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Unit 3: Genes Flashcards

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1
Q

Define a genome

A

Genome Definition: The whole of the genetic information of an organism

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2
Q

What are hierarchy of genetic info?

A

Hierarchy of genetic info:

  1. Genome
  2. Chromosomes
  3. Genes
  4. Allele
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3
Q

What are chromosomes?

A

Definition: Long stretches of DNA which store genes

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4
Q

What is the diploid state of chromosomes?

definition example, location

A

Diploid State Definition: Having a pair of each kind of chromosome. Most eukaryotes are diploid and inherit one copy of each chromosome maternally and the other paternally. Occurs in somatic cells

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5
Q

What is the haploid state of chromosomes?

A

Haploid State Definition: Having one copy of each chromosome.

Location: Gametes

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6
Q

How is Prokaryotic DNA?

A
  • In prokaryotes there’s a single chromosome containing the entire genome, including all necessary genes
  • Not organised around histone proteins
  • Plasmids
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7
Q

What are plasmids?

A

Plasmids = small circular loops of DNA which are easily exchanged between prokaryotes and may contain several genes.
- plasmid may contain one or several genes, usually related to one function
- bacteria can easily exchange plasmids, sometimes even with a different species of prokaryotes. This provides a mechanism where antibiotic resistance spreads. antibiotic-resistant bacteria are a major problem in hospitals
- plasmids are generally not found in eukaryotes, but there are exceptions. For example, saccharomyces cerevisiae which is a unicellular yeast used in baking, containing a small plasmid.

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8
Q

How are eukaryotic chromosomes and how do they change through the cell cycle?

A
  • linear
  • each DNA molecule has two ends like a piece of thread, which are wrapped around histones (basic (alkaline) proteins)
  • In interphase, chromosomes are in chromatin because DNA is in active use. This allows the transcription enzymes to access the genes easily.
  • In the first stages of mitosis and meiosis, the chromosomes condense to form organised structures, forming an ‘X’ shaped structure. The two lines forming this are identical copies of the chromosome, known as sister chromatids. The place where they connect is called the centromere. The supercoiled state lets them be separate without getting tangled and torn
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9
Q

What are homologous pairs?

A

Homologous pairs = the two versions of the same chromosome (maternal and paternal)

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10
Q

What are homologous chromosomes?

A

homologous chromosomes = chromosomes that have the same set of genes in the same locations, but may have small differences between nucleotide sequences. Homologous chromosomes carry the same sequence of genes but not necessarily the same alleles of those genes.

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11
Q

How many chromosomes does the human genome have?

A

Human genome has 23 pairs of chromosomes, and 46 chromosomes total

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12
Q

What are autosomes?

A

Autosomes = chromosomes which do not influence sex determination. They’re numbered according to length. Chromosome 1 is the longest and chromosome 22 is the shortest.

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13
Q

What are haploid nuclei

A

Haploid nuclei contain only one chromosome from each pair and are found only in our gametes. They are produced from diploid cells through meiosis. They carry the same genes ate the same loci, with possibly different alleles.

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14
Q

What type of cell are most cells in the human body

A

Most cells in humans are diploid, meaning nucleus as two copies of each chromosome, 23 homologous pairs

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15
Q

What is a zygote?

A

Zygote = the diploid cell formed by the union of the sperm and egg.

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16
Q

What type of chromosomes are autosomal pairs?

A

all autosome pairs are homologous because the maternal and parental copy contain the same genes in the same positions.

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17
Q

What are some properties of sex chromosomes?

A

sex chromosomes have different genes and lengths, however they have a homologous region allowing them to act like a pair during meiosis.

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18
Q

What type of chromosomes do diploid nuclei have?

A

diploid nuclei have pairs of homologous chromosomes

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19
Q

What are haploid nuclei?

A

haploid nuclei have one chromosome of each pair of homologous chromosomes. Each chromosome in a homologous pair is called a homologue.

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20
Q

What is a tetrad?

A

A structure with two homologus chromosomes is a tetrad.

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21
Q

What is karyotyping?

A

Karyotyping: Aligning homologous chromosomes by length, location of the centromere and by bands of colour differences (striations) induced using dyes.

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22
Q

What is a karyogram?

A

Karyogram: Photograph or image of homologous pairs of chromosomes in decreasing length. Shows the chromosomes of an organism in homologous pairs of decreasing length. Can be used to deduce the sex of an individual, to find missing or extra chromosomes, or to detect mutations. Not able to detect differences in alleles or mutations that affect a single gene.

