Gene Expression

Gene expression is vitally important for living things, well complex living organisms just would not exist without it. The central dogma is the idea that DNA instructions code for amino acids that make protein.

Here are a couple of good links to work through before starting the topic. Link and Link2

PBS learning media has a good link here.

Also I recommend working through the Learn genetics Basic DNA section .

This assessment looks at the Central Dogma or DNA coding proteins which build living organisms. Before we start the topic look at this video about heredity. The knowledge of Heredity came well before we knew what DNA was and it will help to recap the basics from year 11.

Starter Resources

Read the following website How DNA works

Nature magazines online textbook, some excellent information here that I will slowly add to the standard links.

DNAi - Excellent website to work through

Awesome website that covers the basics very well (DNA from the beginning)

A good chapter to start this section here (it becomes above L2 in content after page 5)

Another great animation about DNA

Some excellent "old School" DNA workshops

DNA Structure and Function

(nucleic acid structure and nature of the genetic code)

DNA, or deoxyribonucleic acid, is the hereditary material in humans and almost all other organisms. Nearly every cell in a person’s body has the same DNA. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but a small amount of DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA).

Click on the image to the left for an awesome poster.

Animation of DNA Structure

Another awesome video from Benjamin Himme on YouTube (30 minutes)

Work through the following animation for an intro

And then this one for the structures

And another cool structure activity

The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). Human DNA consists of about 3 billion bases, and more than 99 percent of those bases are the same in all people. The order, or sequence, of these bases determines the information available for building and maintaining an organism, similar to the way in which letters of the alphabet appear in a certain order to form words and sentences.DNA bases pair up with each other, A with T and C with G, to form units called base pairs. Each base is also attached to a sugar molecule and a phosphate molecule. Together, a base, sugar, and phosphate are called a nucleotide. Nucleotides are arranged in two long strands that form a spiral called a double helix. The structure of the double helix is somewhat like a ladder, with the base pairs forming the ladder’s rungs and the sugar and phosphate molecules forming the vertical sidepieces of the ladder.Follow this animation to find out Animation. Next make sure you understand what a gene is here.DNA from the Beginning Good introduction to DNA and geneticDNA is one of the nucleic acids, information-containing molecules in the cell (ribonucleic acid, or RNA, is the other nucleic acid). DNA is found in the nucleus of every human cell. (See the sidebar at the bottom of the page for more about RNA and different types of cells).The structure of DNA powerpoint Link

Nucleotides

Nucleotides are organic molecules that serve as the monomers, or subunits, of nucleic acids like DNA and RNA. The building blocks of nucleic acids, nucleotides are composed of a nitrogenous base, a five-carbon sugar (ribose or deoxyribose), and at least one phosphate group.A gene is a sequence of nucleotides animation Build a DNA molecule

Deoxyribose and/or ribose sugar

The 5-carbon sugars ribose and deoxyribose are important components of nucleotides, and are found in RNA and DNA, respectively.

The sugars found in nucleic acids are pentose sugars; a pentose sugar has five carbon atoms. A combination of a base and a sugar is called a nucleoside. Ribose, found in RNA, is a "normal" sugar, with one oxygen atom attached to each carbon atom.

Deoxyribose, found in DNA, is a modified sugar, lacking one oxygen atom (hence the name "deoxy"). This difference of one oxygen atom is important for the enzymes that recognize DNA and RNA, because it allows these two molecules to be easily distinguished inside organisms.

Phosphate (thanks sparknotes)

A phosphate group consists of a central phosphorous surrounded by four oxygens.

Figure above: Phosphate Group. The phosphorous is single-bonded to three of the oxygens and double-bonded to the fourth. Due to the nature of the chemical bonds, there is a negative charge on each oxygen that has only one bond coming off of it. This negative charge accounts for the overall negative charge on the phosphate backbone of a DNA molecule.

Nitrogenous bases

The nature of the genetic code including triplets, codons and anticodons

The redundancy due to degeneracy within the code.

The genetic code has redundancy due to the fact that two or more codons can specify the same amino acid. (This is known as degeneracy.)

For example, codons GAA and GAG both specify glutamic acid (GLU). [Any example can be given.] This means that there are more codons than amino acids so in any given translation, some codons will be redundant.

This means that there are more codons than amino acids in any given translation.

Proteins - What they are and synthesis

(significance of proteins)

Proteins are the products of gene expression. The significance of proteins is limited to their structural and catalytic (enzymes speeding up reactions) role in living things.

