It means that most genes encode proteins

He was the first to point out the specific relationship between gene and enzyme (first evidencce of specific relationship of gene and enzyme). He delivered a lecture on "Inborn Errors of Metabolism" before the Royal College of Physicians of London in June 1908.

He studied alkaptonuria which is a human disease that turns urine black upon exposure to air.

Garrod made the conclusion that Alkaptonuria is genetically controlled because:

-the Frequency is high in families with alkaptonuria and it is common in first cousin mating but not in mating with unrelated partners.

-Also, it is inherited within family generations, hence it must be genetically controlled.

NORMAL PHENYLALANINE PATHWAY

PHENYLALANINE PATHWAY WITH ALKAPTONURIA

What is the defective enzyme in the pathway involving phenylketonuria?

METABOLIC PATHWAY OF SOMEONE WITH PHENYLKETONURIA

It causes a blockage in the phenylalanine pathway which typically manifests in the form of mental retardation and or excretion of phenylalanine. 

METABOLIC PATHWAY OF SOMEONE WITH ALBINISM

There is mutation in phenylalanine hydroxylase leading to the accumulation of phenylalanine (because it failed to be broken down via normal pathway), and eventually, conversion into phenylpyruvic acid resulting to low serotonin and mental retardation.

There is mutation in the tyrosinase enzyme which blocks the patway, and consequently, no melanin production or no melanin production leading to no pigmentation (found in Humans, birds, snakes, and peacocks).

Archibald Garrod's implications stated that inborn errors of metabolism are due to defective enzyme (defective phenylalanine hydroxylase in phenylketonuria, and defective tyrosinase in albinism), which in turn, may be due to _________ ___________.

They proposed the one gene, one enzyme hypothesis which means that a gene is responsible for an enzyme, and an enzyme in turn, catalyzes a step in a metabolic reaction.

So, if you have a mutan gene, you will not have a functional enzyme, and there will be a block in the metabolic pathway.

One gene, one enzyme hypothesis was modified into this because not all proteins are enzymes; some are or most are structural protein. Proteins are gene products, but not all proteins are enzymes. 

One gene, one protein was further modified into this because they noticed that in hemoglobin, it is composed of:

HEMOGLOBIN - Four polypeptide chains: 2 alpha and 2 beta chains.

In the same way, in antibodies, they are composed of:

ANTIBODIES - Four polypeptide chain: 2 heavy chain and 2 light chain.

Not all proteins are made up of only one polypeptide chain.

Proteins are __________ structures. From proteins, we have the expression of phenotypes.

Different Functions of Proteins and Enzyme that lead to trait expression

Strasr-e

It is a principle that prooves that for all organisms, there is transfer of information from DNA to RNA to Protein.

DNA Replication is a pre-requisite to gene expression.

It contains the information for making one RNA and, in most cases, one polypeptide. 

A DNA sequence to which the transcription enzyme (RNA polymerase) binds.

The main enzyme for transcription.

PROKARYOTIC TRANSCRIPTION

It occurs in conserved sequences in the promoter.

What are the two important bacterial promoter?

PROKARYOTIC TRANSCRIPTION

If you move upstream prior (5' end), you will find  this at -10.

PROKARYOTIC TRANSCRIPTION

If you move upstream even further, you will find this promoter at -35.

PROKARYOTIC TRANSCRIPTION

The promoter sequence along the direction of the transcription.

PROKARYOTIC TRANSCRIPTION

It serves as the DNA template strand for transcription

It requires RNA polymerase and sigma factor.

PROKARYOTIC TRANSCRIPTION

It is a transcription factor that recognizes the promoter sequences so that the RNA polymerase can selectively bind to it.

Together with the RNA polymerase, it will bind to the promoter site and start the complementation of the DNA with RNA bases starting at the +1 Site. 

PROKARYOTIC TRANSCRIPTION

In this stage, the RNA polymerase is mainly used. RNA synthesis via RNA polymerase happens with respect to the elongating RNA. 

RNA Synthesis strand has the same sequence as coding strand, but replace the Thymine with Uracil.

PROKARYOTIC TRANSCRIPTION

When the RNA polymerase reaches the site called terminator site, it will dislodge from the DNA together with the Rho factor that aids in the ____________ of transcription.