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23
Q

What is non-disjunction?

A

Non-disjunction = failure of a pair of homologous chromosomes to separate.

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24
Q

What is a trisomy?

A

Trisomy = condition where zygotes are formed when a gamete has an extra chromosome which creates individuals with three copies of one chromosome. - Trisomy is often fatal. However, if it occurs with chromosome 21, down syndrome occurs.
- Down syndrome causes hearing loss, heart and vision problems, intellectual disability, and slower growth which leads to smaller stature.

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25
Q

What are the two methods to obtain material for fetal karyotyping?

A
  1. Amniocentesis is usually performed between weeks 14 and 20 of pregnancy. A doctor uses ultrasound imagery to guide a syringe needle through the abdomen and uterine wall without piercing the fetus. The needle is then used to withdraw a small amount of amniotic fluid. Amniotic fluid cushions the fetus as it develops in the uterus. Fetal cells floating in the fluid are cultured and karyotyped. Risks: infection, fetal trauma from needle, and miscarriage. Risks of miscarriage are between 0.1 and 1 %
  2. Chorionic villus sampling can happen early in pregnancy when there isn’t enough amniotic fluid to safely perform amniocentesis. It can happen during weeks 10-13. Ultrasound imagine is used to guide the medical professional to avoid harm to the embryo or fetus. Fetal cells are sampled by inserting a suctioning tool (i.e. catheter, syringe) through the vagina or abdomen to reach the fetal cells in the chorion. Chorion is a membrane surrounding the fetus which develops into part of the placenta. Risks include bleeding, infection, and miscarriage. Risk of miscarriage is 0.5 - 2.0%.
  3. Fetal karyotyping using minute amounts of fetal DNA found in maternal blood. Provides same information without risk of miscarriage.
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26
Q

What is audioradiography

A

Autoradiography: Auto = self, radio = radiation, graphy = drawing. Technique that lets X-ray film visualise two-dimensional distribution of a radioactively labelled structure.

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27
Q

Autoradiograph

A

Image formed through autoradiography

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28
Q

What was the first autograph

A
  • First autograph was made from DNA molecules from Escherichia Coli (E. Coli)
    • made thymidine (nucleotide with thymine) labelled with radioactive hydrogen (^3H)
    • grew E.coli bacteria in a medium with radioactive thymidine. When the E. coli cells replicated, they created radioactive DNA.
    • Lysed the cells to release the contents, including the intact DNA onto slides
    • Covered the slides with photographic emulsion and stored them in the dark for two months
    • High energy electrons emitted by the radioactive decay of the radioactive hydrogen caused appearance of dark spots on the photographic emulsion
    • Dark spots indicated the presence of labelled DNA
    • the length of the E. Coli chromosome could be measured and was worked out to be around 1 mm, about 1000x longer than a typical E. Coli cell
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29
Q

What is the term for rupturing cell walls and membranes

A

lyse

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30
Q

Define a gene

A

Short stretches of DNA that influence a specific characteristic. Are heritable

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31
Q

What is a gene locus

A

Gene Locus Definition: Specific location of gene in a chromosome. Identified through gene mapping or sequencing

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32
Q

Define homozygous genes

A

Homozygous Definition: Gene with two copies of the same allele

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33
Q

Define heterozygous genes

A

Heterozygous Definition: Gene with two different alleles

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34
Q

Define an allele

A

Definition: Various, specific forms of a gene that usually vary from each other by one or a few bases. You may inherit the same allele from both parents, or two different.

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35
Q

Define a genotype

A

Genotype Definition: Alleles that you have for a gene

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36
Q

Define a phenotype

A

Phenotype Definition: Traits you possess as a result of your alleles

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37
Q

Explain the TYR gene

A

Example: for the TYR gene, one allele codes for an enzyme that converts amino acid tyrosine into melanin, a pigment in human skin. another allele codes for an altered enzyme that can’t convert tyrosine into melanin. the second allele results in albinism, or the absence of melanin.

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38
Q

What is a SNP

A

Single nucleotide polymorphisms

  • describe changes existing between alleles of a gene. One base is exchanged with another. Multiple SNPs may exist in variations of a gene.
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39
Q

What are causes of mutations

A
  • DNA replication mechanisms make errors
  • Exposure to radiation and mutagens
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40
Q

Define carcinogens

A

Mutagens that cause tumorigenesis

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41
Q

Define base-substitution mutations

A

Mutation where one nitrogenous base is swapped with another.

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42
Q

What is the Human Genome project?