Protein Links

So what is a Protein? Click here

Excellent PowerPoint covering proteins. Protein structure PowerPoint.

Work through this interactive workshop

Protein synthesis Animation (really good)

Another animation

Protein synthesis Animation - Another way

TRANSLATION Animation

Identification of one gene and one polypeptide relationship

An excellent powerpoint can be found here

The significance of proteins

DNA was discovered as a major chemical of the nucleus at about the same time Mendel and Darwin published their work. However, during the early 1900s, proteins were considered better candidates as molecules able to transmit large amounts of hereditary information from generation to generation.Although DNA was known to be a very large molecule, it seemed likely that its four chemical components were assembled in a monotonous pattern — like a synthetic polymer. Also, no specific cellular function had yet been found for DNA. Proteins, on the other hand, were important as enzymes and structural components of living cells. Proteins were also known to be polymers of numerous amino acids. These polymers are called polypeptides. Most importantly, the 20 amino acid "alphabet" of proteins potentially could be configured into more unique information-carrying structures than the four-letter alphabet of DNA.

Animation from the early experiments

Structure

Website that covers the 3 levels of structure

Protein Synthesis

Protein biosynthesis is the process whereby biological cells generate new proteins; it is balanced by the loss of cellular proteins via degradation (being broken down) or export.

What you need to know

· proteins as the products of gene expression: DNA à mRNA à polypeptide or protein

· identification of one gene à one polypeptide relationship

Power-point on Protein synthesis

One gene makes a protein animation

See down the page for more detail on the actual process of the Protein synthesis.

Stages of Protein production - Transcription and translation

The role of DNA sequence in determining the structure of a protein and how that protein is produced (transcription and translation)

The process - Both steps together

Transcription animation

Translation animation

Template and coding strands

The term template strand refers to the sequence of DNA that is used during the synthesis of mRNA.

The opposite strand (that is, the strand with a base sequence directly corresponding to the mRNA sequence) is called the coding strand.

Transcription

Transcription described: mRNA transcribes the code for a polypeptide from the DNA.

transcription is explained: mRNA transcribes the code for a polypeptide from the DNA in the nucleus and carries it to the ribosomes / cytoplasm. So that the original DNA does not get damaged leaving the nucleus.

An enzyme (RNA polymerase) separates / unzips the DNA strand, exposing the gene / bases / nucleotides.
Free nucleotides are match to the exposed bases on the template strand using the base pairing rule, A-U and G-C. Transcription forms a single mRNA strand, with groups of 3 bases (codons) that code for the amino acids.
Transcription is complete when (RNA polymerase reaches the terminator sequence) mRNA detaches and moves out of the nucleus into the cytoplasm and attaches to a ribosome in preparation for translation.

Translation

purpose of translation is described: to use mRNA to make a polypeptide / protein.

purpose of translation is explained: to use mRNA to make a polypeptide / protein. So that the protein can be used for cellular functions (or named example given e.g. to make an enzyme).

mRNA is single stranded (with base Uracil instead of Thymine) and carries the copied genetic sequence from the nucleus to the ribosome.

Process

ribosomes move along the mRNA from the start codon until the stop codons is reached.

Each sequence of 3 bases (codon) on the mRNA is read by the ribosome and matched to the complementary unpaired three base sequence (anticodon) on the tRNA. The specific amino acid attached to the tRNA is then added (peptide bond forms) to the polypeptide chain being made.

Key terms

Triplet: Three consecutive nucleotide bases on the DNA strand. Each triplet is a group of three bases and codes for a specific amino acid.

Codon: the sequence of three consecutive nucleotides on the mRNA strand.

Anti-codon: three consecutive bases on a tRNA molecule that is complementary to mRNA codon.

A triplet is 3 consecutive bases on the DNA strand. The processes of transcription involve attaching free nucleotides to the exposed DNA strand to make mRNA. A codon is 3 consecutive bases on the mRNA strand. One triplet is complementary to one codon.

Similarities and differences between transcription and translation

Similar

both use complementary base pairing

both have mRNA involved in the process

both have a start and stop sequence

both are controlled by enzymes

code on both read in sets off three bases

Different

transcription occurs in the nucleus and requires DNA. Translation occurs in the cytoplasm on a ribosome and involves tRNA and amino acids (explanation for compare and contrast differences)

transcription makes mRNA, translation reads mRNA / makes proteins

transcription uses DNA as a template, translation uses mRNA as a template

transcription involves the pairing of DNA and free RNA nucleotides, whereas translation involves pairing anticodon bases of tRNA and codon mRNA

Awesome video

From NCEA the full description

mRNA is single stranded (with base Uracil instead of Thymine) and carries the copied genetic sequence from the nucleus to the ribosome.

tRNA brings in amino acids / the basic structure looks similar and is sometimes described as a cloverleaf.