PROKARYOTIC TRANSCRIPTION

Protein that binds to the RNA polymerase and disassociates it from the DNA to terminate transcription.

PROKARYOTIC TRANSCRIPTION

A type of rho termination where the Rho factor joins the RNA polymerase so to stop or aid in termination.

PROKARYOTIC TRANSCRIPTION

A type of rho termination for some bacteria that do not require a Rho factor to terminate transcription.

It mediates (acts as an intermediary to) protein synthesis. It carries the message which are read as triplet bases comprising one codon. A succession of codons from the start (AUG) codon.

It transports amino acids to the ribosome. It brings the amino acids to the site of translation/protein synthesis. 

Amino acids are attached to the 3 prime end of the tRNA (at the top)

It is the structural and catalytic component of ribosomes. Is a major component of the ribosomes. Small subunit and large subunit that come together to make up the functional ribosome during translation/protein synthesis.

BASIC TYPES OF RNA

Prokaryotic vs Eukaryotic Transcription

RNA Pol I makes

RNA Pol II makes

RNA Pol III makes

What is the other name for the TATA box of the eukaryotic promoter of transcription? It is upstream -25 to -30.

In the eukaryotic transcription, it is upstream -75 to -85.

In the eukaryotic transcription, it is downstream. It encompasses the TTS (-2 to +5) 

Some RNA remain as RNA like tRNA and rRNA, while some are translated into __________ ______.

It is a three-base sequence in the mRNA that specifies an amino acid.

It is a three-base sequence in a tRNA that base pairs with a specific codon.

The set of 64 codons and the amino acids they stand for. What is means to be a triplet base sequence.

It is triplet, non-overlapping, universal (same genetic code for all organisms), degenerate (one amino acid may be coded for by more than one codon. e.g. UAU and UAC both code for Tyr), wobble (means that the precise pairing occurs in the 1st and 2nd bases of the codon and anticodon), and unambiguous (It is rare that one codon specifies more than one amino acid; can be 1 amino acid coded by many codons, but never many amino acid coded by one codon;

1 codon = 1 amino acid)

A single chain of amino acids linked by peptide bonds.

TRANSLATION

It requires the active utilization of Adenosine Triphosphate (ATP) and the action of the enzyme aminoacyl tRNA synthethase. 

TRANSLATION

What is formed when the amino acids attach to their respective tRNAs at the expense of one ATP molecule?

TRANSLATION

The enzyme responsible for the attachment of amino acids to their respective tRNAs at the expense of 1 ATP molecule.

It stimulates the disassociation of small and large subunits of the ribosomes.

It binds to the small subunit to prevent reassociation of ribosomal unit.

It will fetch the tRNA and will help recognize the start codon

TRANSLATION

It is the reptition of steps that involves EFs, ribosome, mRNA, tRNA with amino acid, and peptidyl transferase.

TRANSLATION

It catalyzes the binding of aminoacyl-tRNA to A site.

It catalyzes the formation of peptide bond between fmet and amino acid carried by tRNA in the A site which forms peptidyl-tRNA or peptide bonds. It forms peptide bonds through the already charged amino acyl-tRNA.

TRANSLATION

It displaces the A site to be available again for the next amino acid-tRNA complex.

TRANSLATION: ELONGATION STAGE

TRANSLATION

TRANSLATION

It is the end stage of translation. 

3 Stop Codons

TRANSLATION

It binds to UAG and UAA

TRANSLATION

It binds to UGA and UAA

TRANSLATION

Its role is assisting or aiding the release factor 1 and release factor 2 to release the polypeptide chain.

As the ribosome moves to the 5 prime to 3 prime direction, eventually, the A site will reach and read the stop codons which are UAG, UAA, and UGA. When this happens, there is no amino acid that enters; no corresponding amino acids.

But, the release factors will bind to the A site in order to initiate what proces in order to release the free polypeptide from the tRNA?

TRANSLATION

After the polypeptide chain is free or is released from the tRNA and the translation is complete, this factor stimulates again the disassociation and disassembly of the large and small subunits for the release of mRNA and the release of the release factors. 

What are the two terminuses of a polypeptide chain?

