Unit 5:

Chapter 14: RNA and Protein Synthesis

Concept 14.1: RNA

Central Dogma of Molecular Biology

Information flows in one direction:

DNA → RNA → protein

How?

Transcription: process where DNA's nucleotide sequence is converted to the form of a single-stranded RNA molecule, which will leave the nucleus and direct the making of proteins in the cytoplasm

DNA → RNA

Translation: process that converts RNA into amino acid chain (called a polypeptide)

RNA → Amino Acid Chain (Polypeptide – AKA “Protein”)

Ribonucleic Acid (RNA)

RNA is the link between DNA and protein.

RNA (ribonucleic acid): The nucleic acid used to make protein

3 Differences of RNA from DNA

Its sugar is ribose (rather than the deoxyribose of DNA)

RNA forms a single, sometimes twisted strand (not a double helix like DNA)

Its nitrogenous bases are ACGU (unlike ACGT in DNA) - U stands for uracil

Uracil (U): A base found in RNA (U takes the place of the T of DNA - similar in structure to T and pairs with A)

Transcription

DNA → RNA

Two DNA strands separate at the place where transcription will start

RNA bases pair with complementary DNA bases

RNA polymerase: The enzymes that links RNA nucleotides together

During transcription, RNA nucleotides base-pair one by one with DNA nucleotides on one of the DNA strands (called the template strand). RNA polymerase links the RNA nucleotides together.

Concept 14.2: Ribosomes and Protein Synthesis

Amino Acids

RECALL: A polypeptide is a chain of amino acids.

Every three nucleotides (called a codon) code for one amino acid.

The Codon

ACGU allows for 64 codon combinations - 61 of the 64 triplets code for amino acids

3 STOP Codons

3 codons do not code for amino acids are "stop codons" (come at the end of each gene sequence)

1 START Codon

The codon AUG not only stands for methionine (Met), but also functions as a signal to "start" translation

Each codon stands for a particular amino acid. (The table uses abbreviations for the amino acids, such as Ser for serine.)

Translation

RNA → Amino Acid Chain (Polypeptide – AKA “Protein”)

The anticodon on tRNA recognizes a particular codon on mRNA by using base-pairing rules

An enzyme specific for each amino acid recognizes both a tRNA and its amino acid partner and links the two together

Ribosome: where translation occurs: it coordinates the functioning of mRNA and tRNA; made of ribosomal RNA (rRNA); has two binding sites: one for mRNA on its small subunit and two for tRNA on its large subunit

Concept 14.4: Mutations

Mutations

Mutation: Any change in an organism's DNA (This is a change in the nucleotide sequence of DNA and can involve anywhere from large regions of a chromosome or just a single nucleotide pair.)

Mutations may or may not affect the phenotype (physical traits) of an organism and/or its offspring.

Types of Mutations

Many types of mutations can occur, especially during DNA replication.

Single gene mutations

Base substitution

Frameshift mutation (insertion or deletion)

Chromosomal mutations

Gene duplication

Gene insertion

Gene deletion

Gene inversion

Gene translocation

Nondisjunction

(We discuss these more in Unit 6.)

Single Gene Mutations

Base substitution: the replacement of one nucleotide with another - can cause anywhere from no change (when new codon codes for same amino acid - called a silent mutation) to drastic changes

Insertion or deletion: insertion or deletion of one or more nucleotides in a gene (usually more disastrous than a base substitution)

Because mRNA is read as a series of triplets, adding or subtracting nucleotides may alter the triplet groupings of the genetic message. Therefore, all the nucleotides that are "downstream" of the mutation will be regrouped into different codons. These new codons code for new amino acids. The result will be a different, and probably nonworking, protein.

Effect of Mutations

Some gene mutations change the phenotype:

A mutation may cause a premature stop codon.

A mutation may change protein shape or the active site.

A mutation may change gene regulation.

Some gene mutations do not affect the phenotype:

A mutation may be silent.

A mutation may occur in a noncoding region.

A mutation may not affect protein folding or the active site.

Some gene mutations don’t affect you but affect your offspring:

A mutation in sex cells can be harmful or beneficial to offspring.

