Bio Exam 3

Genotype

The genetic composition of an organism

The alleles that an organism possess

Phenotype

Represents the outward observable trait or the physical manifestations of a particular genetic combination

Allele

Represent alternate versions of a gene

Dominant allele

The allele that is expressed

Symbolized by a capital letter

Recessive allele

The allele that does not express itself

Symbolized by a lowercase letter

Homozygous recessive

Two recessive alleles

Symbolized by 2 lowercase letters (mm)

Homozygous dominant

Two dominant alleles

Symbolized by 2 uppercase letters (MM)

Heterozygous

One dominant and one recessive allele. Know as a carrier.

Symbolized by one lowercase and one uppercase letter (Mm)

Mendel’s Law of Dominance

When you have 2 different alleles present in an individual, only one expresses itself and gets observed

Mendel’s Law of Segregation

When gametes are formed, the 2 alleles of any gene on homologous chromosomes are going to separate from one another so that the gametes are only going to inherit one of the 2 alleles that were in the parent

Ex. A plant with genotype Aa will produce gametes with either “A” or “a”

Mendel’s Law of Independent Assortment

Each trait is going to be inherited independently of another trait.

Ex. a pea can be either yellow (dominant) or green (recessive) and it can be smooth (dominant) or wrinkled (recessive). These traits are independent but can combine in various ways (9:3:3:1 ratio)

Applies only to traits that are carried on non-homologous chromosomes

Dyhybird cross

Looking at 2 different alleles

Linkage

If genes are located very close together on the same pair of homologous chromosomes, they tend to be inherited together

Incomplete dominant

When there is a dominant allele that cannot completely overpower the recessive one

Ex. Snapdragons plants, the red doesn’t overpower the white causing the F1 generation to look pink

In Hypercholesterolemia, people produce half the number of receptors on the liver to draw in LDL

Codominance

When more the one allele is fully expressed

Ex. Blood typing, A and B are both considered dominant and if you inherit both, you will have AB blood type

Multiple allelism

Some genes have more than 2 alleles available

Ex. Blood typing, there are 3 alleles A, B, and O

Polygenes

When more than one gene can influence on trait

Ex. Skin color in humans is governed by multiple genes that are located on all different chromosomes and together influence skin color (same with height)

Pleiotropy

One single gene can influence more than one phenotypic trait

Ex. Albinism manifests itself in eye, skin, and hair color. It can also affect vision. Sickle cell anemia is when a mutation affects the hemoglobin protein inside of red blood cells

Epistasis

One gene can mask or overpower the effect of a different gene

Ex. Labrador retrievers have genes that determine coat color. Black is considered dominant over brown, but a different allele determines if the coat can result in yellow fur

Epigenetics

Is the study of changes in organisms that are caused by modifications of their gene expression rather than modifications in their genetic code

Ex. Chemicals that can influence whether or not a gene gets turned on or off

Environmental Influences on phenotype

Environmental influences can impact how a gene is expressed

Ex. A person can have alleles that will contribute to them being taller than average, but if that person does not get the proper nutrition when growing up, their height might not show out.

Karyotypes

A visual representation of an organism’s complete set of chromosomes that are arranged in 23 pairs and organized by size and shape

Autosomes

Non-sex chromosomes which are found in both males and females

22 of 23 chromosome pairs are autosomes

Sex chromosomes

Chromosomes that determine the sex of an individual.

Females are described to have two X chromosomes (homologous to each other) and Males are described to have one X and Y chromosome (Y is what determines the male sex and only contains 30 genes)

It is the last chromosome pair on Karyotypes

What is the master gene on the Y chromosome

SRY - it turns on other autosomal genes during embryo development to express themselves, if those genes are not expressed, than a female develops

Understand the concept of hemizygous inheritance in males for X-linked traits

Males only have one X and one Y chromosome.

For a recessive disorder to manifest in males, they only need one copy of the recessive allele on their one X chromosome to express that disorder.

This is because the male lacks a second X chromosome that could carry a normal dominant allele to mask the recessive trait

Explain color blindness to understand X-linked inheritance patterns

Imagine a mother who is a carrier for color blindness and a father who has a normal X chromosome with no color blindness allele

If they have a daughter, she will not be color blind, she will only be a carrier.

