Nucleic Acids

Nucleic Acids

Nucleic acids are one of the 4 major macromolecules found in all living things. A macromolecule is also known as a polymer, which means it is a large molecule made of smaller repeating subunits known as monomers. The monomers of nucleic acids are called nucleotides.

There are two major classes of nucleic acids:

1) DEOXYRIBONUCLEIC ACID (DNA)

DNA is the chemical basis for the gene, the fundamental unit of inheritance and is responsible for governing the activities of the entire cell. DNA is mainly found in the nuclei of cells but is also present in the mitochondria.

2) RIBONUCLEIC ACID (RNA)

RNA molecules are mainly found in the cytoplasm of cells and perform various tasks, such as acting as structural scaffolds or being chemical messengers. There are a variety of different forms of RNA including, mRNA, tRNA, and rRNA.

Nucleotides:

A nucleotide consists of three parts:

i) A nitrogenous base

(so called because nitrogen atoms form part of the rings of the molecule)

There are two types of nitrogenous bases, purines

and pyrimidines.

In DNA, there are two purine bases, adenine and guanine and two pyrimidine bases, thymine and cytosine that are used to make nucleotides.

In RNA, adenine, guanine and cytosine occur, but thymine does not, it is replaced by thepyrimidine uracil.

Pyrimidines

(single ring)

Purines

(double ring)

ii)A 5-carbon sugar (in DNA it is deoxyribose; in RNA it is ribose)

iii)A phosphate group

A nucleic acid polymer consists of alternating chains of sugar and phosphate, with a nitrogenous base attached to a deoxyribose (or ribose) sugar. The nucleotide is held together by covalent bonds that are known as a phosphodiester bond.

A molecule of RNA is a single-stranded structure that often becomes folded, while DNA takes on a double stranded, helical formation. In DNA, bonds are formed between nitrogenous base pairs and are held together through hydrogen bonding.

The nitrogenous base pairs between the DNA double helix always pair up such that adenine and thymine are together and guaninie and cytosine are joined.

Nucleotides are not only important as building blocks of nucleic acids; they also have important functions in their own right. Most of the energy being put to use at any given moment in any living organism is derived from the nucleotide adenosine triphosphate (ATP).

Deciphering the Genetic Code

Genes and Chromosomes

The gene is the major functional sub-unit of DNA. Genes are specific sequences of DNA that have the potential to be expressed and to guide an organism’s development. We often think of genes as the portion of inherited information that defines one particular trait of an organism’s physical characteristics.

The sum of the entire DNA including all of the genes (20 000 - 25 000) within a cell is referred to as the genome.

The specific number, type and arrangement of genes are unique to each species, but even organisms that are only distantly related may carry very similar genes.

In humans genes are organized onto chromosomes. Each chromosome contains linear double-stranded molecules. DNA molecules are held together with proteins called histones. A chromosome is actually 60% protein, 35% DNA, 5% RNA.

Genes are not spaced regularly along chromosomes. The density of genes can vary from one chromosome to another. For example, in humans:

Chromosome 4 – 1.3 billion base pairs = 200 genes

Chromosome 19 – 72 million base pairs = 1450 genes

There is no set relationship between the number of genes on a chromosome and the total length of the chromosome

Central Dogma

DNA provides the information that ultimately codes for a specific protein to be produced. This is a two-step process of transcription, followed by translation.

DNA

Nucleus (

transcription

mRNA

Cytoplasm (

translation 

Proteins

 

Transcription is a process that occurs within the nucleus, where the information from one gene is used as a template to produce a complementary strand of RNA nucleotides (mRNA) that is then moved into the cytoplasm.

Translation is the process where the mRNA transcript is used to generate a sequence of amino acids, which will eventually fold into a three-dimensional structure and become an active protein. This process occurs in the cytoplasm of cells and requires a number of accessory molecules (rRNA and tRNA).

Information for the genetic code is read as a series of three consecutive bases or codons. Each codon ultimately corresponds to a specific amino acid that will be added to a growing polypeptide chain.

Mutations

A mutation is any type of heritable genetic change. There are several types of mutations, some which go unnoticed; others are beneficial, while others still may have serious, deleterious effects.

The following are common mutations that can occur during replication:

Base SubstitutionA different nucleotide is substituted.

Examples:

Silent - same amino acid is specifiedMis-sense - a different amino acid is specifiedNon-sense - codon changed to a stopFrameshift mutationAddition or deletion of a base can throw reading frame off

Example:

SEETHEREDCATANDTHEFATDOG

SEEHEREDCATANDTHEFATDOG

Even without exposure to mutagens, each of your genes undergoes thousands of mutations during your life; most of these are corrected by repair enzymes.