Mutagens

Mutations occur:

When errors are made during DNA replication.

When errors are made during chromosome crossovers in meiosis (that's how mutations are passed on to offspring!).

Mutagens: the things that cause mutations

Most common physical mutagen: high-energy radiation (like X-rays and ultraviolet (UV) light)

Chemical mutagen: when chemicals that are similar to normal DNA bases cause incorrect base-pairing when incorporated into DNA

Fun Fact!: Some mutations can alter a protein in a way that may be beneficial in certain environments.

Concept 14.3: Gene Regulation and Expression

Cell Differentiation

Gene expression: When the embryo promotes expression of particular groups of gene

Cell differentiation: The process when cells develop into their mature forms

What makes each cell different?

A cell’s location in an embryo helps determine how it will differentiate.

A particular cell only expresses genes that code for proteins with functions in that cell.

Though all the genes (DNA) are present in every type of cell, only a small specific fraction of these genes are actually expressed in each type of cell.

Stem Cells

Stem cells: cells that remain undifferentiated - they have the potential to differentiate into various types of cells

Stem cells have the ability to:

Divide and renew themselves

Remain undifferentiated in form

Develop into a variety of specialized cell types

Types of Stem Cells

Stem cells can be classified into different types.

Uses of Stem Cells

Embryonic stem cells can be grown indefinitely by scientists in lab cultures.

(1) Egg is fertilized by sperm cell in petri dish. (2) Egg divides, forming an inner cell mass. (3) Cells are removed and grown with nutrients. (Scientists control how the cells specialize by adding or removing certain molecules.

Some types of tissues, such as nervous tissue and heart muscle, do not have stem cells that exist in the adult individual. Yet, embryonic stem cells may be able to help people with disabling diseases that affect such tissues, but some people question the ethics of this technology.

Chapter 16: Biotechnology

Concept 16.2: The Process of Genetic Engineering, 16.3: Applications of Biotechnology, and 16.4: Ethics and Impacts of Biotechnology

Manipulating DNA

Scientists use various tools to manipulate DNA for their research.

Chapter 16 discusses technologies such as:

Selective breeding

Increases to genetic variation

Polymerase Chain Reaction (PCR)

Restriction enzymes

Recombinant DNA technology

Cloning

Transgenic organisms (GMOs)

Gel electrophoresis / DNA fingerprinting

Bioinformatics

Some of these forms of genetic engineering are discussed in the class using the following slides.

Polymerase Chain Reaction (PCR)

PCR: A technique that makes many copies of a certain segment of DNA without using living cells (copy machine)

(PCR can generate 100 billion identical molecules from a single strand in just a few hours!)

PCR is similar to DNA replication.

Result

Each PCR cycle doubles the amount of DNA molecules.

Using PCR to produce multiple copies of a DNA sample can:

Make further analysis of the sample much easier.

Enable scientists to make copies of very rare DNA (such as 5,000-year-old human remains, a 40,000-year-old wooly mammoth frozen in a glacier, or a 30-million-year-old plant fossil).

Make it possible to detect viral genes in cells infected with the virus that causes AIDS.

Restriction Enzymes

How does a biologist remove a gene from one DNA molecule in order to better study it for their research?

Restriction enzymes: Cut DNA

Each restriction enzyme recognizes particular short nucleotide sequences (called restriction sites) in DNA molecules, and cuts sugar-phosphate bonds in the DNA backbone at specific points within these sequences.

Different restriction enzymes cut DNA in different ways.

Gel Electrophoresis

Gel electrophoresis: a technique for seeing DNA fragments by length

Each DNA sample is copied using PCR and then cut up into fragments by restriction enzymes and placed in the gel. All DNA molecules are negative, so they move through pores in the gel toward the positive pole.

The shorter DNA fragments slip more easily through the pores of the gel. Therefore, the shorter DNA fragments will travel further through the gel. The DNA fragments show up as a series of bands in each "lane" of the gel.

DNA Fingerprinting

DNA fingerprint: an individual unique branding pattern on an electrophoresis gel, determined by restriction fragments of the person's DNA

The probability that two people share identical numbers of repeats in several locations (resulting in an identical fingerprint) is very small.