If they have a son, he will be color blind because he can inherit the affected allele from his mother and has no second X chromosome to provide a normal allele

Explain hemophilia to understand X-linked inheritance patterns

Hemophilia is another X-linked recessive disorder that primarily affects males

Because males have one X chromosome, if they inherit the recessive allele for hemophilia, they will have those conditions

Females, on the other hand, will need 2 copies of that recessive allele for them to have those conditions

Chromosome structural changes - Deletions

When a fragment of a chromosome gets lost and that chromosome ends up missing certain genes

Chromosome structural changes - Duplication

When a chromosome gets an extra segment because that portion gets duplicated and reinserted

Chromosome structural changes - Inversions

When a chromosome segment breaks off, flips around and gets reinserted

EX. BCD → DCB

Chromosome structural changes - Translocations

A fragment of a chromosome is moved to a different chromosome

Sometimes, the cell will not survive

How do chromosome structural changes lead to the disorder Cri du Chat syndrome?

This disorder is caused by a deletion of a portion of chromosome 5 and can lead to severe intellectual disability

How do chromosome structural changes lead to the disorder, Chronic Myelogenous Leukemia

This disorder is caused by translocation. A portion of chromosome 22 is exchanged with a fragment from chromosome 9.

This leads to a shortened chromosome 22, which causes an uncontrolled cell cycle progression

Nondisjunction

When chromosomes do no separate properly

Describe the role of nondisjunction in causing abnormal chromosome number

In Meiosis 1, homologous chromosomes can fail to separate, causing one gamete to receive both or more chromosomes,

In Meiosis 2, sister chromosomes can fail to separate, which can lead to one gamete having more chromosomes/less chromosomes than necessary

How do abnormal chromosome numbers contribute to Down Syndrome (Trisomy 21)

Down syndrome occurs when nondisjunction happens to chromosome 21 creating 3 copies of that chromosome instead of 2

The karyotype will show 47 chromosomes leading to mental delay developments, heart defects, characteristic facial features, and short heights

Having children after the age of 35 increases the risks of having Down Syndrome (49 - 1 in 10)

X inactivation

One of the X chromosomes in females undergoes a process in which that chromosome will condense down, and some genes will not express themselves

Once it happens in a cell, all the daughter cells will have the same X chromosome inactivated. This results in a mosaic pattern of gene expression in females

Mosaicism example - X inactivation

Tortoiseshell Cats- their fur color is determined by two different alleles (black and orange) Some cells express the black fur allele and others the orange fur allele

Abnormal number of sex chromosomes - Turner Syndrome (Monosomy X)

When an individual inherits only 1 X chromosome (XO), meaning it only affects females

1 in 2500 females will have undeveloped sex characteristics and infertile, short, webbed necks and potential learning difficulties

Abnormal number of sex chromosomes - Klinefelter Syndrome

Occurs when a male has an extra X chromosome (XXY)

1 in 1000 males will be infertile and have underdeveloped sex organs and maybe develop feminine traits (enlarged breasts) and are taller than average

Abnormal number of sex chromosomes - XYY Syndrome

Occurs when males have one X and 2 Ys (XYY)

1 in 1000 males will be taller than average, have severe acne, and lower intelligence but are fertile

Abnormal number of sex chromosomes - Trisomy X

Occurs when a female inherits 3 X chromosomes (XXX)

1 in 1000 females will be taller than average with slightly wider set eyes, will have some learning disabilities

Amniocentesis

One example of fetal testing performed at around 15 weeks

An ultrasound guides a thin needle into the amniotic sac (which surrounds the fetus)

A small amount of amniotic fluid is drawn out, which contains fetal cells that can then be tested for genetic conditions by culturing them

Chorionic Villus Sampling (CVS)

One example of fetal testing performed at around 10 weeks

A thin catheter is inserted into the placenta and collects chorionic villi that are made up of fetal cells which can be analyzed by genetic disorder

Fetal cells proliferate rapidly allowing for quick karyotyping

What is the role of DNA in genetics and inheritance?

