Molecular Biology

UNIT 3

MOLECULAR BIOLOGY

Genetic information & nucleic acids

INDEX

1. What is molecular biology?

2. Nucleic acids

3. Genetic messages

4. DNA replication

5. Expression of genetic information

6. The genetic code

7. Mutations

8. Genetic engineering

9. Biotechnology

10. Bioethics

What is molecular biology?

Molecular biology is the science that studies the structure, the function and other aspects of nucleic acids (and other macromolecules present in the cells). It is related to biochemistry and genetics.

The nucleic acids

2.1. Composition of nucleic acids

2.2. Types of nucleic acids

2.3. Nucleic acid structure

2.4. Nucleic acid function

NUCLEIC ACIDS

• Organic macromolecules.
• Macromolecules are polymers; molecules made up of similar subunits called monomers
• Involved in all the processes of storage and expression of genetic information

2.1. Composition of nucleic acids

• Since nucleic acids are polymers, they are formed by groups of nucleotides.
• One nucleotide is made up by 3 basic elements:
1. A phosphate group, derived from H3PO4.
2. A carbohydrate, one pentose monosaccharide.
3. A nitrogenous base, one out of 5 different possiblities (A, C, G, T or U)

2.2. Types of nucleic acids

RNA

DNA

Ribonucleic acid

Deoxyibonucleic acid

• The pentose is an oxyribose.
• The nitrogenous bases found in RNA are:
• Adenine (A)
• Cytosine (C)
• Guanine (G)
• Uracil (U)

• The pentose is an deoxyribose.
• The nitrogenous bases found in DNA are:
• Adenine (A)
• Cytosine (C)
• Guanine (G)
• Thymine (T)

VS

2.2. Types of nucleic acids

RNA

DNA

Ribonucleic acid

Deoxyibonucleic acid

VS

2.3. Nucleic adic structure

PRIMARY STRUCTURE

• Thousands of millions of nucleotides, bonded in order to form long chains.
• One nucleotide's phosphate group bonds with the next nucleotide's pentose.
• This way, the nitrogenous bases remain free.

2.3. Nucleic adic structure

PRIMARY STRUCTURE

• It is present in both RNA and DNA

2.3. Nucleic adic structure

SECONDARY STRUCTURE

• It is present just in DNA (RNA has only primary structure).
• Two chains of nucleotides bond, linking their nitrogenous bases and folding forming a helix that is:
• Antiparallel: they run in opposite directions.
• Complementary: nitrogenous bases are paired.

2.3. Nucleic adic structure

SECONDARY STRUCTURE

• The nitrogenous bases join with hydrogen bonding.
• Each base bonds only with its complementary partner.

2.3. Nucleic adic structure

SECONDARY STRUCTURE Nitrogenous bases pairing

• Adenine always bonds with thymine, or viceversa: A - T / T - A They establish 2 hydrogen bonds.
• Cytosine always bonds with guanine, or viceversa: C - G / G - C They establish 3 hydrogen bonds.

2.3. Nucleic adic structure

SECONDARY STRUCTURE Nitrogenous bases pairing

• Sometimes, RNA also can have paired bases.
• If this happens, cytosine bonds with guanine, the same than DNA.
• However, since there is not thymine in RNA, adenine bonds with uracile.

2.4. Nucleic adic functions

TYPES OF RNA

• Messenger RNA (mRNA). It carries the genetic message with the information to create proteins.
• Transfer RNA (tRNA). It transports the molecules needed to create proteins.
• Ribosomal RNA (rRNA). It forms the ribosomes.

2.4. Nucleic adic functions

DNA FUNCTIONS

• Storing genetic information. It is found in the nuclei of eukaryotic cells.
• Transmitting the hereditary information. That is why it replicates, generating identical copies.
• Controlling the processes of genetic information via transcription and translation in order to build proteins.

2.4. Nucleic adic functions

DNA FUNCTIONS

• Having this in mind, it makes sense that the DNA is the most protected part of the cell: by the plasma membrane, nuclear membrane, folding system...
• It is the key molecule for cells, where all the information they need to function correctly lays. If an invasive agent gets to modify it, it could be lethal for the cell.