A
  • began 1990
  • aimed to determine the complete sequence of the human genome and identify every gene it contains
  • multinational and multidisciplinary initiative
  • whole human genome was estimated to be around 3.2 billion bases
  • anticipated to take around 15 years, but ended up being finished in 2003 due to technological advancements
  • personal genome sequencing is also possible
  • knowing which alleles a patient has tells doctors which medicines are likely to be effective
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43
Q

What is sickle cell anemia?

A
  • common genetic disease where malaria is endemic (regularly occuring)
  • most common type of sickle cell disease
  • 1/3 rd of the population in africa may carry the sickle cell allele
  • 2% of children are born with sickle cell anemia
  • Possible Symptoms: increase events of extreme pain, weakness, heart attack or stroke, pneumonia, bone malformations, death
  • single-base substitution. ‘T’ instead of ‘A’ once in the genome.
  • occurs when a person is homozygous for HbS
  • sickled cells need to be broken down and eliminated which strains the liver and causes a shortage of functioning red blood cells, anemia
  • new red blood cells need to be made in bone marrow to replace lost blood cells, and the extra work might damage bone structure
  • sickling events are triggered by low oxygen in blood, dehydration, infection, and sudden external temperature changes
    • In sickle cell anemia:
      • hemoglobin proteins polymerise into long fibres. There’s hundreds of hemoglobin molecules in each red blood cell
      • Red blood cells take a sickled shape when they’re stretched out by the hemoglobin fibres inside of them
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44
Q

What is chromosome 11 and the HBB locus

A
  • human chromosome 11 has a length of about 135 million DNA base pairs, and is about 4% of the human genome. it has around 1300 protein-coding genes.
  • codes for beta subunit of hemoglobin, a polypeptide 146 amino acids long
  • two copies of beta subunits combine with two alpha subunits and four heme groups, forming a hemoglobin molecule
  • standard Hb^A allele reads G A G at the 6th triplet instead of G T G
  • when HBB locus is transcribed, the mRNA from HbA has GAG for the 6th codon, which is glutamic acid. the mRNA from HbS has codon GUG which codes for valine.
  • glutamic acid interacts well with water, keeping hemoglobin molecules dissolved in the erythrocyte
  • valine is hydrophobic, allowing the beta subunits to join together.
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45
Q

What is hemoglobin

A
  • hemoglobin = protein found in erythrocytes (red blood cells) which carries oxygen through the body
  • every red blood cell has about 270 million hemoglobin molecules
  • homoglobin normally formed using HbA or HbS normally has the same ability to carry oxygen
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46
Q

What happens when hemoglobin from HbS alleles polymerises into long fibres

A
  • ability to carry oxygen is reduced
  • long fibres poke into the cell membrane, distorting the shape and making it curved and ‘sickle’ type
    • can get stuck and clog blood vessels anywhere. if happens in brain, the person could have a stroke
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47
Q

What is the term for when one gene has multiple effects

A

Pleiotropy

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48
Q

What happens when chromosome 11 has HbAHbA or HbAHbS

A
  • when person’s alleles are HbAHbA, their hemoglobin will never polymerise and their erythrocytes will never sickle
  • if HbAHbS, the hemoglobin has some beta subunits with valine and some with glutamic acid. the cells then only sickle when infected by plasmodium falciparum, the parasite that causes malaria. body eliminates sickled red blood cells so malaria is eliminated with it. in areas where malaria is present, it’s an advantage to have one HbS allele. Having 2 leads to sickle cell anemia, and doesn’t protect people from malaria.
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49
Q

What are the genotypes for sickle cell anemia

A
  • HbAHbA - homozygous for normal hemoglobin, no sickling, no protection from malaria
  • HbAHbS - heterozygous, carriers of the sickle cell trait, protection from malaria
  • HbSHbS - homozygous for altered hemoglobin, sickle cell anemia, no protection from malaria
50
Q

What is malaria?

A

Malaria is an infectious disease caused by protozoan parasites transmitted to humans by infected mosquitoes

51
Q

Define meiosis and its location, products, pre-requisites, usage, advantages, species

A

Definition: Process to produce nuclei with exactly one copy of each gene.