DNA is the genetic material that carries instructions for an organism’s traits. It is made up of genes that tell the body how to make proteins.

When organisms reproduce, they pass their DNA to their offspring, which is how traits are inherited

Describe the structure and composition of DNA and how nucleotides are linked

DNA is made up of nucleotides (a sugar, a phosphate, and a nitrogenous base)

The sugar is deoxyribose which is made up of 5 carbons

Attached to carbon 1 is the nitrogenous base (ATGC)

Attached to carbon 5 is the phosphate group

Linked to carbon 3 is the phosphate group as they stack up on each other

DNA is a double helix structure and is antiparallel. The ends are going to be 5 prime and 3 prime ends, and vice versa

Alfred Hershey and Martha Chase

Concluded that DNA, not protein, functions as the genetic material and inheritance

Hershey won a Nobel Prize along with Salvador Luria and Max Delbruck, but Martha was left out.

Erwin Chargaff

discovered the amount of adenine always equaled the amount of thymine and the amount of guanine always equaled the amount of cytosine

The amount of bases differed between species

Maurice Wilkins and Rosalind Franklin

Used X-ray crystallography to study the structure of DNA

Photograph 51 - DNA has a helical shape, and a width of about 2 nanometers, and nitrogenous bases are in the center of the DNA

James Watson and Francis Crick

Obtained Photograph 51 and proposed DNA was a double helix and that the sugar and phosphate form the outer backbone

Nitrogenous bases are in pairs in the center of the helix, and each pair is spaced 0.34 nanometers apart. It takes ten base pairs to make one complete turn of the helix (3.4 nanometers in height)

Explain the process of DNA replication, including the roles of each enzyme and the difference between leading and lagging strands

The process begins at specific spots on DNA known as origins of replication

An enzyme called DNA helicase comes in and unwinds the DNA, separating the 2 strands which creates a “Y” shape known as a replication fork

Another enzyme called primase adds a short piece of RNA called a primer to each strand. The primer acts as a starting point for the next steps.

Then, DNA polymerase, the main enzyme for making new DNA, attaches to the primer. It will start adding new DNA nucleotides to create a new strand. This happens continuously on one strand called the leading strand because DNA polymerase moves in the same direction that the helicase is unwinding DNA (5’ to 3’)

On the other strand, there’s the lagging strand. Here, DNA polymerase has to work in short sections because it moves in the opposite direction of helicase (discontinuously). It makes short pieces of DNA (called Okazaki fragments), and each fragment also starts with a primer

The newly created fragments on the lagging strand are eventually linked together by another enzyme called DNA ligase

In the end, each new DNA molecule is made up of one original strand and one newly made strand, which makes the replication process semiconservative.

Also movies from 5’ to 3’ prime and DNA polymerase has to attach to 3’

What is the significance of telomeres and telomerase in DNA replication and aging

The process of cell division and DNA replication can lead to the shortening of chromosomes. This is because of telomeres, which are at the ends of DNA strands and cannot be fully replicated

So, each time a cell divides and has to replicate the DNA, telomeres protect important information from being lost. They postpone erosion because they are repetitive sequences of DNA

Somatic cells usually divide up to 50 times, and each time, the telomeres get shorter, and when they become too short, they can cause cell death (and is also linked to aging processes since older cells have shorter telomeres)

Telomerase is an enzyme that restores telomeres to their original length, adding back those repetitive sequences.

Adult somatic cells don’t have active telomerase, so telomeres do shorten with each division as we age.

Elizabeth Blackburn

Discovered the enzyme telomerase

What are some types of DNA repair mechanisms and potential consequences of mutation

In proofreading, DNA polymerase checks for errors during replication. If it encounters an incorrectly paired nucleotide, it removes the incorrect one and replaces it with the correct one

In mismatch repair, if DNA polymerase overlooks an error that has incorrectly paired nucleotides, other enzymes will cut out the incorrectly paired nucleotide and replace it with the correct one

In nucleotide excision repair, damage to DNA by things like UV can result in thymine dimers (where 2 adjacent thymines bond). Enzymes will remove that damaged section and replace it with an undamaged section

If the errors are not corrected, there can be permanent changes in the DNA (mutations), which can lead to genetic disorders or diseases

What are the applications of DNA knowledge in forensics and criminal justice

DNA fingerprinting which is used to identify unique patterns in DNA in each organism

This method was used to exonerate Kirk Bloodsworth who was put on death row.