The genetic message

The central tenet of molecular biology

• DNA's information has to reach the ribosomes, which are the creators of proteins.
• So, that infromation undergoes several processes:
• The DNA's infromation flows to the mRNA in the transcription process.
• Then the mRNA binds to ribosomes and, with the intervention of tRNA, proteins are built thanks to the translation process.

The central tenet of molecular biology

• The previous processes happen during the greater part of the cell cycle.
• However, during S phase, the genetic information is identically copied from the DNA molecule already existing in the cell, in order to create the 2 DNA molecules that the daughter cells will incorporate. This DNA duplication is known as replication.

The central tenet of molecular biology

The central tenet of molecular biology

The central tenet of molecular biology

• All this processes are directly related with the expression of genetic information, this is, the interpretation of the data in our genes for them to be actually present in real life:
• Replication: DNA > DNA
• Transcription: DNA > RNA
• Translation: RNA > protein
• This processes essentialy consist of chemical reactions, so enzymes are going to be crucial.

The DNA replication

4.1. The replication process

4.2. Characteristics of DNA replication

4.3. Biological importance of DNA replication

4.4. Genes: the basis of life

• Replication is the process by which DNA makes a complementary, identical copy of itself.
• It happens in the S phase of the cell cycle:
• in the nucleus (eukaryotic cells)
• in the cytoplasm (prokaryotic cells)

4.1. The replication process

1. Unwinding and separating the double helix.
2. Building new chains for the new DNA strand.
3. Correcting errors.

4.1. The replication process

1. UNWINDING & SEPARATING

• Helicase enzymes separate a small section of the DNA's double helix, creating the replication fork.
• The fork advances and, by being separated, the strands can act as templates to create a new copy of the DNA.
• So, each of the new double helixes will be formed by one strand of the former DNA and a newly built one.

4.1. The replication process

1. UNWINDING & SEPARATING

4.1. The replication process

2. BUILDING NEW STRANDS

• Two new chains are built thanks to the action of the DNA polymerase enzyme:
• It moves along each template strand.
• It recognises the nitrogenous bases on the template strand.
• It adds the complementary bases to the new strand.

4.1. The replication process

2. BUILDING NEW STRANDS

4.1. The replication process

3. CORRECTING ERRORS

• Once the new chains of nucleotides are complete, different enzymes correct the errors.
• By doing this:
• No nitrogenous bases are wrongly paired.
• The information in the DNA stays unaltered.

4.1. The replication process

3. CORRECTING ERRORS

4.2. Characteristics of DNA replication

1. Semi-conservative. Each new molecule of DNA keeps one chain of the original DNA molecule, the one that was used as template.
2. Bidirectional. The new chain is built in both directions from the replication fork.

4.3. Biological importance of replication

• The new copy of the DNA molecule includes the same unique sequence of nucleotides than the original one. This ensures that the daughter cells conserve the same genetic information than the parental cell. Like this, genetic information will last over time.
• Nontheless, changes might happen: mutations, making evolution possible.

4.4. Genes: the basis of life

• A gene is a biologically significant segment of DNA, this is, the basic unit of genetic information.
• Each gene has a specific number of nucleotides, that encode a very specific order to make a specific protein.
• Genes cannot perform biological functions on their own, proteins are the one that make a genetic trait a reality.

The expression of genetic information

5.1. Transcription

5.2. Translation

• We call genetic expression to the fact of making the information coded on genes real.
• This means the information in genes have to be interpreted to build proteins, which are the molecules that build cells and help them in performing their functions.

5.1. Genetic TRANSCRIPTION

• Transcription is the process by which a chain of messenger RNA is formed from a fragmen of DNA (one specific gene).
• It takes place in the nucleus (or in the cytoplasm if the cell is prokaryotic).
• It has 3 steps: initiation, elongation and termination.

5.1. Genetic TRANSCRIPTION

1. INITIATION

• The chromatin unpacks.
• The RNA polymerase recognises the promoter, a specific region of each gene in the DNA.
• Then the transcription begins, and the RNA polymerase uses one of the two strands of DNA as template.