Cell Division

You are made up of approximately 100 trillion cells. This is amazing considering that all these cells started from one fertilized egg. Even now cells are dividing in your body! Cell division is needed for:

1.Growth - organisms increase in size by creating more cells

2.Repair - old and damaged tissue is replaced by new cells

3.Reproduction – single celled organisms reproduce by splitting in two

How does cell division occur?

Cell division occurs in three stages:

1.Replication – Making an exact copy of DNA

The replication process must be relatively quick and it must be accurate for cells to survive. Remarkably, cells are able to duplicate their DNA in a few hours, with an error rate of approximately one per billion nucleotide pair!

2.Mitosis - The division of chromosomes in the nucleus

3.Cytokinesis - The division of the cytoplasm and cell organelles

The end result of these stages are TWO identical cells from one original cell.

In order to describe the events of the cell cycle, the process has been divided into several phases:

INTERPHASE:

· The cell is doing its job

· DNA in the form of chromatin – cannot be seen

· Cell grows

· At the end of interphase the DNA has replicated

PROPHASE:

· Nuclear membrane disappears

· Nucleolus disappears

· DNA shortens and thickens and becomes visible - chromsomes

· Spindle fibres form and can be seen

· Centrioles move apart

METAPHASE:

· Chromosomes line up at equator of cell

· Centrioles are located at poles

· Spindle fibres attach to centromeres and centrioles

ANAPHASE:

· Centromeres split and single-stranded chromatid move to opposite poles

· Pulled by spindle fibres

TELOPHASE:

· Opposite of prophase

· Nuclear membrane reappears

· Nucleolus reappears

· Spindle fibres disappears

· Chromatid become longer and thinner and cannot be seen

(chromatin)

FINAL RESULT OF CELL DIVISION:

· Cytokinesis occurs (division of cytoplasm)

· Two genetically identically daughter cells

Meiosis

Different characteristics are displayed by different people. This variation in characteristics is shown because each person comes from a different family. Even within a family there are differences.

Each human cell has 46 chromosomes in total or 23 pairs of chromosomes. Each pair of chromosomes resembles each other in size, shape and genetic information. You receive one member of each pair from your father and the other from your mother. These pairs of chromosomes are called homologous chromosomes. Your genes are located on these chromosomes.

Meiosis is the process by which a diploid cell (2n) produces haploid (n) gametes or sex cells.

Meiosis occurs only in the sex organs of most living things:

Spermatogenesis = sperm production in the testes

Oogenesis = egg/ovule production in the ovaries

Plants = pollen (microspores) in the anther and ovules/eggs (megaspores) in the ovaries

Meiosis Terminology

Diploid

· Two sets of chromosomes (2n)

· Body cells (somatic) are diploid cells

· Human cells have 46 chromosomes or 2 sets (2n) of 23 chromosomes

Haploid

· Single set of chromosomes (n)

· Sperm or egg (gametes) are haploid cells

· Human sex cells have 23 chromosomes

Homologous chromosomes (homologues)

· Two chromosomes similar in shape and size that carry the same genetic information

· Inherit one chromosome from each parent

Zygote

· The cell that results when an egg and a sperm unite (fertilization)

Synapsis

· The pairing of homologous chromosomes

· Occurs in prophase I of meiosis

Tetrad

· Two homologous chromosomes form a loose connection of 4 chromatids

Crossing over

· The process where the ends of chromosomes (adjacent) become twisted or tangled together and break apart

· The ends of the homologous chromosomes may switch or exchange places

· Explains why all offspring will be different (except identical twins)

Non-disjunction

· During meiosis one chromosome does not get pulled to the proper end of the cell

· One cell may get too many chromosomes and others too few

Stages of Meiosis (Interphase occurred first)Phase

Diagram

Key events

Prophase I

· Same as prophase of mitosis

· Nuclear membrane and nucleolus disappear

· Chromosomes become visible (previously chromatin)

· Spindle fibres appear

· Synapsis occurs as homologous chromosomes pair up

· The exchange of information occurs in a process called crossing over

Metaphase I

· Tetrads line up at the equator of the cell

· Chromosomes align randomly and differently each time through meiosis (law of independent assortment)

Anaphase I

· Tetrads separate and double stranded chromosomes move to the poles of the cell

Telophase I

· Two cells forming, with ½ the number of chromosomes

· Each strand is different because of crossing over

· Chromosomes still must be separated into single stranded chromatid

Prophase II

· Same as mitosis prophase

Metaphase II

· Double stranded chromosomes line up at the equator

· Same as mitosis metaphase

Anaphase II

· Double stranded chromosomes separate into single stranded chromatids

· Same as mitosis anaphase

Telophase II

· Four cells with the haploid number of chromosomes

· Each cell is genetically different from each other and different every time meiosis occurs

Mendelian Genetics

Early Ideas About Genetics

Aristotle (384-322 BC)

Pangenesis - every part of the body was involved in the production of the “seeds” of the parents; seeds fused to give rise to a new individual.

