MCB 2210 Lecture Notes - Lecture 2: Morphogenesis, Cytoskeleton, Mitochondrion

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blackwallaby3

11 Sep 2017

School

UConn

Department

Molecular and Cell Biology

Course

MCB 2210

Professor

David Daggett

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Document Summary

Lecture 2 cells & genes: genomes, genes, and proteins, we now know the complete sequences to predict the complement of proteins (the. Proteome) of many organisms: how many different proteins (protein-coding genes) does it take to make a cell, prokaryote minimum about 475 in mycoplasma. Typically, 1000-4000: eukaryote simple single-celled: 6300. I(cid:374) a give(cid:374) cell, so(cid:373)e ge(cid:374)es are (cid:858)tur(cid:374)ed o(cid:374)(cid:859) or (cid:858)tur(cid:374)ed off(cid:859); so(cid:373)e are expressed at high levels, some low. This is referred to as differential gene expression. + leads to changes in which proteins are expressed: cells with the same genes can display different behaviors depending on their environment, cellular organization in suspension and adhesion. Adhered on a surface proteins distribute differently: dna and its associated histone proteins can become chemically modified, by methylation or acetylation. Lecture 2 cells & genes: causes the underlying genes to be held in a transcriptionally active or inactive, semi-permanent state. Sometimes these modifications can be stably inherited from one cell to another.

Related Questions

QuestionGroup: #21 Gene expression 2

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Homework

The direct end result of gene expression is which of the following?

Amino acids

Translation

Proteins

Carbohydrates

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QuestionGroup: #22 Mutation

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Homework

Which of the following is the ways in which nucleotide mutations lead to altered proteins?

One nucleotide is substituted by another nucleotide, which can cause an early stop codon to be incorporated into the amino acid sequence resulting in a truncated protein.

One nucleotide is replaced by another nucleotide, which can change an amino acid in the protein sequence

Nucleotides are inserted into a nucleotide sequence causing a frameshift in the sequence.

All three choices may cause mutations.

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QuestionGroup: #23 Mutation 2

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Mutations are the result of which of the following?

Change in the normal nucleotide sequence in the DNA directly resulting in different carbohydrates

Change in the normal nucleotide sequence in the DNA directly resulting in different proteins

Change in the order of transfer RNA to messenger RNA so that the transfer RNA take over the role of Messenger RNA

Primarily an alteration in the sequence of nucleotides in the abnormal proteins

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QuestionGroup: #24 Cell division

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There are two major kinds of cell division. Which of the following plays a major role in promoting genetic diversity?

Meiosis since it causes the cells to make more daughter cells than mitosis

Mitosis since it causes the cells to duplicate and eventually have mutations

Meiosis since it causes the DNA sequences to be separated into new patterns in the daughter cells.

Mitosis since it essential for the ovaries in humans to separate and duplicate

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QuestionGroup: #25 Cancer

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Homework

Genes that slow down or stop the cell cycle are called...

Apoptotic genes

Oncogenes

Restriction genes

Tumor suppressor genes

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QuestionGroup: #26 Cancer2

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The common theme in the development of all cancers is...

Mutation

Evolution

Infection

Syncopation

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QuestionGroup: #27 Genetics

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Homework

Punnett's square is which of the following?

Example of all possible combinations of alleles

Example of all possible combinations of chromosomes

Example of only certain combination of alleles since some will not be expressed.

Example of all possible combinations of DNA

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QuestionGroup: #28 Embryo development

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Which of the following is the end of the cleavage phase?

A fetus

Formation of a blastocyst

Implantation to the lining of the uterus

Fewer number of cells

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QuestionGroup: #29 Development of organ system

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Homework

For organs to be differentiated, which of the following is the first step?

Stem cells trigger the development of differentiated cells

Tissues assemble into organ systems such as blood

Tissue specific genes in stem cells are triggered

Differentiated cells form tissues

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QuestionGroup: #30 Development and society

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Homework

A pregnant mother ingests a chemical which her mother said would be great for the baby. When the baby was born, it had a large head and flippers for arms. What caused this phenotype?

