Molecular and Cell Biology Ch 10

1865 Gregor Mendel

• discovered the basic rules of heredity using garden peas

• father of genetics

• An individual has two alternative heredity units for a given trait, what are they?

the heredity unit for a given trait can either be dominant or recessive

1869 Johann Meischer

• discovered DNA and named it nuclein

• in 1899 nuclein was renamed to nucleic acid

Mendel chose to focus on (blank) clearly definable traits: list them

seven

1. height

2. seed color

3. seed shape

4. flower color

5. flower position

6. pod color

7. pod shape

list the 7 dominant and recessive alleles for mendel’s pea plants

Dominant allele

Height: tall

Seed color: yellow

Seed shape: round

Flower color: purple

Flower position: along stem

Pod color: green

pod shape: inflated

Recessive allele

Height: dwarf

seed color: green

seed shape: angular (wrinkled)

flower color: white

flower position: at stem tips

pod color: yellow

pod shape: constricted

1. Gregor Mendel’s work became the foundation for the science of (blank)

2. how did Mendel establish which traits were dominant vs recessive

3. Mendel established the laws of (blank) based on his studies on peas

1. genetics

2. mendel crossbred plants through several generations and counted the number of individuals with various characteristics

3. inheritance

1. define gene

2. each trait is controlled by (blank) forms of a gene called (blank)

3. alleles can be (blank) or (blank)

4. what happens when alleles are nonidentical

1. the unit of inheritance that governs the characteristics of organisms

2. two, alleles

3. identical, nonidentical

4. the dominant allele masks the recessive allele

1. define gamete

2. a gamete contains (blank) gene for each trait

3. how do somatic cells arise

4. (blank) alleles controlling each trait are inherited; (blank) from each parent

5. pairs of genes are (blank) during gamete formation

6. genes controlling different traits arise (blank) of one another aka (blank)

1. reproductive cell

2. one

3. somatic cells arise from the union of male and female gametes

4. two, one

5. separated/segregated

6. independently, independent assortment

• how were chromosomes first observed

• how are chromosomes divided during cell division

• chromosomes are (blank) prior to cell division

• chromosomes were observed in dividing cells via a light microscope

• chromosomes are divided equally among the two daughter cells during cell division

• chromosomes are double prior to cell division

1. DNA is the (blank) principle

2. describe Frederick griffith’s experiment

1. transforming

Frederick Griffith was working with streptococcus pneumonia bacteria trying to find a cure for pneumonia. during his experiment, he injected mice with:

live pathogenic strain of bacteria: killed the mice

live non-pathogenic strain of bacteria: mice lived

heat-killed pathogenic strain of bacteria: mice lived

mix heat-killed pathogenic and non pathogenic bacteria: mice died

because the mice still died when treated with the heat-killed pathogenic strain and non pathogenic strain mix, something that had disease-causing properties passed from the dead bacteria to the live bacteria to change their phenotype

DNA is the transforming principle

describe the Avery, McCarty and MacLeod experiment

• scientists purified both DNA and proteins separately from streptococcus pneumonia bacteria

• when the protein was injected into bacteria, no effect was seen

• when DNA was injected into bacteria, the harmless bacteria was transformed into virulent bacteria

• conclusion: DNA is the transforming principle that transmitted the disease-causing properties

Explain the Hershey and Chase Experiment

• this experiment served as definitive proof that DNA is the transforming factor and not protein

• scientists wanted to know if viruses injected DNA or proteins into bacteria to pass their genetic instructions

• the scientists used T2 bacteriophages (viruses that infect bacteria)

• Protein coats were tagged with radioactive sulfur-35 (proteins contain sulfur but DNA does not)

• DNA was tagged with radioactive phosphorus-32 (DNA contains phosphorus and proteins generally do not)

• the radioactively labeled bacteriophages attached to the bacteria cells and injected their genetic material

• bacteria cells were agitated (blended) to detach the viral protein coats from the outside of the bacterial cell

• sulfur-35 stayed outside the cell, remaining in the liquid medium, but phosphorus-32 was found inside bacterial cells and proved that DNA was injected and served as the transforming principle that carries genetic instructions

1. define genetics

2. define genome

3. what is biological information encoded in

4. True or false: the genome includes both the genes and non-coding sequences of the DNA/RNA

1. studies the molecular structure and function of genes, heredity, and variation in living organisms

2. the sum of all genes, the genome contains all of the biological information needed to build and maintain an organism

3. deoxyribonucleic acid (DNA)

4. true

• what is the backbone of DNA made up of

• what forms the “teeth” of a DNA molecule

• how is the double stranded helix of DNA held together

1. phosphate and deoxyribose (sugar-phosphate backbone)

2. the nitrogenous bases

3. hydrogen bonding between nitrogenous bases

• (blank) is the genetic material in all organisms

• what is the structure of DNA

1. DNA

2. DNA is made up of nucleotides, which are composed of a phosphate group, pentose sugar (in this case deoxyribose), and a nitrogenous base, which can either be a purine or pyrimidine