Julius Ruffin served more than 20 years in prison for a crime he did not commit but was exonerated because of DNA fingerprinting

What is the fundamental concept of gene expression

It is the 2 step process by which DNA directs the synthesis of proteins

The sequence of nucleotides in DNA specifies an order of amino acids in a protein

The sequence that amino acids are connected in a protein is very important

Describe the structure and composition of RNA

It is similar to DNA but is single-stranded

It is made up of nucleotides (a sugar, phosphate, and base) the sugar is ribose

The phosphate group is always attached to carbon 5 and the base is always attached to carbon 1

The bases are (A, G, C, U in place of thymine)

What are the 3 main types of RNA? Describe their functions

Messenger RNA (mRNA) carries the code for instructions for protein synthesis from DNA to the ribosome

Ribosomal RNA (rRNA) is a structural and functional component of ribosomes, without it, ribosomes won’t function

Transfer RNA (tRNA) is responsible for carrying specific amino acids to the ribosome during protein synthesis

Ribosome

Is what is going to assemble the amino acids into a polypeptide as it is directed by mRNA

What is an analogy for how the different RNAs work together

Recipe for a cake (DNA) but you ask a French baker for help to bake it but need to translate the recipe first and deliver it (mRNA) to the French baker (ribosome). This baker has helpers (tRNA) that will help deliver all the ingredients (amino acids) to the baker as he is putting the cake together, the cake (protein) is the final product

Describe the steps of transcription and how RNA can be made from a DNA template

The first step is Initiation, where RNA polymerase binds to the promoter sequence on DNA, which then leads to the separation of the DNA stands at that location, exposing the template for transcription

The next step is elongation, where RNA polymerase creates a complementary RNA strand in the 5’ to 3’ directions (using uracil in place of thymine)

This then moves on to termination, where RNA polymerase reaches a termination sequence and separates itself from the DNA which leads to the release of a new RNA molecule from the DNA

What are the modifications that occur to mRNA after transcription (post-transcriptional processes)

Following is RNA processing, where a 5’ cap and poly-A tails are added so that the RNA can enter the cytoplasm and it will protect it. 5’ cap will allow ribosomes to attach for translation

Lastly in RNA splicing, introns are removed from the RNA, leaving behind exons and leading to the formation of mRNA (which can now leave the nucleus

Describe the steps of the translation process the difference between codon and anticodon

The first step is initiation, where the small subunit of the ribosome attaches to the mRNA and 5’ prime end, which leads to the first tRNA coming in a bringing AUG (methionine) the start codon

Next, the large subunit of the ribosome clicks onto the small subunit and tRNA making an initiation complex, making an

Then is elongation, where the mRNA strand passes through the ribosomal subunits, leading to each codon being read one at a time. The tRNA with the corresponding anticodon pairs bring in the correct amino acid

A peptide bond forms between the amino acids, which leads to the tRNA releasing its amino acids and shifting to allow a new tRNA, allowing the peptide chain to grow

The process stops when a stop codon is encountered on the mRNA which triggers the release of the completed polypeptide chain and the ribosomal structure disassembles

What is the difference between codon and anticodon

Codon is a sequence of 3 nucleotides on the mRNA that specifies an amino acid

Anticodon is the corresponding sequence of the codon, it is not the sequence read for amino acid.

Understand the concept of gene regulation and the levels at which regulation can occur

Gene regulation is the process by which cells control the expression of genes

This can lead to differences in the types and amounts of proteins produced in various cell types

Regulation occurs at the DNA level where DNA is wrapped around proteins. If the DNA is tightly coiled, the gene is not expressed, but if it is unpacked, proteins can be made.

It can also occur during transcription where various proteins determine whether a gene gets transcribed into mRNA

It can occur during mRNA processing and export, where mRNA needs to be recognized by nuclear receptors to exit the nucleus

During translation, where proteins control the initiation, which leads to the timing of mRNA degradation affecting how much protein is created

And, during post-translational modifications of proteins where altercations may be needed for the protein to function

Learn about gene mutations, their types, and their causes.