Location: Gametes

Products: Four haploid cells per diploid nucleus

Pre-Requisites: DNA is replicated during the S phase of interphase before meiosis

Species: Eukaryotes

Usage: Dividing genetic material to prepare for combining with another parent

Advantages: Genetic diversity in offspring

52
Q

What are the stages of meiosis

A
  1. Meiosis I
    1. Prophase I
    2. Metaphase I
    3. Anaphase I
    4. Telophase I
  2. Meiosis II
    1. Prophase II
    2. Metaphase II
    3. Anaphase II
    4. Telophase II
53
Q

Draw meiosis

A

https://file.notion.so/f/f/e52fcf8a-d6ea-4a2d-a3c3-d8bce0c54560/b992951b-6131-42e5-b78f-d151af085c3a/Untitled.png?id=e92d5311-b27f-44c2-aede-eb354e0ae6e8&table=block&spaceId=e52fcf8a-d6ea-4a2d-a3c3-d8bce0c54560&expirationTimestamp=1714867200000&signature=DDihrvlWm4IfNIafswqjZxGomtUI-TZQiCS-RNDPW6o&downloadName=Untitled.png

https://file.notion.so/f/f/e52fcf8a-d6ea-4a2d-a3c3-d8bce0c54560/d80ad02f-ad4e-4aac-8c8b-663a4def6f0d/Untitled.png?id=8eb395d2-8e81-43ce-84da-e899382811f2&table=block&spaceId=e52fcf8a-d6ea-4a2d-a3c3-d8bce0c54560&expirationTimestamp=1714867200000&signature=no-l9jkP313VNak2bgcIsdmuz5EeGo0QRjJ5p7dTUyk&downloadName=Untitled.png

https://file.notion.so/f/f/e52fcf8a-d6ea-4a2d-a3c3-d8bce0c54560/de59af72-da36-4c96-a251-17a5c2c1172c/Untitled.png?id=6de2d145-4cc2-4562-9ac5-0ebf2fe82e5b&table=block&spaceId=e52fcf8a-d6ea-4a2d-a3c3-d8bce0c54560&expirationTimestamp=1714867200000&signature=YyQr4keVmW7GacoBqLBuF7PXobRHh6bUL7BE1b5AUYs&downloadName=Untitled.png

54
Q

What problem can occur in meiosis

A

Problems: Non-disjunction (when two copies of a chromosome don’t separate properly, so gametes have one extra or one missing chromosome, occurs more often in older parents, more commonly mothers). Non-disjunction can cause trisomy (three copies of a chromosome) or monosomy (one copy of a chromosome) in offspring

55
Q

What does n represent in meiosis

A

n=number of chromosome types

56
Q

What is a trisomy

A

Trisomy = Three copies of a chromosome

57
Q

What is a monosomy

A

Monosomy = One copy of a chromosome

58
Q

What is the formula for mitosis vs meiosis with respect to n

A
  • Mitosis: diploid cell (2n) → two diploid (2n) daughter cells.
  • Meiosis: diploid cell (2n) → four haploid (n) daughter cells.
59
Q

Summarize what happens during Meiosis I

A

Reduction division. Going from diploid (2n) to haploid (n)

60
Q

What are the steps of prophase I of meiosis

A
  1. Chromosomes supercoil and become visible
  2. they form closely linked homologous pairs (known as tetrads/bivalents. two homologues have two chromatids each, for a total of four)
  3. Non-sister chromatids crossover at a point called the chiasmata (singular: chiasma), and exchange segments of DNA. This can happen over multiple times in the same tetrad. This contributes to genetic variation amongst the gametes.
  4. Centrioles go to opposite poles and the spindle fibres start forming
  5. Nucleolus and nuclear membrane disintegrate
61
Q

What happens during metaphase I of meiosis

A
  1. Homologous pairs move to the metaphase plate, halfway between the poles
  2. Maternal and paternal homologues show random orientation towards the poles. Alleles
  3. spindle fibres attach to centromeres of each chromosome and align them along the metaphase plate
  4. Spindle fibres connect each centromere to one pole

Resulting Changes from Being Arranged in Pairs, Not Individually:

  1. Reduction division — daughter cells have half the information from the parent. Daughter cells have two chromosomes each, and are haploid with one version of each chromosome.
  2. Random Orientation — When the pairs line up, the the maternal or paternal could be on either side. The way that one homologous pair is lined up doesn’t impact the other. This makes the assortment of each gamete random.
62
Q

What happens during Anaphase I of meiosis

A
  1. Microtubules shorten and pull homologous chromosomes towards opposite poles
  2. Sister chromatids remain connected at the centromere and move to the same pole
63
Q