Uses of DNA Fingerprinting

Evidence in criminal cases

Paternity tests

Immigration requests

Studying biodiversity

Tracking genetically modified crops

Making a DNA Fingerprint

Using PCR and gel electrophoresis, a DNA fingerprint can be made from cells in a single drop of blood or from a hair follicle.

DNA is extracted from the small sample.

Multiple copies are made using PCR.

Genetic markers are then compared using a gel.

In most cases, the probability of two people having identical genetic markers is small—somewhere around 1 in 1 billion.

Cloning

Clone: a genetically identical copy of a gene or of an organism

Cloning occurs in nature:

Bacteria (binary fission)

Some plants (from roots)

Some simple animals (budding, regeneration)

Mammals can be cloned through nuclear transfer.

Nucleus is removed from an egg cell.

Nucleus of a cell from the animal to be cloned is implanted in the egg.

Benefits

Organs for transplant into humans

Save endangered species

Concerns

Low success rate

Clones “imperfect” and less healthy than original animal

Decreased biodiversity

Genetically Modified Organisms (GMOs)

Genetically modified organism (GMO): any organism that has acquired one or more genes by artificial means.

GM Bacteria

Transgenic bacteria can be used to produce human proteins.

Examples:

Bacteria that break down certain chemicals and help to clean up toxic waste sites

Bacteria engineered to mass-produce useful chemicals, from pesticides to therapeutic drugs

Bacteria produce human insulin that can be used in the treatment of some types of diabetes

Bacteria used in the development of effective vaccines against disease-causing microbes

GM Plants

Transgenic plants are common in agriculture.

How? Transgenic bacteria infect a plant, then the plant expresses the foreign gene.

Many crops are now genetically modified (GM).

Using recombinant DNA technology, scientists are able to improve various characteristics (like delayed ripening, improved nutritional content, and resistance to spoilage or disease) of certain crop plants.

GM Animals

Transgenic animals are used to study diseases and gene functions.

Transgenic mice are often used to study development, disease, and gene function.

Genetically modifying animals is more difficult than producing GM plants.

Goals of genetically modifying an animal might include:

To make a sheep with better-quality wool

A pig with leaner meat

A fish that will mature in a shorter time

To make a transgenic animal that produces a large amount of an otherwise rare biological substance for medical use (like adding a gene for a desired human protein, such as a hormone, to the genome of a farm mammal)

GMO Concerns

Questions that scientists have include:

Are crops carrying artificially inserted genes safe?

Could they be harmful to human health or to the environment?

Concern to Environment: GM crops could pass their new genes to closely replaced .

Concern to Human Health: GM plants or animals could have unkown risks to human consumers. (Some consumers think labeling that clearly identifies GM products should be required.)

Additional Biotechnology (not directly covered in Chapter 16)

Genomics

Genomics: the study of genes, gene functions, and entire genomes

(including the sequencing of genomes and comparisons of genomes within and across species)

Gene sequencing: determining the order of DNA nucleotides in genes or in genomes

The genomes of several different organisms have been sequenced.

Human Genome Project

1990: advances in DNA technology enabled scientists to tackle the challenge of completely sequencing the human genome

The government-funded Human Genome Project began.

2000: rough draft of the entire sequence was completed

The DNA sequences determined by the Human Genome Project are entered into a database that is available to researchers all over the world through the Internet.

Scientists are still working to identify and map all human genes.

Benefits

Comparing human sequences with those from other species allows for insight into human embryonic development and evolutionary relationships.

For human health, identifying genes will aid in diagnosing, treating, and possibly preventing many common ailments.

Vaccines

vaccine: used to stimulate the body's immune response against disease

There are a variety of types of vaccines. Some include:

inactivated

examples: hepatitis A, flu, polio, rabies

live-attenuated

examples: measles, mumps, rubella, smallpox, chickenpox

subunut

examples: hepatitis B, HPV, shingles

mRNA

examples: COVID-19

mRNA vaccine: a vaccine that introduces a piece of mRNA that corresponds to a viral protein (usually a small piece of protein found on the virus's outer membrane)