes, a single promotor

(D) genes, a single promotor

An operon is a group of genes under the control of a single promotor.

The Lac operon is a group of genes that code for the enzymes that help e. Coli break down:

(A) a polypeptide
(B) a disaccharide
(C) a phospholipid
(D) a hormone

(B) a disaccharide

The Lac operon is a group of genes that code for the enzymes that help e. Coli break down lactose, the disaccharide found in milk.

Why is regulating the lac operon important for e. Coli?

e. Coli does not need any enzymes to breakdown lactose when there is no lactose present in the first place. Using regulation, e. Coli is able to be more efficient in which proteins it produces.

What binds to the promotor versus the operator?

RNA Polymerase will bind to the promotor. The repressor protein will bind to the operator.

Fill in the blanks: The Lac-Operon is a famous example of a(n) ____________. The trp (Tryptophan-producing) Operon is a famous example of a(n) __________________.

(A) Repressible System, Repressible System.
(B) Inducible System, Repressible System
(C) Repressible System, Inducible System
(D) Inducible System, Inducible System.

(B) Inducible System, Repressible System

The Lac-Operon is a famous example of an Inducible System. The trp (Tryptophan-producing) Operon is a famous example of a Repressible System.

What is the difference between a repressible and inducible operon?

A repressible operon is on until it is turned off ("repressed").

An inducible operon is off until it is turned on ("induced").

What does it mean to say that the repressor protein is "constitutively expressed"?

To say that something is "constitutively expressed" means that its gene is always turned on; thus, in this case, the repressor protein is always being produced.

Describe how the repressor protein regulates gene expression of the lac operon when lactose concentration is high? low?

When high concentrations of lactose are present in e. Coli, allolactose binds to the repressor, thus removing the repressor and allowing RNA polymerase to transcribe the lac operon genes in order to make enzymes to break down the lactose.

CAP is an example of an activator protein. Describe the role and mechanism of action of Catabolite Activator Protein (CAP) in e. Coli.

In E. Coli, cyclic adenosine monophosphate (cAMP) is produced during glucose starvation. Consequently, cAMP binds to a protein called CAP which causes a conformational change that allows the CAP protein to bind to a DNA site adjacent to the promoter. Then the CAP protein recruits RNA polymerase to the promoter..
It is an example of an activator protein because it interacts with the RNA polymerase to help it attach to the promoter sequence thus encouraging the expression of a gene

Describe how a normal inducible system would act

repressor binds to operator --> blocks RNA Polymerase from transcribing structural gene --> decrease transcriptional activity

Describe how an inducible system would act in the presence of an inducer

inducer binds to repressor --> forms inducer-repressor complex --> this complex cannot bind to operator --> allows RNA Pol to move down the gene and transcribes it --> increases transcriptional activity

Describe what is going on in the Lac operon in the absence of lactose

in the absence of lactose --> Lac repressor is made --> lac repressor binds to operator --> inhibits transcription --> decrease transcriptional activity

Describe what is going on in the Lac operon in the presence of lactose

lactose binds to repressor --> forms complex that cannot bind to operator --> allows RNA pol to transcribe gene --> increase transcriptional activity

According to the Jacob-Monod Model an operon contains:

Structural gene
Operator site
promoter site
regulatory gene

What do each of them do?

Structural gene: codes for the protein of interest (target of regulation)
Operator site: region of DNA capable of binding to repressor protein
promoter site: provides place for RNA polymerase to bind
regulatory gene: codes for a repressor that influences the expression of the structural gene

Draw out an operon and place the sites in the correct order

regulatory gene, promoter, operator, structural gene

Explain the function of the DNA binding domain and Activation domain of transcription factors

DNA Binding Domain: binds to specific nucleotide sequences in promoter region to help in the recruitment of transcriptional machinery

Activation Domain: allows for binding of several transcription factors and other regulatory proteins

How is gene expression controlled in prokaryotes

controlled by transcription factors that are transcription activating

Briefly describe how a repressible system operon would normally work

repressor cannot bind to operator --> RNA polymerase moves along the gene and transcribes it --> increases transcriptional activity

Briefly describe how a repressible system operon would function in the presence of a co-repressor

co-repressor binds to repressor to form a complex --> complex binds to the operator site --> prevents transcription by blocking RNA polymerase --> decreases transcriptional activity

Describe how the trp operon acts during high levels of trp

high levels of trp acts as a co-repressor --> Trp binds to repressor and binds to operator site --> prevents transcription by blocking RNA pol --> decrease transcriptional activity

Describe what is going on in the trp operons in the absence of trp

in the absence of trp the trp repressor is inactive --> operon is turned on --> increase transcriptional activity

Which of the following are different between prokaryotic and eukaryotic transcription?

Prokaryotic transcription occurs in the cell cytoplasm and, in prokaryotes, both transcription and translation happen simultaneously. Eukaryotic transcription occurs in the cell nucleus and, in eukaryotes, transcription and translation differ in space and time.

How does transcription differ between bacteria and eukaryotes quizlet?

What about transcription in bacteria and eukaryotes is true? Bacteria use only one RNA polymerase to transcribe RNA, whereas eukaryotes use three.

What is the difference between eukaryotic transcription and bacterial transcription?

Bacterial transcription differs from eukaryotic transcription in several ways. In bacteria, transcription and translation can occur simultaneously in the cytoplasm of the cell, whereas in eukaryotes transcription occurs in the nucleus and translation occurs in the cytoplasm.