5.1. Genetic TRANSCRIPTION

2. ELONGATION

• The RNA polymerase travels along that single chain of DNA, using it as template.
• It recognises each nitrogenous base and creates the strand of mRNA with the complementary one.
• Since mRNA cannot have thymine, when the RNA polymerase reads an A in the template, it adds a U to the new chain.

5.1. Genetic TRANSCRIPTION

3. TERMINATION

• There is a specific section in the DNA that each gene has that marks that transcription must end at that point.
• The RNA polymerase reads this section and stops the process, having built a new chain of mRNA.
• Possible errors are then corrected.

5.1. Genetic TRANSCRIPTION

5.2. Genetic TRANSLATION

• Translation is the process by which proteins are built from a mRNA chain, with the help of tRNA and ribosomes.
• It takes place in the cytoplasm or in the RER, the places where we can find ribosomes in the cell.
• It has 3 steps that are also named initiation, elongation and termination.

5.2. Genetic TRANSLATION

• CODON: a group of 3 (triplet) nitrogenous bases in the mRNA chain.
• ANTICODON: the complementary triplet to the codon that is present in a molecule of tRNA.
• AMINO ACID: each of the basic components of proteins, each one of them is carried through the cytoplasm by a specific tRNA.

5.2. Genetic TRANSLATION

1. INITIATION

• It begins when the first tRNA comes to the ribosome. This tRNA has to carry:
• the anticodon that corresponds to the first codon in the mRNA chain.
• the amino acid corresponding to that codon.
• Once there, the codon and the anticodon are paired and the first amino acid of the protein is settled.

5.2. Genetic TRANSLATION

2. ELONGATION

• The ribosome travels alongside the mRNA chain, reading it.
• Each time it recognises a codon, it joins the tRNA with the corresponding anticodon in the same place.
• The amino acids attached to the tRNA bind to one another, establishing a peptidic bond.
• Like this, the protein is being enlarged.

5.2. Genetic TRANSLATION

3. TERMINATION

• The ribosome recognises the "STOP codon".
• The tRNAs can no longer join to the ribosome.
• The peptidic chain is finished: the protein is already built.
• Possible errors are corrected.

The genetic code

6.1. Organisation of genetic code

6.2. Properties of the genetic code

6.3. Alterations in reading genetic code

• DNA and RNA contain a genetic message that needs to be 'translated' into proteins.
• The cell knows what genetic information corresponds to what amino acid thanks to the genetic code.
• The genetic code is the dictionary that matches the language of nucleotides in the mRNA with the language of amino acids in proteins.

6.1. Organisation of the genetic code

THE BASE TRIPLETS OR CODONS

• The genetic code is organised into groups of 3 nitrogenous bases: triplets or codons.
• By combining the 4 possible letters in mRNA, there are 64 possible triplets.
• Each triplet is coded to determine one of the 20 amino acids that make up proteins. There are also 3 triplets that mark the end of translation, the "STOP codons".

The genetic code

• The AUG codon determines methionine and also the beginning of translation (triangle).
• The UAA, UAG and UGA codons determine the end of the translation (big spot).

6.2. Properties of the genetic code

1. It is degenerate or redundant. This means there are more triplets than amino acids: several triplets code the same amino acid (synonymous triplets).
2. It is unambiguous. Each triplet always codes the same amino acid.
3. It is universal. Every single living being has the same genetic code, from the simplest to the most complex.
4. It is unidirectional. This is because mRNA is always read in the same direction, without interruptions or gaps

6.3. Alterations in reading the genetic code

• The process of reading the mRNA and interpreting the genetic code is strictly designed: each triplets codes its amino acid only.
• Occasionally, the ribosome calls for the wrong tRNA, which then provides the wrong amino acid.
• Like this, the sequence of amino acids in the protein changes, and the function of the resulting protein will also change.

Mutations

7.1. Types of mutations

7.2. Mutations and genetic variability

7.3. Mutations and evolution

MUTATIONS

• A mutation is a change in DNA which usually has effects on the expression of genetic information.
• They have different characteristics:
• They occur in one specific way.
• They can be passed by heredity.
• They can have no effect.
• They are neutral in themselves.