The chemicals were teratogens which influenced oxidative phosphorylation causing the changes in the phenotype.

The chemicals influenced the expression of different stem cells.

There is no way to assume the chemicals caused the phenotype since we have no data on other mothers who took this medicine. It could have been purely by chance.

The chemicals were teratogens which caused the baby to show early signs of evolution.

Class 6: Viruses (and Cells, continued)

Making connections: viruses and microbes Match the cell biology concept (on page 1) with an important application of that concept (on page 2). Then answer the follow-up questions at the bottom of page 2.

Cell Biology concepts
1. Bacteria that cannot construct new cell wall material become fragile and break down.
2. During influenza infection, the viral enzyme neuraminidase is required to release new viruses from the host cell in which they were made. Once released, the new viruses can infect many additional cells.
3. Thermus aquaticus is a bacterium found in hot springs and can live at temperatures up to ~80Â°C (175Â°F). It has adapted so that its enzymes are most functional at the elevated temperatures, compared with many organismsâ enzymes that function best ~37Â°C (98Â°F).
4. Until the isolation and investigation of retroviruses, scientists thought that RNA could be copied from DNA, but DNA could not be copied from RNA. Research on this class of viruses led to an update to this âCentral Dogmaâ of biology.
5. Some bacteria have adapted, so that the enzymes involved in making cell wall materials have a slightly different shape and can no longer be bound by certain drugs.
6. Rhizobia are bacteria that colonize the roots of certain plants (legumes, including beans and peas). The host plant benefits from the prokaryotesâ ability to âfixâ nitrogen, converting N2 from the atmosphere into a form that is usable by the plant.
7. Many species of bacteria contain the enzyme cellulase. More than 10 billion such bacteria and other symbiotic microbes may be found in a single milliliter of material from inside the digestive system of ruminant mammals.
8. Fungi, including those that cause athleteâs foot, use ergosterol to maintain healthy membranes. Animal cells do not make ergosterol, they use a similar lipid â cholesterol.
9. During retrovirus infection, a DNA copy is made of the virusâs RNA genome. A cut is made in the host cellâs DNA and the DNA copy of the viral genome is pasted into the host chromosome by a viral enzyme called integrase.
10. Prokaryotic cells contain smaller ribosomes (â70Sâ ribosomes) than eukaryotic cells (â80Sâ ribosomes). Both types of ribosomes synthesize proteins, but the macromolecules they use to do it are somewhat different.

2
Applications
_______ Oseltamivir, also called Tamiflu, binds and inhibits the viral protein neuraminidase.
_______ Clotrimazole is a drug that is used to treat certain infections. It interferes with synthesis of ergosterol, a lipid involved in phospholipid membranes.
_______ Penicillin is a drug that interferes with synthesis of peptidoglycans (these are biological molecules that are part protein and part carbohydrate) that are present in certain cell walls.
_______ HIV is often treated with several drugs that inhibit different parts of the viral replicative cycle. Raltegravir is an example of a drug that interferes with the integration of viral genes into the host cellâs chromosome.
_______ Cows, like other vertebrates, lack the ability to breakdown cellulose. Yet they are able to live on a diet of grass and other vegetation high in cellulose.
_______ Enzymes isolated from extremophiles have been very useful in laboratory research. For example, Taq polymerase facilitates PCR, a revolutionary technique for production of DNAs of particular sequences, which requires cycling reactions through high temperatures.
_______ Plants and animals require nitrogen to make biological macromolecules, however theyâre unable to convert atmospheric nitrogen (N2) into a biologically useful form.
_______ Azithromycin is a drug that binds to 70S ribosomes and blocks synthesis of any new proteins.
_______ Methicillin-Resistant Staphylococcus aureus (MRSA) can cause life-threatening infections of the skin and bloodstream. One of the reasons MRSA infections are so serious is that they are resistant to treatment by many antibiotics, including methicillin and penicillin.
_______ The enzyme reverse transcriptase, isolated from retroviruses, is an important tool in molecular biology research. Scientists interested in learning what genes are turned on in particular cells use it to make DNA copies of RNAs they are studying (The DNA copies are useful because they are more stable).