Mutation - a permanent change in the DNA sequence (which can affect the structure and function of proteins that DNA codes for)

Missense mutation is a change in a single nucleotide pair that leads to a change in amino acid sequence (Ex. Sickle Cell Anemia, glutamic to valine changes hemoglobin properties)

Silent mutation is when a change in the base pair does not affect the amino acid production (multiple codons can code for the same amino acid

Nonsense mutation when there is a premature stop codon because of a nucleotide pair sub

Insertion/Deletion are part of frameshift mutations, it is when one or more pairs are either inserted or deleted (even more than one nucleotide base pair can be deleted

Mutagens

physical and chemical agents that induce mutations

Biotechnology

the industrial use or altercation of biological molecules for practical applications for using or altering biological molecules or organisms for practical goals

Practical Applications of Manipulating DNA - Agriculture

Farmers have been using selective breeding for generations to obtain describable traits in crops (Ex. Juicer corn kernels or larger potatoes)

Scientists can use genetic engineering to create plants that are drought-tolerant or disease-resistant

Practical Applications of Manipulating DNA - Medicine

Genetic engineering allows us to use bacteria to create proteins for medication (Ex. Create human insulin)

Genetic Engineering

Manipulating genetic material by either adding, deleting, or transplanting genes into new or the same organism

Restriction enzymes, PCR and Vectors- Biotech

Restriction enzymes cut DNA at specific sequences, allowing scientists to extract any gene of interest

PCR is used to amplify a specific DNA sequence (developed by Kary Mullis). Involves heating and cooling DNA to separate strands then using heat-loving DNA polymerase from bacteria to synthesize new strands rapidly

Vectors - Biotech

Vectors are carriers that can deliver DNA from one organism to another (usually plasmids or viruses)

Plasmids are circular, self-replicating pieces of DNA

If a restriction enzyme cuts a plasmid, it creates “sticky ends” that can be with complementary sequences, allowing the insertion of desired genes

Explore the creation of transgenic organisms and their significance (how genes from one species

Transgenic organisms are created by inserting DNA from one species into the genome of another, allowing the expression of those traits

People with type 1 diabetes used to rely on insulin extracted from pigs/cows. Now we can insert human insulin gene into bacteria using plasmids as vectors

These plasmids are cut with restriction enzymes, creating sticky ends. The same restriction enzyme is used to cut out human insulin gene.

We can then insert the human insulin gene into the plasmid and becomes recombinant DNA, which combines genetic material from different species

Then the modified plasmid is ,introduced into a bacterium to produce human insulin

Genetically modified organisms

Represents any organism that has modified DNA

GMO applications in agriculture

Making food more nutritious

Golden rice - hundreds of thousands of children with vitamin A deficiency become blind and die within 12 months of losing their eyesight, to counteract this, rice was inserted with a vitamin A gene

Innate potato - potatoes have been modified with DNA from other potatoes to reduce the production of an amino acid called asparagine (which becomes a carcinogen when fried)

Bt-corn - Bacillus thuringiensis is a bacterium toxic to some insects and is sprayed/injected in plants. Scientists have now just taken the gene from the bacterium and inserted it in corn

Gene therapy

a genetic engineering technique where you can add the right gene to a person who has a defective one (or edit a broken gene)

What are the scientific and ethical considerations of gene therapy

Scientific considerations focus on how to safely and effectively fix/replace defective genes

It has shown success in treating Severe Combined Immunodeficiency, where corrected genes are inserted into a patient’s blood stem cells

Another one is Leber’s congenital amaurosis, where gene therapy has been used to restore vision

Ethical considerations view gene therapy as unnatural and immoral, where others see it as a moral obligation to fight diseases if there is the ability to do that

Describe how the CRISPR-Cas9 system can be used for gene editing.

CRISPR-Cas9 finds a target sequence in the DNA and edits it in its precise location

Cas9 acts like scissors, cutting the DNA at the targeted spot which triggers the cell to repair the break

A short strand of DNA with the correct genetic sequence is supplied, which the cell uses a template