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Biochemistry > Regulation Of Gene Expression > Flashcards

Regulation Of Gene Expression Flashcards

1
Q

What is a gene?

A

General definition: Basic unit of inheritance of a characteristic.
Biological definition: Sequence of nucleotides in DNA ( a segment) that is transcribed to produce a functional RNA.
Genes act as instructions for the synthesis of aspecific protein (e.g. an enzyme)

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2
Q

State the structure of a gene

A

DNA & RNA are nucleic acids made up of nucleotides.
NUCLEOTIDES are made up of nitrogenous bases( Purines and Pyrimidines) , Sugar( Ribose and Deoxyribose) and a phosphate group

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3
Q

List the types of nitrogenous bases and their subtypes

A

PURINES( Adenine and Guanine)
PYRIMIDINES ( Cytosine, Thymine, Uracil)

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4
Q

State the modified and other bases that make up nucleotides

A

MODIFIED BASES: 3 methyl cytosine, 5 OH methyl cytosine and methylated guanine in mRNA.
OTHER BASES: Hypoxanthine, xanthine, uric acid

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5
Q

What are the functions of nucleotides?

A
  1. Form of energy in the cell- ATP,GTP,UTP
  2. Intermediates in metabolic reaction- UDPglucose.
  3. Second messengers-cAMP
  4. Coenzymes: NAD, FAD & Coenzyme A.
  5. Building blocks of nucleic acids
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6
Q

Describe the synthetic bases and anti-metabolites that are used in therapy

A

A. 5Fluorouracil: Analogue of Uracil. it is converted to 5 Flourouracil monophosphate an inhibitor of thymidylate synthase that catalyses the conversion deoxyuracil monophosphate to deoxy thymine monophosphate.
B. methotraxate: Analogue of dihydrofolate. It inhibits dihydrofolate reductase that catalyses the reduction of Dihydrofolate to tetrahydrofolate an esssential coenzyme in DNA synthesis. Rapidly dividing cells like cancer cells are more susceptible.
C. Allopurinol:- Analoque of xanthine and hypoxanthine. It inhibits the enzyme xanthine oxidase.

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7
Q

Via which pathways are nucleotides synthesized?

A

De novo
Salvage

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8
Q

Briefly describe the de novo synthesis of nucleotides

A

Purine ring: synthesized while attached to Ribse 5 Phosphate. synthesis from simple molecules amino acids glycine, glutamine and aspartate, carbon dioxide and formate donated by tetrahydrofolate
Pyrimidine ring: the pyrimidine ring is attached to ribose 5 phosphate after the ring has been synthesized. The synthesis of pyrimidine begins with the construction of the nitrogenous base and ends with the addition of the sugar and phosphate group

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9
Q

What happens in the salvage pathway of nucleotides?

A

Nitrogenous bases and nucleosides from the breakdown of old nucleotides are recycled to synthesize new nucleotides

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10
Q

Draw the purine structure and identify the sources of its atoms

A

Nitrogen 1(N1) = aspartate.
Carbon 2(C2)= N10 formyl tetrahydrofolate.
Nitrogen 3( N3)= amide nitrogen of glutamine.
Carbon 4, carbon 5 and nitrogen 7 ( C4,C5, N7)= glycine
Carbon 6( C6) = carbon dioxide
Carbon 8(C8) = N10 formyl tetrahydrofolate.
Nitrogen 9( N9)= amide nitrogen of glutamine.

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11
Q

Outline the reactions in purine biosynthesis

A
  1. Ribose 5 P + ATP →5-phosphoribosylpyrophosphate+ AMP (PRPP SYNTHETASE) committed step
  2. 5-phosphoribosylpyrophosphate +glutamine→ 5-phosphoribosylamine +PPi+ glutamate (PRPP AMIDOTRANSFERASE/ Glutamine PRPP amidotransferase)
  3. 5- phosphorobosylamine +glycine+ ATP→ 5-phosphoribosyyglycinamide + ADP + Pi (5- phosphoribosyl glycinamide SYNTHETASE/GAR Synthetase)
  4. Glycinamide ribonucleotide + formyl T4F → formyl glycinamide ribonucleotide + T4F (GAR TRANSFORMYLASE) FIRST OF 2 THF DEPENDENT RX
  5. FGAR +glutamine+ ATP → formyl glycinamidine ribonucleotide + ADP+ Pi (FGAR AMIDO TRANSFERASE)
  6. FGAM + ATP→ 5-amino imidazole ribonucleotide ADP+ Pi (glycinamidine ribonucleotide CYCLASE)
  7. AIR + CO2→ carboxyamino imidazole ribonucleotide (AIR CARBOXYLASE)
  8. CAIR + aspartate + ATP → N succinylo 5 amino imidazole 4 carboxamide ribonucleotide+ ADP +Pi (SAICAR SYNTHETASE)
  9. SAICAR → N 5 amino imidazole carboxamide ribonucleotide+ fumarate (adenylo succinate LYASE)
  10. AICAR + formyl T4F → FAICAR + T4F (AICAR TRANSFORMYLASE)
  11. FAICAR → inosine monophosphate + H2O (IMP SYNTHASE)
    Once formed, IMP is rapidly
    converted to AMP and GMP
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12
Q

Draw the pyrimidine structure and identify the sources of its atoms

A

The sources of atoms of the pyrimidine ring.
C2 and N3 = carbamoyl phosphate
C4, C5, C6 and N1 = aspartate

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13
Q

What metabolic defects can result from purine synthesis?

A

Gouty arthritis,
Lesch Nyhan disease

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14
Q

What metabolic defects can result from pyrimidine synthesis?

A

orotic aciduria types 1 and 2

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15
Q

What are the fundamental features of replication?