What happens during telophase I of meiosis

A
  1. Ends when chromosomes arrive at the poles
  2. each chromosome still has a pair of chromatids
  3. Chromatids partially uncoil and a nuclear membrane forms around each nucleus
  4. Cytokinesis occurs
  5. Results in two daughter cells with haploid nuclei
64
Q

Summarize what happens in meiosis II

A

Definition: Separation of chromatids in haploid cells. n→n. Similar to mitosis

65
Q

What happens in prophase II of meiosis

A
  1. Chromosomes condense
  2. Centrioles go to opposite poles and the spindle fibres start forming
  3. the nucleolus and nuclear membrane disintegrate
66
Q

What happens in metaphase II of meiosis

A
  1. Spindle fibres attach to the centromere and connect each centromere to both poles
  2. Pull to align the sister chromatids at the equator
67
Q

What happens in anaphase II of meiosis

A

Centromeres divide and chromatids move to opposite poles through spindle fibres

68
Q

What happens in telophase II of meiosis

A
  1. Chromosomes go to opposite poles and uncoil
  2. Nuclear envelopes form
  3. Cytokinesis
  4. 4 haploid daughter cells are made and each is genetically distinct
69
Q

What is genetic variation: source and advantages

A

Source: Mutation, sexual reproduction, crossing over in prophase I, random orientation in metaphase I

Advantages: Allow a population to adapt

70
Q

What is non-disjunction and how does it happen

A

Definition: When the sister chromatids fail to separate during anaphase II or anaphase I

Products: Gamete with two copies of a chromosome and one with none

  • when the gamete with extra chromosome is fertilized by a normal gamete, the zygote will have three copies of a homologue. this is called trisomy
  • If occurs during early embryonic development, it is called mosaicism and accounts for 2% of down syndrom cases
  • Many trisomies cause severe symptoms causing the embryo to not develop
  • Only survivable monosomy in humans is having a single X chromosome for the sex pair
  • positive correlation between age of mother and incidence of chromosomal differences. After 30-34 there’s a sharp increase. With higher age, there’s a higher chance of non-disjunction.
71
Q

Who was gregor johann mendel and what did he do

A

Mendel discovered the basic principles of heredity through work on garden pea plants (Pisum sativum). He covered each flower until it could be hand-fertilized with the pollen of a parent plant, then examined traits of the offspring. This resulted in Mendel’s law.

72
Q

What are mendel’s laws of inheritance?

A

Applicable to: Sexually Reproducing species

  1. The law of segregation - the inheritance of each characteristic is controlled by a pair of alleles in an individual. The two alleles are separated during meiosis so each gamete has only one allele for each gene. Alleles are passed down as distinct units. Exceptions to this is the genes in the sex chromosomes and the mitochondrial DNA.
  2. The Law of independent assortment - allele inherited for one trait doesn’t affect which allele will be inherited for a different trait. A gamete has one copy of each gene. The copy it gets during meiosis is the result of random orientation during metaphase I. There’s an exception for genes whose loci are close together on the same chromosome. These called are linked genes.
  3. the law of dominance - in an organism with with two alleles, one will determine the phenotype. The expressed one is dominant and unexpressed is recessive. There can also be co-dominance.
73
Q

What are gametes, segregation, and zygotes

A

Segregation: Alleles are segregated during meiosis

Gametes: Reproductive cells carrying the haploid copy of the genome produced during meiosis.

Zygote: Diploid cell formed when a sperm and ovum fuse in fertilisation.

74
Q

What is the ABO gene

A

ABO Gene determines which blood group an individual has. The ABO gene is most important for transfusions, but other genes also affect blood groups (i.e. positive or negative is determined by RHD gene which indicates if a Rh factor protein is present)

75
Q

What is the genotype for A blood type

A

I^A I^A, or I^A i

76
Q

What is the genotype for blood type B

A

I^B I^B or I^B i

77
Q

What is the genotype for blood type AB

A

I^A I^B

78
Q

what is the genotype for blood type O

A

ii

79
Q

What does the I in alleles for the ABO gene (i.e. allele I^A) stand for?

A

Isoagglutinogen

80
Q

What do alleles I^A and I^B do for the blood molecule?

A

all alleles make the same base molecule, but I^A and I^B make different additions to the molecule. The modified molecules are called antigens since they make in immune response to foreign things. ‘i’ doesn’t produce an antigen.