When you have completed the matching activity, answer these follow-up questions:
â¢ What types of infections can be treated with the following drugs?
o Penicillin
o Clotrimazole
o Azithromycin
o Tamiflu
o Raltegravir
â¢ Why are these drugs (above) safe for you to take? That is, why donât they kill your cells?
â¢ Cancer cells are your own human cells that have become deregulated so that they divide and pile up in an uncontrolled way. Many chemotherapy drugs treat cancer by interfering with cell division and other cell processes.
o Why are there so many more side effects for individuals undergoing chemotherapy than for individuals taking antibiotics?

The bacterium E. coli, which is a major model system for the study of genes and DNA, has a singular circular chromosome of about 4x106 bp. In contrast, human diploid cells have __1__ chromosomes, of __2__ different types (donât forget that the X Â¹ Y!). The total amount of DNA found in a haploid cell such as a sperm or egg is called the organismâs âC-valueâ; the human C-value is __3__.

Also in contrast to the E. coli circular chromosome is the fact that eukaryotic chromosomes are not circular, but instead are __4__. Eukaryotic chromosomes are complexed heavily with protein to form a DNA-protein complex generically called __5__. The proteins found can be considered to fall into two general classes: __6__ and __7__. The first class is made up of 5 major proteins called __8__, __9__, __10__, __11__, and __12__. On a weight to weight basis, these proteins make up about __13__% of the total mass of a chromosome. Since these proteins must associate relatively non-specifically with DNA, they are rich in the basic amino acids __13__ and __14__, which gives the proteins a net __15__ charge.

One goal of packaging the DNA into chromatin is to compact the genome so it will fit into a nucleus. The basic unit of chromatin structure is the __16__, which has __17__ base pairs of DNA wrapped around a âcore particleâ composed of __18__ copies each of the core histones. Each nucleosome is separated by a stretch of âlinkerâ DNA so that the repeating unit is approximately 200 bp. Lets do a little arithmetic: If we consider that the nucleosome is approximately __19__ nm in diameter, that there is about 200 bp in this structure, and that 200 bp of DNA would normally occupy __20__ nm if stretched out straight (recall that each base is spaced about 0.34 nm from the next), we can see that the nucleosome alone allows for a __21__-fold compaction ratio.

The nucleosome structure is further compacted by histone __22__, which is not a part of the core particle. Instead, this histone __23__ (does what?) to cause the nucleosomal 10 nm fiber to condense into a higher-order structure referred to as the __24__ nm fiber. In the nucleus, chromosomes do not just float around freely: they are tethered to a proteinaceous structure called the __25__ at specific DNA regions called âSARsâ, which stands for __26__. SARs are rich in topoisomerases, to allow the winding and unwinding of the DNA that accompanies replication and transcription to occur, despite this constraint.

The 30 nm fiber discussed above is the form in which transcriptionally active DNA is believed to exist in the nucleus; however, further condensation leads to a highly condensed inactive form called __27__; in this terminology, the active form is referred to as __28__. The inactive condensed form can be divided into two types: one type is essentially invariant between cell types, and since it is âon all t timeâ, it is referred to as __29__. The other type comes and goes, depending on the expression of the genes present in that region of the chromosome; it is referred to as __30__.

Eukaryotic chromosomes carry the genes, of course, but also have other functional regions. One such region is the place where the spindle apparatus attaches during mitosis and meiosis; this region of the chromosome is called the __31__. Another important part of the linear eukaryotic chromosome is the ends; these are called __32__. In humans, the end of each chromosome is composed of many repeats of the short sequence __33__. One more type of functional region on each chromosome is the place where DNA replication starts; in humans, each chromosome has several of these __34__. Thus, eukaryotic chromosomes carry several different types of functional sequences, which together allow for their __35__ during S phase, __36__ during mitosis and meiosis, and the __37__ of their genes

MCB 2210 Lecture Notes - Lecture 2: Morphogenesis, Cytoskeleton, Mitochondrion

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