MUTATIONS

• They occur randomly:
• As replication errors that are not corrected by the enzymes.
• As a result of mutagens: elements that have the power of changing the DNA, such as
• Ultraviolet radiation
• Chemical substances (tobacco, alcohol)
• Viruses

MUTATIONS

• They can be inherited:
• If they take place in the gametes they can affect the new individual.
• Also if the organism reproduces thanks to asexual reproduction.

MUTATIONS

• They can be silent (they can have no effects):
• This happens when, even if the mutation has affected the genes, this change does not involve changes in the phenotype.

MUTATIONS

• They are neutral (they are not good nor bad):
• In themselves, they are just genetic alterations.
• Nontheless, they can have good or bad effects on the organism.
• This is why mutations are the main source of genetic variability, because without mutations new traits would never appear.

7.1. Types of mutations

• Genetic mutations: they affect genes, this is, the sequence of nucleotides (changes in the "letters" that make up the DNA)
• Chromosomal mutations: they affect chromosomes, this is the arms can be misplaced.
• Genomic mutations: they affect the genome, this is, the number of chromosomes.

7.1. Types of mutations

A) GENETIC MUTATIONS

• Substitution: one nucleotide is exchanged.
• ATTCGAG > ATACGAG
• Addition: one extra nucleotide is added.
• ATTCGAG > ATGTCGAG
• Deletion: one nucleotide is deleted.
• ATTCGAG > AT_CGAG > ATCGAG

7.1. Types of mutations

A) GENETIC MUTATIONS They can be also classified due to their EFFECTS

• Silent mutation. Substitution. The nucleotides change, but the mutant triplet encodes the same amino acid.
• UUU > UUC | Both triplets encode phenilalanine.

7.1. Types of mutations

A) GENETIC MUTATIONS They can be also classified due to their EFFECTS

• Missense mutation. Substitution. The nucleotides change and the amino acid also changes.
• UUU > UUG | The first triplet is for phenilalanine, but the second is for leucine.

7.1. Types of mutations

A) GENETIC MUTATIONS They can be also classified due to their EFFECTS

• Nonsense mutation. Substitution. The nucleotides change and the mutant triplet is a STOP codon. The mutant protein will be shorter.
• UGU > UGA | The first triplet is for cysteine, but the second is a STOP codon. Even if the other codons do not change, the protein will end here.

7.1. Types of mutations

A) GENETIC MUTATIONS They can be also classified due to their EFFECTS

• Frameshift mutation. Additions & deletions. Since the total number of nucleotides change, completely new codons will be created, thus resulting in completely different amino acids.
• UGU UCC AGA CGC > Cys - Ser - Arg - Arg
• UGU AUC CAG ACG G... > Cys - Ile - Ser - Thr

7.1. Types of mutations

B) CHROMOSOMAL MUTATIONS

Involving just one chromosome:

• Deletion: one fragment of the chromosome is deleted.
• Duplication: one fragment of the chromosome is duplicated
• Inversion: the genes of one fragment of the chromosome are in the inverse order

7.1. Types of mutations

B) CHROMOSOMAL MUTATIONS

Involving two chromosomes:

• Insertion: one fragment of one chromosome is removed from it and placed in another chromosome.
• Translocation: two fragments from two different chromosomes are exchanged.

7.1. Types of mutations

C) GENOMIC MUTATIONS

• Polyploidy: a whole set of chromosomes is gained (If we have a 2n individual suffering a polyploidy, it will be 4n).
• Aneuploidy: individual chromosomes are gained or lost.

7.2. Mutations and genetic variability

• We have seen that mutations affect both the genetic information and the structure and function of proteins that are built thanks to that information.
• Mutations and mutant proteins can cause diseases or they can simply supply the organism with a new trait that other members of the spieces don't have.
• This is known as genetic variability.

7.3. Mutations and evolution

• Mutations occur spontaneously and naturally on all the cells of every living organism.
• They are not negative: they can cause illnesses, but they are also the essence of biodiversity. Thus, they are the motor of evolution.
• Mutations allows the existance of different genetic messages among organisms of the same species.

7.3. Mutations and evolution

• Having different traits in a population of the same species allow this species to adapt to changes in the environment, because they have different genetic information.
• Mutations allow each individual of the same species to face changes with different tools and following different strategies.