Anton van Leeuwenhoek (1632-1723)

The idea of an “animalcules” in the semen of males – a tiny preformed embryo.

19th Century

Blending theory of inheritance

Charles Darwin

Offspring had variations of their parent's characteristics; but he could not explain why.

Gregor Mendel (1822-1884)

Developed the fundamental principles that became the modern science of genetics.

Mendel’s Experiments

Gregor Mendel was a monk, whose studies included mathematics and botany. He conducted a series of experiments on pea plants over an eight-year period.

Mendel used pure bred (or true breeding) pea plants for his experiments, which are plants that produced predictable offspring (Example - tall or short).

Mendel actually studied seven different traits, each trait that had only two possible variations. Mendel obtained pure bred plants through selective breeding.

Useful terminology:

P generation = Parent Generation

F1 generation = Offspring of parents (first filial generation)

F2 generation = Offspring of F1 (second filial generation)

Mendel bred pure breeding tall plants with pure breeding short plants.

All of the offspring were tall. The tall pea plants were then crossed with each other.

The resulting offspring showed a 3:1 ratio of tall plants to short plants.

These results led Mendel to conclude that the trait for tall plants must be dominant and the trait for short plants to be recessive. When both a dominant and a recessive trait are present, only the dominant one will manifest itself.

Mendel conducted theses experiments many times, using the seven different traits. For each test, he obtained the same results.

In addition, Mendel came up with the Law of Segregation:

i) The inherited traits (or genes) are determined by pairs of ‘factors’ or alleles.

ii) The alleles segregate (or separate) in the formation of gametes (eggs or sperm)

iii) The alleles are inherited – one from each parent.

Using the information obtained from Mendel’s experiments, we can look at his experiments again from the point of view that every trait is associated with a different allele.

Symbols are assigned to the alleles. Capital letters for dominant traits and lower case for recessive.

Examples: T = tall and t = short

The genotype are the alleles for a particular trait.

The phenotype is how the alleles physically manifest themselves.

Genotypes can be either homozygous or heterozygous.

Homozygous means that both of the alleles are the same (TT or tt).

Heterozygous means the two alleles are different (Tt).

Punnett Squares

Comparing one trait at a time in breeding experiment is referred to as a monohybrid cross. The results can be organized in a Punnett square; a way of calculating the probability of inheriting a particular trait. It is a simple method of illustrating all possible combinations of gametes from a given set of parents.

Examples:

In guinea pigs, black fur is dominant to white fur. What would the F2 generation look like if you started with a male homozygous for white fur and a female homozygous for black fur?

Cross a white furred male with a female from the F1 generation.

Test Cross

A test cross is a type of breeding experiment that can be used if the phenotype of an organism is known, but the genotype is unknown.

The test cross is always performed between the organism with an unknown genotype (that carries a dominant allele – heterozygous or homozygous dominant) and an organism that has a homozygous recessive genotype.

A test cross would NOT be employed to determine human genotypes.

Sample Problem:

Having blue flowers is dominant (B) is a dominant characteristic to the recessive trait of having pink flowers (b). By performing a test cross with an plant of unknown genotype that has blue flowers, determine the possible outcomes that could result.

When performing a test cross there are only two possible outcomes that can occur:

1.All offspring will appear to have the dominant trait. This would suggest that the unknown organism has a genotype that is homozygous dominant.

2.Half the offspring would have the dominant trait and half would have the recessive trait. This would suggest that the unknown organism has a genotype that must be heterozygous.

Test crosses have proven to be a useful tool in the process of selective breeding. Selective breeding is the crossing of desired traits from plants or animals to produce offspring that have one or several of the desired characteristics.

Selective breeding commonly employs the techniques of either inbreeding or hybridization.

Hybridization is the mating of two different parents to produce offspring with desirable characteristics of both parents.

Inbreeding is the process by which mating occurs between closely related individuals for the purpose of maintaining or perpetuating certain characteristics. Inbreeding can often result in rare recessive features/conditions manifesting themselves.

Practice Questions

If you are given a dominant round (R) seed pea plant and you need to know the genotype of this plant, you need to do a test cross. What pea plant genotype would you cross this mystery dominant plant with?