Codon – mRNA bases are in a code of three bases at a time.

Anti-codon – Three unpaired bases on the tRNA are known as an anticodon.

A start codon initiates the translation / protein synthesis and a stop codon ends translation / protein synthesis.

RNA is a ribose sugar whereas DNA is a deoxyribose sugar.

The Ribosome is the cell organelle which is involved in the translation of messenger-RNA into a polypeptide chain

3 bases on mRNA / codon correspond to 3 bases on tRNA / anti-codon which carries an (specific) amino acid.

Codon-anticodon ‘matches’ combine with base pairing, thus bringing the (correct / specific) amino acid to the next part of the sequence. The start codon and stop codons indicate the start and end of a protein. They are important for ensuring correct protein length / structure.

The determination of phenotype via metabolic pathways

(specific names of enzymes are not required)

Enzymes

Enzymes are biological catalysts that speed up the rate of reactions or allow reactions to take place in conditions where it would not otherwise be possible.

Enzymes function in specific conditions. Outside of these conditions the enzymes will not function as well.

Enzymes are proteins.

Biochemical reactions are catalysed by specific enzymes and every enzyme is coded for by a specific gene(s)

Enzymes PowerPoint - A good source of information

Enzymes notes

Phenotype is determined by the presence, absence, or amount of specific metabolic products.

Advanced - Protein folding Probably not needed for L2 but interesting.

Metabolic pathways

A metabolic pathway is a series of biochemical reactions that are connected by their intermediates: The reactants (or substrates) of one reaction are the products of the previous one, and so on.

Because there are a series of biochemical reactions, each one usually controlled by an enzyme, there are multiple places where the end result can be affected.

As with most metabolic pathways in our body, the first compound in a pathway is converted to the next compound by the action of an enzyme. For example, in the simple pathway A ® B ® C, the conversion of compound A to B occurs because of the action of enzyme 1, and the conversion of B to C occurs because of the action of enzyme 2.

A mutation can occur which stops the function of enzyme 1, then the end product can not be made even if enzyme 2 is fully functional.

In another individual, a mutation can occur which stops the function of enzyme 2, then the end product can not be made even if enzyme 1 is fully functional.

There are a number of possible combinations to the way in which a condition can be inherited because the metabolic pathway has at least two points where different genes are controlling the outcome.

If both parents have porphyria, they must both have alleles, which result in the deficiency of one of the enzymes at one of the points of the pathway.

Normal children can be born, because if the points which are affected in the parents are different, then each one of those can be dominated by an allele inherited from the other, resulting in normal production of the enzyme.Phenotype is determined by the presence, absence or amount of specific metabolic products (animation)

· biochemical reactions are catalysed by specific enzymes and every enzyme is coded for by a specific gene(s)

· biochemical reactions do not occur in isolation but form part of a chain reaction so that the product of one becomes the substrate of another step in metabolism

· phenotype is determined by the presence, absence, or amount of specific metabolic products

The effect of environment on genotype through mutation

Some key definitions to remember:

Phenotype is the observable physical / characteristics of an organism.

Genotype is the set of alleles in our DNA, which is responsible for a particular trait an individual possesses.

A mutation is a change in the base sequence / genetic code of a gene. (The markers will NOT accept change in genetic code which results in a new allele).

· mutagens (specific mutagens are recognised but their effect at molecular level is not required)

· the potential effect on genotype and phenotype of gene mutations at the gene level.

Gametic and somatic mutations

Somatic mutations can occur in any of the cells of the body except the germ cells (sperm and egg) and therefore are not passed on to the offspring. AND Gametic: (may be called germ line, which is acceptable) occur in the gametes and CAN be passed on.

Somatic: Alterations in DNA that occur after conception. Somatic mutations can occur in any of the cells of the body except the germ cells (sperm and egg) and therefore are not passed on to the offspring.

Gametic: (may be called germ line, which is acceptable). A heritable change in the DNA that occurred in a gamete (germ cell) – a cell destined to become an egg or sperm. When transmitted to the offspring, a gametic mutation is incorporated in every cell of their body

NCEA EXAMPLES

Inherited mutations are able to be passed on to the next generation and occur in gametes (sperm or egg).