7.3. Mutations and evolution

Biston betularia is a species of moth that can have two patterns: white or black. They live on the birch tree's bark (which are naturally white), so white moths are camouflaged againts that bark.

7.3. Mutations and evolution

Biston betularia is a species of moth that can have two patterns: white or black. They live on the birch tree's bark (which are naturally white), so white moths are camouflaged againts that bark.

7.3. Mutations and evolution

This means that, since white moths have a better camouflage, birds could not see them, so they captured the black ones to eat them. Like that, white ones could reproduce more and they were more abundant.

7.3. Mutations and evolution

In the 19th century, the pollution increased due to the Industrial Revolution, and the birch tree's barks were darkened. In this new environment, black moths had a better camouflage.

7.3. Mutations and evolution

The birds began to see the white moths better than the black ones, so the black moths could reproduce more and they finished outnumbering the white ones.

Genetic engineering

8.1. Recombinant DNA technique

8.2. Polymerase chain reaction (PCR)

8.3. Cloning

GENETIC ENGINEERING

• Genetic engineering is a set of techinques used to manipulate an organism's DNA.
• The organism that has undergone a genetic engineering technique is called a genetically modified organism, or GMO.
• GMOs include transgenic organisms, which are created by introducing genes from a different species into their own genome.

8.1. Recombinant DNA technique

• It adds fragments of other organisms' DNA into the genome of an organism.
• This fragments may be from an organism of the same species (just GMO) or from an organism of a different species (GMO & transgenic).
• We call recombinant DNA to that molecule of DNA that has been added a fragment of external DNA.

8.1. Recombinant DNA technique

8.2. PCR - Polymerase Chain Reaction

• PCR is a technique that replicates small fragments of DNA:
• in vitro
• in short periods of time
• It allows us to have many copies of the same sample of DNA.

8.2. PCR - Polymerase Chain Reaction

• The process is divided into cycles. In a cycle, each DNA molecule is replicated, meaning that we will obtain 2 new molecules from each previous molecule.
• One cycle consists of 3 phases: DNA denaturation, alignment and elongation.

8.2. PCR - Polymerase Chain Reaction

DNA denaturation The temperature increases insde the machine, forcing the two strands of DNA to separate. Alignment Primers (DNA fragments that allow the replication to begin) bind to each of the single strands. Elongation The DNA polymerase attaches the corresponding nucleotides, creating the complementary strand.

8.2. PCR - Polymerase Chain Reaction

8.2. PCR - Polymerase Chain Reaction

PCR in medicine It allows us to compare one sample of DNA with an already known molecule, to see wether they match or not. Having many copies of the sample is helpful to prove it with different possible known DNA molecules.

• Forensic medicine
• Parental screening
• PCR tests for illneses (COVID-19)

8.3. Cloning

• Cloning is making identical copies of one original organism, one original cell or one original DNA molecule, thanks to genetic engineering techinques.
• We can find 2 types of cloning:
• Therapeutic cloning , it clones somatic cells.
• Reproductive cloning , it clones embryos.

8.3. Cloning

8.3. Cloning

• Depending on what destiny will this cells have:
• Therapeutic cloning , the stem cells are cultivated to create different organs and tissues that can be transplanted to somebody.
• Reproductive cloning , the egg cell with the nucleus of the donor continues the embryonic development; in the end we will get an individual with the same DNA than the donor (clon).

Biotechnology

Set of techniques that use living organisms or their substances to create productsfor human use.

Biotechnology: past and present

Classic biotechnology Humans use biotechnology since ancient times:

• The use of microorganisms to produce aliments goes back to the Ancient Egypt.
• Products like bread, beer, wine, cheese and yoghourt are made thanks to yeast or bacteria.
• This microorganisms usually perform fermentation processes (alcoholic or lactic fermentation).

Biotechnology: past and present

Modern biotechnology

• We understand the reactions of the processes that living beings perform.
• We can increase the efficiency of this processes by manipulating the DNA of the organisms.
• Like that, we change the production methods of many processes: this is modern biotechnology.

10

Bioethics