Purines: adenine, guanine

Pyrimidines: cytosine, thymine, uracil (in RNA)

1. DNA is composed of (blank) chains of nucleotides that form a double helix shape

2. the two strands of DNA are (blank)

3. nitrogenous bases of DNA

4. adenine and thymine make how many hydrogen bonds

5. guanine and cytosine make how many hydrogen bonds

1. two

2. antiparallel

3. adenine, thymine, guanine, cytosine

4. 2

5. 3

3 functions of genetic material

1. storage of genetic information

2. self duplication and inheritance

3. expression of the genetic message

what is DNA’s major function

• coding for proteins

• information is encoded in the order of nitrogenous bases

1. how wide is the double helix

2. (blank) are always paired with (blank)

3. a DNA molecule has a (blank) groove and (blank) groove

4. the double helix makes a turn every (blank) residues

5. the two chains of DNA are (blank) to each other

1. 2 nm

2. purines, pyrimidines

3. major, minor

4. 10

5. complementary

1. what technology can help us show the differences in conformation between circular and supercoiled DNA

2. what happens to an underwound DNA molecule

3. Supercoiling of DNA can only occur in

4. what is the definition of DNA supercoiling

• EM and gel electrophoresis

• it spontaneously assumes a negatively supercoiled conformation

• closed-circular DNA or linear DNA where the ends are fixed

• DNA that is more compact than its relaxed counterpart

1. enzymes that change the level of DNA supercoiling

2. cells contain a variety of (blank): list them

topoisomerases

Type I: change the supercoiled state by creating a transient break in one strand of the duplex

Type II: make a transient break in both strands of the DNA duplex

what is genetic engineering

• the removal of a gene from the DNA of one organism and the insertion of that gene into another organism

give an example of genetic engineering

• genetic engineering is exemplified by the production of insulin from bacteria by inserting the human insulin gene into bacteria and growing the bacteria to produce lots of insulin quickly, economically and efficiently

list the steps of insulin production via genetic engineering

1. A starter bacteria cell is identified and contains a ring of plasmid DNA

2. plasmids are extracted from the bacterial cell

3. a section of the plasmid DNA is cut via enzymes

4. the gene for insulin production is cut from part of the human DNA genome using enzymes

5. gene for insulin is inserted into plasmid ring of DNA

6. modified plasmid is inserted back into bacterial cell

7. bacterial cells are cultured so they rapidly reproduce and create more insulin

8. insulin is extracted from bacterial cell for medical and commercial use

Green Fluorescent Protein

• Green fluorescent protein (GFP) is a naturally fluorescent protein first isolated from the jellyfish Aequorea Victoria

• GFP can be used to tag neuronal stem cell cultures: utilizing fluorescent tags to visually separate stem cells (orange/yellow tag) from their offspring (blue/green/purple tag). This process involves altering the cell’s genome by incorporating foreign DNA into its genome.

Recombinant DNA

• artificially engineered DNA molecule created by joining or splicing genetic material from two or more different sources or species

• Chromosome

• nucleosome

• chromosomes numbers are (blank) for an organism

• n- (blank) number

• 2n- (blank) number

• double stranded DNA molecule packaged by histone and scaffold protein

• the basic structural and repeating unit of chromatin in eukaryotic cells, responsible for packaging long DNA molecules into a compact, organized form inside the nucleus

• constant

• haploid

• diploid

• karyotype

• the number and appearance of chromosomes in the nucleus of a eukaryotic cell, this term is also used for the complete set of chromosomes in an individual organism

1. karyotypes describe the (blank) of chromosomes, and what they look like under a (blank) microscope. For example: their (blank), the position of the (blank), (blank) pattern and differences between (blank) chromosomes

1. number, light, length, centromeres, banding, sex

1. chromosomes are (blank) in most human cells, leading to (blank) chromosomes

2. chromosomes are (blank) in gametes, leading to (blank) chromosomes

1. diploid, 46

2. haploid, 23

what percent of genes do you share with a mouse

92%

1. the human genome, the genetic code in each human cell, contains (blank)/(blank) DNA molecules each containing from (blank) thousand to (blank) million nucleotide pairs

2. DNA molecules of this size are (blank) to (blank) cm long when uncoiled, or about 5 cm on average

3. you have about (blank) cells in your entire body, if you stretched out your DNA and all your cells end to end, they’d stretch over 774 million miles

4. about (blank) percent of the human genome contains DNA that helps “build” us or maps for proteins, the other 98.5% is (blank) that we dont use

1. 23/46, 500, 2.5

2. 1.7, 8.5

3. 10 trillion

4. 1.5, junk

key features of Fluorescence in situ hybridization (FISH) (FPG)

• fluorescent probes are generated towards a specific DNA sequence

• probes are hybridized to DNA

• Gene/DNA locations are determined from fluorescent “spots”