81
Q

What blood type is the universal donor

A

Blood type O is the universal donor since individuals of any group can receive O blood safely

82
Q

What is the frequency, mode of inheritance, and chromosome location of PKU (phenylketonuria)

A

Mode of inheritance: Autosomal recessive
Chromosomal location: 12

83
Q

What is the frequency, mode of inheritance, and chromosome location of Tay-Sachs disease

A

Mode of inheritence: Autosomal recessive
Chromosomal Location: 15

84
Q

What is the frequency, mode of inheritance, and chromosome location of Duchenne muscular dystrophy

A

Mode of inheritance: Sex-linked recessive
Chromosomal location: X

85
Q

What is the frequency, mode of inheritance, and chromosome location of Marfan’s syndrome

A

Mode of inheritance: Autosomal dominant
Chromosomal Location: 15

86
Q

What is cystic fibrosis

A

Type: Autosomal recessive disease

  • recessive allele was formed by mutation in the CFTR gene, which codes for a chloride channel in mucous membranes
  • on chromosome 7 and is involved in secretion of sweat, mucus, and digestive juices

Effects: Build up in lungs, causing dangerous infections and damaging lung tissue. Mucus also builds up in the liver and pancreas, so it’s more difficult to digest food.

  • 1/20 people are carriers
87
Q

What is Huntington’s disease?

A

Type: Autosomal dominant disease

  • Neurodegenerative disorder affecting people between ages 30-50

Cause: Dominant allele developed through mutation of HTT gene on chromosome 4

Symptoms: Loss of muscle coordination, cognitive decline, and psychiatric problems. Once these symptoms appear, the average life expectancy is 10 years.

Population Percentage: 1 in 10 000

88
Q

What is Red-Green Colour Blindness

A

Type: Sex-linked recessive

  • codes for non-functional copy of one type of photoreceptor protein in the retina
  • present in 8% of males in northern europe
89
Q

What is haemophilia?

A
  • where protein needed for blood clotting is not made
  • small injuries can cause excessive bleeding and even death

Type: Sex-linked recessive. Gene needed for clotting factor VIII is on the X-chromosome.

90
Q

What are the causes of mutations

A

Causes: Chemical mutagens and radiation. These increase the mutation rate and can cause genetic diseases and cancer.

91
Q

What are mutagens?

A

Definition: Agent that increases frequency of mutations by triggering changes in the genetic material

  • includes radiation and chemicals
  • can lead to cancer, in which case the mutagens are also called carcinogens
  • are only passed on if present in DNA of cells that make gametes
92
Q

What is ionising radiation

A
  • occurs when energy is emitted in the form of waves or particles
  • lower levels are harmless since they lack the energy to break chemical bonds
  • Higher energy radiation called ionising radiation can break bonds between atoms, including DNA, leading to mutation
  • If radioactive iodine is incorporated into the thyroid hormones it increases the mutation rate and can cause cancer.
93
Q

What type of radiation can cause DNA damage

A

UV light, X-rays, alpha, beta, and gamma radiation from decay of radioactive elements

94
Q

What are the variations of dominance

A
  • complete dominance
  • co-dominance
    • new phenotype because both alleles are being expressed
    • i.e. red x white = pink
    • new notation
95
Q

What makes a blood type positive?

A

Positive mean you have a D-antigen. Negatives make anti-bodies against the D-antigen.

96
Q

Define gel electrophoresis

A

Using an electrical current to move molecules through a semisolid medium. This causes molecules(DNA or RNA or protein) to be separated by their size and amount of charge to identify the alleles at a few loci.

97
Q

What property of DNA and RNA and proteins allows for gel electrophoresis to occur

A

Property that allows for this to happen: DNA and RNA have a negative charge so they will move towards the positive end in an electric field. The thing can be adjusted based on the charge of proteins, but it works because they’re charged particles.

98
Q

What is the role of restriction endonucleases in gel electrophoresis

A

Restriction endonucleases: DNA is usually too long to be separated by electrophoresis. To get fragments to the right size (250-30 000 base pairs in length), restriction endonucleases cut the backbone of the DNA double helix at highly specific sequences to make shorter DNA segments and distinctive fragment patterns which can be used to make DNA profiles

99
Q

What is the process of gel electrophoresis

A

Samples with DNA fragments are loaded into small depressions called wells on one end of the gel (jelly-like polymer). The gel is submerged in a buffer solution and an electric current is run through it. The samples start near the negative pole, so they spread out as they go towards the positive pole.

100
Q

What type of gel is used in gel electrophoresis and why is it useful

A

Consistency allows separation of DNA fragments by size. The gel is made of long polymers, often polysaccharide agarose, which binds together in an interwoven mesh. The DNA has to then travel through the spaces between the polymers. Smaller pieces slip through more easily, making them travel further along the gel. By using higher concentrations of polymer, the average size of the pore can be reduced and smaller pieces of DNA can be separated.