Mutations that occur during the organism’s lifetime occur in body cells (may say somatic) and affect that individual only / gametes and affect the next generation.

Named diseases which occur in an organism’s lifespan, such as most colon cancers or melanomas.

Cystic fibrosis is an inheritable recessive condition (stated in question), so it can be passed on from generation to generation. Most individuals will receive a ‘normal’ dominant gene from the other parent so will not actually get cystic fibrosis but will be carriers. Only an individual who gets two recessive alleles will get the condition.

Conditions caused by somatic mutations are often due to environmental factors such as diet, exposure to sunlight, toxins etc and impact on an individual but not on the genetics of their offspring. However, environmental factors such as chemicals and toxins can mutate gametes and effect the next generation.

Mutagen

is a physical or chemical agent that changes the genetic material, usually DNA, of an organism and thus increases the frequency of mutations above the natural background level, eg:

• radiation

• toxins

• virus.

Mutagens can alter the genotype by causing an increase in the rate of a gene mutation or a chromosome mutation. In both cases the genotype is changed.

A gene mutation is a change in the base sequence of a gene (do NOT accept change in genetic code), which results in a new allele.

Gene Mutations

Gene mutations can be of three different kinds:

Base substitution

In this case, one base in the DNA is substituted for another. Eg, instead of CAT there could be CGT. Only one triplet code is affected, so the likely outcome of the mutation will usually be less significant.

Explain

A single nucleotide change / swapped, which may result in a codon that codes for a different amino acid. (Not all substitutions result in a new amino acid, due to redundancy of the code.)

On the DNA strand, a single nucleotide is substituted / swapped for another so the strand still has the correct number of bases and the protein can be made. However, the different amino acid may cause the final protein to fold slightly differently, and therefore not function correctly.

Base insertion

These occur when a base is inserted, changing the reading frame of each triplet code.

Base deletion

These occur when a base is deleted, changing the reading frame of each triplet code. Insertion and deletion mutations lead to Frame Shifts: thus changing the reading frame of each triplet code and altering the amino acid sequence / final protein.

Deletion mutation may cause severe disease because more than a single nucleotide can be deleted, causing an amino acid not to be in the final protein. Thus the protein is not folded into the exact shape.

Substitution mutation does not cause severe disease because one nucleotide is exchanged for another, causing a different amino acid to be added to the polypeptide chain.

The shape may be slightly different; (however it can still reach the cell membrane and carry out its function to a reduced level.)

Gene Regulation

Interesting article covering environments role in expression

Effect of environment on expression of phenotype

The phenotype of an organism results from the interaction between the genotype and the environment. It is the composite of the characteristics shown by the cell or organism under a particular set of environmental conditions.

Environmental factor can be an internal or external factor that affects the organism’s phenotype.

Environmental factors vary widely, but can include temperature, wind, salinity, available nutrients etc. (Any reasonable / appropriate environmental factors can be accepted). The genotype provides the instruction set for a particular structure or function, but this may not be able to be fully expressed if the environmental conditions work against it. Eg, plant height is controlled by both genotype and environment. If a cutting is taken from a plant that is prostrate (grows close to the ground) due to the environmental factor of the wind, when it is grown in a sheltered garden the genotype is expressed fully and the result is a tall plant. The genotype of the plant has not changed at all, so this is not the case of a tall plant genotype vs. a prostrate genotype.

Wikipedia article

Examples of gene mutations influencing expression

Sickle cells

Sickle cell anemia (sickle cell disease) is a disorder of the blood caused by an inherited abnormal hemoglobin (the oxygen-carrying protein within the red blood cells). The abnormal hemoglobin causes distorted (sickled) red blood cells. The sickled red blood cells are fragile and prone to rupture.

https://www.dnalc.org/resources/3d/17-sickle-cell.html

Cystic fibrosis

Cystic fibrosis (CF), also known as mucoviscidosis, is a genetic disorder that affects mostly the lungs but also the pancreas, liver, kidneys and intestine.Long-term issues include difficulty breathing and coughing up sputum as a result of frequent lung infections. Other symptoms include sinus infections, poor growth, fatty stool, clubbing of the finger and toes, and infertility in males among others. Different people may have different degrees of symptoms.

New Zealand Contexts

https://www.nsu.govt.nz/pregnancy-newborn-screening/newborn-metabolic-screening-programme-heel-prick-test

https://www.tvnz.co.nz/shows/why-am-i