In doing this cross, you find that the offspring are all round. What does this indicate about the mystery parent genotype?

In doing this cross, you find that the offspring show a 1:1 ratio of round:wrinkled. What does this indicate about the mystery parent genotype?

In corn, the allele for purple kernels is dominant to the alleles for yellow kernels. Determine the likely genotypes of the parents if the offspring that results from pollination produce 47 purple kernel producing plants and 14 yellow kernel producing plants.

This idea of using the phenotypes of offspring to predict the genotypes of parents is employed when studying human inheritance patterns. This is called Pedigree Analysis.

Pedigree Analysis

Pedigree chart: a graphic presentation of a family tree that shows the pattern of inheritance for a single gene.

From the point of view of individual III - 1, the symbols represent the following relationships:

I - 1 = grandfather I - 2 = grandmother

II - 1 and II - 2 = aunts II - 3 = uncle II - 4 = father II - 5 = mother

III - 2 = fraternal twin sister III - 3 = brother

Practice Problem #1

The following Pedigree shows a family with the trait of shortsightedness. The allele for shortsightedness (E) is dominant to the allele for normal vision (e). Predict the genotypes for each individual in the family.

Practice Problem #2

Phenylketonuria (PKU) is a genetic disorder caused by a dominant allele. People with PKU are unable to metabolize a naturally occurring amino acid, phenylalanine. If phenylalanine accumulates it inhibits the development of the nervous system, leading to major cognitive delays. The symptoms of PKU are not evident at birth, but can develop quickly if the child is not placed on a special diet. The pedigree chart below shows the inheritance of the defective allele in one family.

a) How many generations are shown in the pedigree?

b) How many children were born to the parents of the first generation?

c) What are the genotypes of individuals 1 and 2 in generation I?

d) How is it possible that in generation II, some of the children showed symptoms of PKU, while others did not?

e) Individuals 6 and 7 in generation II had a child without PKU. Does this mean that they can never have a child with PKU? Explain your answer.

Incomplete Dominance and Codominance

Not all alleles interact under the principle of dominance and recessive. Incomplete dominance is when both alleles contribute equally to the phenotype of the organism, creating a blend of traits in a heterozygous genotype.

Example:

In four o'clock flowers, red flowers (CR) is incompletely dominant to white (CW). The heterozygous plants (CRCW) are pink in colour. What are the possibilities for the F2 generation starting with a cross between a red and white flower?

Codominance:Two dominant alleles are expressed at the same time. No blending.

Example:

In cattle, red hide colour (R) is codominant to white (W). Cows that are heterozygous for this trait have a roan hide colour (RW), where the red hair and white hair both appear on the animal.

Cross two roan cows and determine the chance of getting a white animal.

Sometimes it is a benefit for an individual to inherit two different alleles for the same trait. This is called heterozygous advantage. An example is a person who is heterozygous for the sickle cell gene; they have some normal red blood cells and are resistant to malaria.

Dihybrid Crosses

1. What is the frequency of tossing one dice and having it roll the number one?

2. What is the frequency of tossing two dice and having both roll one?

3. What is the frequency of tossing a Yahtzee! Five dice that all roll the number one?

The above examples illustrate that the result of one toss of the dice has no affect on the outcome of future rolls, that is, one’s dice action is segregated from the others and independent.

In his studies Gregor Mendel discovered that like the dice, alleles assort independently from each other. Mendel termed this, The Law of Independent Assortment. The law states that:

If genes are located on separate chromosomes, then they will be inherited independently of each other.

This simply means that the inheritance of alleles for one characteristic does not affect the inheritance of alleles for another characteristic (as long as the alleles are on different chromosomes).

Example:

Whether a human has attached or free earlobes has no effect upon whether or not their hair is curly or straight. The characteristics are independent from one another.

Mendel came up with the idea for the law of independent assortment while studying the inheritance of two separate traits in crossbreeding (following the same procedures he had used for studying single traits). This kind of approach is called a dihybrid cross.

There are two approaches we can take to determine the probability for each of the possible outcomes to occur in a dihybrid cross.

Approach #1

You can solve a dihybrid problem by completing two separate monohybrid crosses, one for each of the characteristics being examined. Then the crosses can be combined to calculate the probabilities of the dihybrid crosses.

Example:

In garden pea plants the pod colour yellow (Y) is dominant over the recessive allele green (y); while round seed shape (R) is dominant over wrinkled (r). Following mating between parents with the genotypes YyRr x YyRr, what are the probabilities of obtaining offspring with the following characteristics:

· Yellow pods and round seeds

· Green pods and round seeds

· Yellow pods and wrinkled seeds

· Green pods and wrinkled seeds

Pod ColourProbabilitySeed ShapeProbabilityCombined Probability

YellowRound

GreenRound

YellowWrinkled

GreenWrinkled

Approach #2

The alternative method to solving dihybrid problems has you come up with all the possible combinations of alleles that can occur during a cross, and then completing a giant Punnett square. The first step is to identify the complete genotype of each organism in the cross (this will include 4 alleles, two for each trait being examined).