RESEARCHERS INVOLVED IN DECIPHERING THE GENETIC CODE

He proposed the need for a genetic code system.

RESEARCHERS INVOLVED IN DECIPHERING THE GENETIC CODE

In 1961, Francis Crick and his students established some rules for the genetic code. Which of the following IS NOT true?

RESEARCHERS INVOLVED IN DECIPHERING THE GENETIC CODE

They made synthetic RNAs using polynucleotide phosphorylase enzyme, with which they were able to make synthetic RNAs. This study eventually lead to the discovery of the genetic code.

The enzyme that Marianne Grunberg-Manago and Severo Ochoa used to make synthethic RNAs.

It is an important enzyme that is used in the laboratory to synthesize artificial RNAs from which, later on, could be used to deduce the genetic code.

RESEARCHERS INVOLVED IN DECIPHERING THE GENETIC CODE

They used the findings of Marianne Grunberg-Manago and Severo Ochoa.

They produced artificial mRNA and introduced it into a cell-free system to have translation in a test tube. 

When they put together a series of U, it gave polyphenylalanine.

When they put together a series of C, it gave polyproline.

He constructed synthetic mRNA with different repeating nucleotide combinations. He used repeating dinucleotide, trinucleotide, tetranucleotide synthetic mRNA. He contributed the final identification of the codons for the 20 amino acids. Thus, he won the Nobel Prize in 1968 with Marshall Nirenberg (and Holley) for their Contribution to the Genetic Code.

8 NATURE AND CHARACTERISTICS OF THE GENETIC CODE

COLINEARITY OF A GENE AND PROTEIN

He discovered the linear correspondence between the DNA sequence and the order of amino acids. It means that the nucleotides of the DNA sequence correspond to the linear sequence of the amino acids they code for. 

He compared the positions of mutations in the DNA with the amino acid alterations in the protein, and they proved to match. Hence, the DNA sequence has a direct correspondence to the order of amino acids. 

What is the 21st amino acid encoded by UGA (a stop codon)? It is found in Archae, Eubacteria, and Animals.

What is the 22nd amino acid encoded by UAG (a stop codon)? It is found in Archae, specifically Methanosarcina barkeri.

OMICS TECHNOLOGIES

It is the molecular analysis of the entire genome of species. 

It is the genome-wide gene expression profiling. 

Systematic study of all proteins in a cell or tissue; amounts of the different proteins, modifications, interactions, localization, and functions. 

High throughput characterization of the small molecule metabolites in an organism. 

Totality of genes

Totality of RNA

Totality of proteins

Totality of sugars, nucleotides, amino acids, and lipids (lipodome)

Metabolites lead to what?

3 Eukaryotic Processing after Transcription, Before Translation (pre mRNA)

The addition of a 5 prime 7-methylguanosine cap which protects the mRNA from degradation and assists in ribosome binding during translation. 

3 Eukaryotic Processing after Transcription, Before Translation (pre mRNA)

Removal of introns and joining of exons.

Are intervening DNA sequences found in between the exons.

Sequences in a gene that code for amino acids. They contain codons.

3 Eukaryotic Processing after Transcription, Before Translation (pre mRNA)

This protects the mRNA from degradation in the cytoplasm. It aids in transcription termination and helps in the export of the mRNA from the nucleus to the ribosomes for translation.

SPECIAL TRANSFERS

The ability of the cells to determine which genes should be expressed, when these genes should be expressed, where these genes would be expressed, and how much of each gene product should be expressed.

Switching on (being transcribed and translated) and switching off (not being transcribed nor translated) of genes in response to the needs of a cell or the organism.

Constantly being transcribed

expressed all the time

Gene products are essential for maintenance

Always expressed because they constitute the cell and are important for survival. For example, genes for all enzymes in the glycolitic pathway are essential for energy generation.

Needs repressors in order to stop (entails the use of repressor). Tryptophan Operon is an example of this.

Needs activators to start (entails the use of activators to turn on). Lac Operon is an example of this.

A group of functionally related genes.

With multiple coding sequences which encodes several proteins.

A group of genes encoding enzymes for lactose utilization. Lactose as source of energy. System is normally turned off. Inducible System.