101
Q

What is ethidium bromide used for in gel electrophoresis

A

Dye used which binds to DNA and then fluoresces in UV light. Ethidium bromide binds strongly to DNA so it makes a clear signal but is mutagenic, so safer alternatives may be used sometimes.

102
Q

What is the purpose of gel electrophoresis

A

Can be used whenever source of DNA must be identified. For example, can determine which type of bacteria is causing an epidemic, or be used to solve crimes. Can also be used to determine paternity and other family relations.

103
Q

Define PCR

A

Polymerase chain reaction repeatedly copies fragments of DNA, resulting in a large enough sample to do a thorough analysis.

104
Q

What are the steps to PCR

A
  1. DNA is places in a reaction chamber with many free nucleoside triphosphates, primers that will allow replication to occur from the desired point, and Taq polymerase
  2. DNA is heated enough to break hydrogen bonds and separate the two strands of the double helix. This happens at 98 degrees celsius
  3. The sample is allowed to cool and short primer sequences anneal to(bond with) complementary sequences in the DNA sample
  4. Taq polymerase replicates DNA by using the primer as a starting point
  5. After replication, DNA strands are heated to the point of separation and the process repeats
105
Q

What is Taq polymerase

A

Heat-stable version of DNA polymerase originally found in bacteria that live in hot springs.

106
Q

Define DNA profiling

A

Technique examining variable portions of DNA to make a profile or ‘fingerprint’ unique to the individual. After amplifying with PCR, the resulting mix of DNA fragments is separated using gel electrophoresis.

107
Q

What is satellite DNA

A

Short repeated DNA sequences present in most genomes

108
Q

What are restriction endonucleases used for in DNA profiling

A

Used to chop satellite DNA into fragments that vary in length depending on the number of repeats.

109
Q

What are GMos

A

GMOS: Genetically modified organisms also known as transgenic organisms resulting from DNA transfer between species.

110
Q

Why are GMOs possible

A

Reason for being possible: Genetic code is universal, so the information stored in DNA will be translated to the same polypeptide.

111
Q

What are the techniques for genetic modification

A

Techniques: All involve the target gene being identified and isolated, then copied and inserted into the genome of a different species

  • Inserting target gene into a virus and allowing it to infect the organism
  • shooting cells with tiny gold pellets dipped into a solution with the target gene (microprojectile bombardment
112
Q

How has escherichia coli been genetically modified

A

Produces human insulin due to genetic modification

113
Q

What is the process of gene transfer to bacteria

A
  1. Isolate desired gene from the original species by using reaction endonucleases.
    1. If the gene is eukaryotic, use reverse transcriptase to make an edited version of it because eukaryotes delete parts of RNA before it leaves the nucleus to be translated. Bacteria have no nucleus, so scientists make DNA without the parts that should be deleted
  2. Isolate an appropriate plasmid
  3. Cut the plasmid with the same restriction endonuclease that was used to remove desired genes, in order to open the loop of the plasmid, forming a string with two ends
    1. Most restriction endonucleases leave ‘sticky ends’ where half of the the helix extends beyond the other, leaving some unpaired bases. By using the same restriction endonuclease, the gene and plasmid get complementary unpaired sequences that ‘stick’ together by hydrogen bonding
    2. Use a restriction endonuclease that makes blunt ends for both the gene and the plasmid. Then add guanine nucleotides to the 5’ ends of the gene, and cytosine nucleotides to the 5’ ends of the plasmid. This makes complementary sequences that allow them to stick together
  4. Mix many copies of the target gene and cut plasmid together to allow complementary unpaired sequences to join together, thus adding the gene into the plasmid
  5. Use DNA ligase to covalently bond DNA backbones of the gene and plasmid together, sealing the gene into a plasmid loop
  6. Transfer the plasmid with the target DNA (recombinant plasmid) back into the bacteria
114
Q

What are the benefits and risks of genetic modification of crops, with examples for each

A

Benefits:

  • Introduction of new positive trait to crop. For example, golden corn has three added genes to provide precursors of vitamin A, and could prevent cases of vitamin A deficiency
  • Economic advantages since GMOs can have a greater yield. For example, Bt corn has an added gene to resist pests, and thus can produce 20-40% more corn per unit of land than conventional corn
  • Environmental advantages as higher yields mean less needed land for farming. For example, there’s a drop in sprayed pesticides on farms using Bt potatoes