Using the previous example of Yellow (Y) and green (y) pea pods and round (R) and wrinkled (r) pea seeds:

What is the probability of obtaining green and wrinkled peas?

Predict the chance of a yellow and round pea from the following parents:

yyRr x Yyrr

Multiple Alleles

Many traits in humans and other species are the result of the inheritance of more than two alleles for one gene. A gene with more than two alleles is said to have multiple alleles.

Blood Types

In humans a single gene determines a person's ABO blood type. This gene determines what type of an antigen protein, if any, is attached to the cell membrane of red blood cells. An antigen protein is a molecule that stimulates the body's immune system. The gene is designated "I" and it has three common alleles: IA, IB and i. The different combinations of the three alleles produce the four different phenotypes of blood.

A & B are dominant to O. A & B are codominant. The possible genotypes for blood typing are:

IAIA -

IBIB -

IAi -

IBi -

IAIB -

ii -

Examples:

A man with hybrid type A blood and a woman with type AB blood wish to know the possible blood types for their children.

A rich couple are confronted by a man who claims to be the man's son from a previous marriage. The son's blood type is "O" and both the man and his ex-wife are hybrid type A. What is the probability that the young man is telling the truth?

Rh Factor

In addition to the substances that cause A, B, and O blood types there is another factor called the Rh factor that can be found in blood. The genes for having the Rh factor are completely dominant to the genes for not having the Rh factor.

For example: Let:R - have the Rh factor

r - absence of the Rh factor

Therefore, RR and Rr produce people that are Rh positive & rr only produce an Rh negative individual.

What are the possibilities for a man that is pure type B and pure Rh positive with a woman who is hybrid A and Rh negative?

In addition to the many traits being controlled by one gene with multiple alleles, there are also many traits that are polygenic, which means they are controlled by more than one gene. Examples of polygenic traits include, height, skin colour and eye colour. These traits tend to exhibit continuous variation in which the phenotype varies gradually from one extreme to another.

Sex Linkage

Linked genes are genes that are on the same chromosome and that tend to be inherited together. These genes DO NOT exhibit Mendel's law of independent assortment and therefore do not follow the Mendelian inheritance patterns that have been previously discussed.

Sex Determination

Human cells contain 46 chromosomes (23 pairs). The first 22 pairs are referred to as autosomes; these chromosomes carry the majority of our traits. Your 23rd pair of chromosomes are called your sex chromosomes; these are the ones that determines your sex, but they also carry some traits. Males have one X and one Y chromosome (XY), while females have two X chromosomes (XX).

Sex Linkage

Thomas Hunt Morgan (1866-1945) was an American geneticist who worked with fruit flies (Drosophila melanogaster) and developed theories on gender and inheritance.

Fruit flies are an ideal subject for study in genetics because:

· They reproduce rapidly

· Offspring can mate shortly after leaving the egg

· Females produce over 100 eggs each mating

· You can study many generations in a short period of time

· They are small – can be housed in a single culture tube

· Males can be easily distinguished from females.

Morgan’s Experiment

Morgan explained his experiments by concluding that the X and Y chromosomes contain different genes, and that in his fruit flies, the Y chromosome does not carry the gene to determine eye colour.

Morgan called characteristics that are controlled by genes located on the sex chromosomes as sex-linked traits.

In humans there are numerous sex-linked traits:

· Hemophilia

· Nearsightedness

· Colour blindness

· Hairy ears (Y linked)

· Juvenile Glaucoma

· Muscular Dystrophy

Males and females produce the same amount of proteins coded by genes located on the X chromosome. However, females have two copies of this chromosome while males only have one. Experiments have shown that one of the X chromosomes in each female cell is inactivated. Which one is inactivated is random, and therefore different X chromosomes are active in different cells. The inactivated X chromosome is called a Barr Body.

Sex-Linked Problems

What are the possible offspring for a cross between a normal female and a colour-blind male

Let:X- Normal gene for colour-blind male

Xc- Recessive gene for colour-blindness

In humans, baldness is sex-linked and recessive to normal amount of hair. For hair colour, black is incompletely dominant to blonde, heterozygous have brown hair colour.

Show the possible offspring for a man who is bald and had brown hair and a woman who is blonde and a carrier for baldness.

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