COMPONENTS OF AN OPERON IN GENERAL

Gene that codes for a repressor protein that can bind to the operator to regulate the activity of the operon. Lac I for Lac Operon and Trp R for Trp Operon

COMPONENTS OF AN OPERON IN GENERAL

Where RNA polymerase bind to initiate transcription

COMPONENTS OF AN OPERON IN GENERAL

Beside the promoter

Regulatory DNA sequence located near or within the promoter (near if Lac Operon, within if Trp Operon). Acts as binding site for a repressor protein.

COMPONENTS OF AN OPERON IN GENERAL

The actual genes within the operon that encode proteins needed for a specific function.

COMPONENTS OF AN OPERON IN GENERAL

Signals the end of transcription

LAC OPERON

The regulatory gene which codes for the repressor that will bind to the operator in order to regulate how operon activates; codes for and transcribes protein. Its product is an active repressor that is ON by default.

LAC OPERON

Codes for B-galactosidase which breaks down lactose into glucose and galactose as well as converts it into allolactose which will serve as the inducer.

LAC OPERON

Codes for lactose permease which transports lactose into the cell.

LAC OPERON

Codes for thiogalactosidase transacetylase which is for lactose metabolism; needed by the cell in order for the toxic byproducts of lactose metabolism to not accumulate and not cause toxicity. No direct function but cleans up the byproducts of lactose breakdown.

Mnemonics for the Essential Genes and Regions for Lac Operon

What if there is no Lac I or if the Lac I is mutant?

What if there is No Lac P or If it is a Mutant P?

What is there is No Lac O or if it is a Mutant O?

What if there is No Lac Z?

What if there is no Laz Y?

What if there is no Lac A?

Group of genes encoding enzymes for tryptophan synthesis/biosynthesis. System is normally on, so you must turn it off if too much. Repressible System. REPRESSIBLE

The body needs tryptophan because it is an essential amino acid for metabolic processes like melatonin production.

TRYPTOPHAN OPERON

The regulatory gene in the tryptophan operon which codes for the repressor that is the inactive repressor. Repressor is OFF by default.

TRYPTOPHAN OPERON

The promoter site of tryptophan operon

TRYPTOPHAN OPERON

The operator site of the tryptophan opperon. It lies within the promoter since the tryptophan promoter and tryptophan operator are overlapping/they overlap. So, if the repressor binds to operator, it also prevents the binding of RNA polymerase on the promoter since trp promoter and trp operator overlap.

TRYPTOPHAN OPERON

The one that binds or attaches to the aporepressor (inactive repressor), and it is the tryptophan itself, in order to make the aporepressor active and able to attach to the tryptophan Operator.

TRYPTOPHAN OPERON

Structural genes that code for anthranilate synthetase, indole glycerol phosphate synthethase, and tryptophan synthetase which are the enzymes that are functional for the production of tryptophan/tryptophan synthesis. 

If one of these are lost, the tryptophan synthesis would cease to exist.

EUKARYOTIC GENE REGULATION

Genes are quickly turned on and off

Rapid adjustment to local environment or physiological changes

EUKARYOTIC GENE REGULATION

Events required for an organism to develop and differentiate.

What is the name of the eukaryotic transcription model?

Which of the following is NOT a component of the Britten-Davidson Eukaryotic Transcription Model?

Regulatory network where multiple integrators allow each sensor to control multiple structural genes. Regulatory network where multiple receptor sites allow expression of structural genes by several activator RNAs. 

Hormonal Control of Gene Expression is an example of a eukaryotic gene regulation where the steroid hormones (estrogen) enter the cell, and once inside the cell, it binds to the receptor to make the hormone-receptor complex which enters the nucleus. 

Consequently, it would be the sensor which activates the integrator gene to transcribe the activator RNA. Then, the activator RNA triggers the receptor which leads to the structural gene to induce transcription and translation into polypeptide.

Further foldings of the polypeptide chain makes it a functional protein; either structural or enzyme protein.

Protein bases on the structural protein.

The sequence of the gene reflects on the RNA where the codon is. When the codon is translated, it leads to expression of phenotype.

DNA to Protein — hardware of the cell to produce a trait. For example, why this gene color is expressed given a DNA, and the enzymes for melanin synthesis.