A

i) semi conservative,
ii)begins at the origin and proceeds bidirectional at the replication folk,
iii) semi discontinous

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16
Q

Briefly state the functions of the main enzymes involved in replication

A

DNA Polymerase I (gap filling, repair and recombination.
DNA Polymerase II(proof reading and repair).
DNA Polymerase III processitivity{ number of nucleotides added before the enzyme dissociates} and strand synthesis)

17
Q

What are histones?

A

proteins attached to chromosomes. have a role to play in gene expression

18
Q

What are the mutations seen in sickle cell due to replication fault?

A

For example point mutation seen in Sickle Cell.
Glutamate Codon
GAA GUG
GUU
GUC

Valine Codon GUA
GAG

19
Q

List the type of DNA damage

A
  1. Single base alteration- deamination of cytosine to uracil, Insertion or deletion of a nucleotide.
  2. Two Base alterations . Formation of thymine dimer
  3. Chain breaks by UV light
20
Q

What are the mechanisms of DNA repair?

A

Mismatch repair.
Nucleotide excision.
Base excision repair

21
Q

Briefly describe transcription

A

Only one strand serves as a template- the template strand.
The other strand is the coding strand and runs in the same direction as the RNA molecule that is being transcribed( 5’ to 3’ direction).
Initiation, elongation, termination, post transcription modification.
RNA: Single stranded They are Four types( mRNA,rRNA,tRNA and sRNA)

22
Q

Briefly describe translation

A

The linear sequence of DNA that was transcribed into mRNA is translated into linear sequence of amino acid residues of a protein
The mRNA sequence that specifies for the AA sequence in the protein is called the genetic code with 64 triplet codons.
The features of the genetic code.
The stages of protein synthesis.

23
Q

Describe the first step of gene expression

A

THE TRANSCRIPTION OF THE SEGMENT OF DNA INTO RNA.
Transcription is a regulated process that allows a cell or organism to adapt to environmental changes. For example, it controls on when a protein should be produced and how much.
Gene expression process involves modulation(control) of Gene Transcription
In the control of gene transcription specific regulatory proteins bind to regions of DNA in the controlled gene which causes: positive(activate) or negative(inhibit) effect on transcription.

24
Q

Explain the mechanism of gene regulation / transcriptional control

A
  1. Using specific binding proteins that bind to the regulatory (promoter) segment of a gene.
  2. Gene regulation is influenced by chemicals such as hormones.
  3. Gene expression can also be modulated by gene amplification which leads to increase in the number of copies of the gene. This is seen in cancer cells which cause the cancer cells to grow and multiply uncontrollably.
  4. Gene rearrangement mechanisms. Reconstitute a gene from gene segments in gene recombination. This is seen in Genetically Modified Organisms.
  5. Post transcriptional modifications of RNA also contribute to control of gene expression
25
Q

What is a cistron?

A

The smallest unit of genetic expression is called a cistron. One cistron codes for only one polypeptide

26
Q

What is polycistronic mRNA?

A

a gene can code for an mRNA that encodes more than one separately translated protein. Such an mRNA is referred to as polycistronic mRNA

27
Q

What is an operon?

A

In bacteria, genes involved in one metabolic pathway are often present in a linear array called and operon.
An operon is regulated by one promoter or regulatory region

28
Q

Operons and polycistronic mRNAs are common in…?

A

Operons and polycistronic mRNAs are common in prokaryotic systems but not in eukaryotes

29
Q

Briefly describe a well-studied example of an operon

A

A well studied example of an operon is the Lac operon in the intestinal bacterium E.coli.
This is a sequence of three genes encoding for enzymes involved in metabolism of lactose

30
Q

Who described the operon model?

A

Jacob and Monod in 1961 described the operon model.
They observed lactose metabolism by an intestinal bacterium E.coli

31
Q

Describe the gene and enzyme system for LAC operons

A

Three genes code for three enzymes as follows:
-Lac Z is the gene for b-Galactosidase responsible for hydrolysing lactose.
- Lac Y is the gene responsible for producing the protein that assists in permeation of galactose into the cell.
-Lac A is a gene encoding Thiogalactoside
transacetylase.(unknown function)

32
Q

What constitutes a LAC operon?

A

The structural genes for these three enzymes along with the lacl gene (lac operon repressor), CRE( cAMP response element), lac promoter, lac operator are physically associated to constitute a Lac operon
This genetic arrangement for structural genes and the regulatory genes allows for coordinate expression of the 3 genes that produce the three enzymes in lactose metabolism
Each protein is translated separately with its own start and stop signals.

33
Q

Describe the role of glucose as a carbon source for a LAC operon

A

When glucose is present the lacl gene produces the lac operon repressor protein that binds to the Operator and prevents the RNA polymerase to bind to the Promoter gene to initiate the transciption of the 3 genes for the three enzymes because the 3 enzymes are not needed under the circumstances.

34
Q

Describe the role of lactose as a carbon source in a LAC operon

A

When lactose is present, adenyl cyclase is activated to produce cAMP which binds to the cAMP activator protein(CAP) to form CAP-cAMP complex which binds to the CRE(cAMPResponse Element). This activates the binding of the RNA Polymerase to the Promoter gene activating the transcription of the 3 genes

35
Q

What is an inducible gene?

A

inducible gene is one whose expression increases in response to an inducer or activator, a specific positive regulatory signal.
Inducible genes have low basal rates of transcription

36
Q

What is a housekeeping gene?

A

Housekeeping genes are genes whose expression is constitutive, meaning that they are expressed at a reasonably constant rate and not known to be subject to regulation. For example genes that produce enzymes that are in major metabolic pathway

Biochemistry (12 decks)

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