Risks:

  • Ecosystem damage since GMOs may accidentally outcompete native species. For example, GM soybeans resistant to herbicide led to documented increase in the amount of sprayed herbicide used. There’s also GM creeping bentgrass which is hybridised with wild grasses, spreading the gene into the wild. Then there’s mirid bugs which used to be minor corn pests. When Bt-sensitive pests were killed, mirid populations increased.
  • Increasing monoculture since GMO crops have very low biodiversity, since they’ve been cloned from an original modified plant. For example, corn earworm and rootworm pests have developed resistance to Bt in corn
  • Corporate control over food supply since not all farmers can make GMOs. Monsanto sues farmers for planting GM seeds saved from the previous season. Some subsistence farmers near large GMO farms also have very high numbers of pests, causing them damage.
  • Human health concerns since it results in exposure to new genes and protein. For example, anaphylaxis, a life-threatening allergic reaction, might have been caused by accidental exposure to GM StarLink corn. And an attempt to improve soybeans by adding a Brazil nut protein showed people allergic to nuts were also allergic to GM Soybeans.
115
Q

What are clones

A

Groups of genetically identical organisms, derived from a single original parent cell.

116
Q

What are methods of natural cloning

Provide examples and descriptions

A

Methods of natural cloning:

  • Binary fission in bacteria
    • Example: E.coli
    • Description: Chromosome is copied and cell splits in half, making two cells with a copy of the chromosome
  • Runners in Plants
    • Example: Strawberries
    • Specialised stems grow along the ground and put down roots, making a cloned individual a short distance from the parent plant
  • Bulbs in plants
    • Example: Garlic cloves
    • Each clove contains a cloned shoot of the parent plant, as well as stored food to allow development of another plant
  • Tubers in plants
    • Example: Potatoes
    • Enlarged stems(potatoes) or roots(sweet potatoes) have small buds called ‘eyes’ which can each grow into a cloned plant
  • Budding in fungus
    • Example: Yeast
    • The nucleus is copied and passed into a small bud formed on the side of the parent cell. The daughter cell is a clone, usually smaller than the parent cell.
  • Budding in animals
    • Example: Hydra
    • A new multicellular individual grows from the parent body using mitosis. When the cloned individual is large enough it breaks off.
  • Parthenogenesis in animals
    • Example: Marbled crayfish
    • The adult lays eggs containing 100% of her genetic information. The eggs develop into clones. There are no males in this species.
117
Q

What are the means of deliberately cloning animals

A
  1. Splitting or fragmentation of an embryo to clone an animal before cells have differentiated
  2. Using differentiated cells and somatic cell nuclear transfer to clone adult animals
118
Q

What are the origins of DNA in animal clones produced through somatic-cell nuclear transfer

i.e where is nuclear DNA from, mitochondrial DNA

A

Nuclear DNA is from the donor
Mitochondrial DNA is from the egg donor

119
Q

What are the steps to somatic-cell nuclear transfer

A
  1. Donor somatic (body) cells are taken from the organism that will be cloned and cultured in the lab.
    1. Somatic cells with the least DNA inactivation should be chosen. In this case, cells were taken from the udder of the donor sheep.
    2. The cell is starved so that the amount of cellular material other than the nucleus is reduced.
  2. An unfertilised egg is taken from another individual.
  3. The unfertilised egg is enucleated (the nucleus is removed).
    1. In this case, the nucleus was removed using a tiny pipette.
  4. The enucleated egg is fused with a donor cell.
    1. In this case, the cells were placed next to each other and an electrical current was used to disrupt the cell membranes enough so that they would fuse together.
  5. The fused cell is allowed to divide until a small embryo has formed.
  6. The embryo is transplanted into the uterus of a surrogate mother.
  7. The pregnancy and birth of the offspring proceed normally.
120
Q

What is the GM Maize and how does it affect the environemtn

A

GM Maize: Modified maize that produces a protein called Bt toxin from Bacillus thuringeinsis bacteria. One concern is that the pollen also contains the toxin, and since maize is a wind-pollinated plant, its pollen spreads to surrounding areas including milkweed, which is the main source of food for monarch butterfly larvae. However, the risk to monarchs from the toxin was minimal

121
Q

What is the Bt Toxin and why is it detrimentalz

A

Lethal to corn borer larvae of the moth, Ostrinia nubilalis, and many other insects, It allows farmers to apply less pesticide as the toxin is already eliminating the corn borers.

Biology (7 decks)

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