Steps in Fluorescence in situ hybridization (My Dogs Play All Summer)

1. Mitotic chromosomes on a glass slide contain double-stranded DNA

2. Denature DNA with a hot salt solution, separating it into single strands

3. Probe: slide is incubated with a biotinylated DNA probe, and wash to remove any unhybridized probes, forming a double stranded DNA hybrid

4. (Fluorescent) avidin binds to DNA probe (to reveal location) and the chromosomes are counterstained so they appear red

5. Satellite DNA is localized specifically to the centromeres

General process of fluorescence in situ hybridization (FISH) used for bacterial pathogen identification (Infected Owls Prefer Bright Flying Nuts)

• infected tissue sample taken from patient

• oligonucleotide complementary to the suspected pathogen’s genetic code is synthesized and chemically tagged with a fluorescent probe

• tissue sample is chemically treated in order to make the cell membranes permeable to the fluorescently tagged oligonucleotide

• fluorescent tag is then added and only binds to the complementary DNA of the suspected pathogen

• if the pathogen is present in the tissue sample, then the pathogen’s cells will fluoresce after treatment with the tagged oligonucleotide

• no other cells will grow

what is satellite DNA

non-coding DNA sequences found in centromeres of eukaryotic chromosomes

The Human Genome Project

• started from 1990s and directed by the US Department of Energy and NIH

• had primary goal of mapping and sequencing all of the base pairs that make up human DNA

• complete genome was announced in 2003

• how many genes does the human genome have

• what accounts for several proteins from one gene

• what accounts for different protein functions

• 30,000

• alternate splicing of messenger RNA

• post-translational alterations

• the genome varies among different individuals due to (blank)

• what is the most common variability among humans

• sites of single nucleotide difference in humans are called

• structural variants

• true or false: intermediate-sized variants are more common than previously thought

1. genetic polymorphisms

2. at the single nucleotide difference

3. single nucleotide polymorphisms (SNPs)

4. changes in the segment of a genome which may involve large segments of the DNA (50 base pairs or larger)

5. true

genetic polymorphism

• simultaneous occurrence of two or more distinct alleles or DNA sequence variations at a single locus in a population where the least common variant occurs in at least 1% of the population

• unlike disease-causing mutations, polymorphisms are normal parts of a species genetic makeup and explain why healthy individuals have different traits such as different eye color, blood types or natural ability to better metabolize drugs or food

Conrad Hal Waddington

• introduced the idea of epigenetics

• he defined as: causal interactions between genes and their products which bring phenotype into being

• epigenetics

• epigenome

• study of how behaviors and environmental factors modify genes (turn them on or off) without altering the underlying DNA sequence

• global analyses of epigenetic changes across the entire genome

Explain how epigenetics drive differentiation

• differentiation is driven by epigenetics

• as a cell moves from a totipotent, to pluripotent and finally multipotent state, epigenetic changes (turning on or off of genes) lock in cell identity so that muscle cells, neurons and blood cells perform their unique roles without sharing identical genetic material

• what defines the epigenetic profile

• what is the effect of DNA methylation

• what is the affect of histone acetylation

• what is the affect of histone deacetylation

• modifications of DNA (cytosine methylation) and proteins (histones)

• when a methyl group is added to cytosine bases in a DNA molecule, it typically acts to “turn off” or repress gene transcription by compacting chromatin so transcription machinery cannot reach the genes

• histone acetylation adds an acetyl group to lysine, which loosens chromatin and generally activates gene expression

• histone deacetylation removes an acetyl group from lysine, leading to tighter chromatin packing and gene repression

• what are the enzymes associated with DNA methylation

• what are the enzymes associated with histone acetylation/deacetylation

• DNA methyltransferases: Dnmt1 Dnmt3a

• Histone acetyltransferases (HATs) and Histone deacetylase (HDAC)

explain the phenomenon occurring in this picture

• in the normal cell state, the CpG island (a region of DNA rich in CG sequences located close to gene promoters) is unmethylated. Because the promoter region is clear, transcription machinery can bind and gene expression is on.

• in the cancerous cell state, there is hypermethylation (^mCG for methylcytosine) clustered around the CpG island at the gene promoter region. This heavy methylation packs chromatin tightly, blocking transcription factors from reaching the gene and turning gene expression off.

NOTE: cancer cells will use DNA hypermethylation to silence vital tumor suppressor genes, allowing the cell to grow uncontrollably.

describe twins and epigenetics

• identical twins are from the same zygote, so they begin life with the same genetic information, including epigenetic tags

• over time, the twins’ environments will diverge, resulting in individual epigenetic tags to form for each twin

• this makes twins different by the time they get older

• genetic tags are passed through (blank)

• what happens to epigenetic tags when the zygote is formed

• are parent’s experiences passed to offspring

• generations

• many epigenetic tags are removed from the chromosomes of the parents, but some remain

• parents experiences are passed on to offspring via epigenetic tags