1. Overview of the Cells

Describe the kind of stem/differentiated cells of the following: 1. Cells that have the ability to divide 2. Neutrophils 3. Hematopoietic Stem Cells 4. Inner Cell Mass Cells 5. iPS Cells

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Describe the structures and purposes of the endomembrane system. Eukaryote or Prokaryote?

- A group of membranes and organelles that works together. - Includes: nuclear envelope, lysosomes, the ER, and Golgi apparatus. - Modify, package and transport lipids and proteins.

Critical characteristics of stem cells:

- Ability of self-renewal/duplication - Ability to differentiate into specific cell types

What are Adult Stem Cells? Example?

- Adult stem cells are found in differentiated tissue - such as bone and skin. They are groups of cells that differentiate to renew and replace cells in the adult body. - One medically relevant cell that has been used for years are bone marrow stem cells - ASCs can be used for transplants for a variety of reasons: - - Leukemia - - Aplastic anemia - - Sickle cell anemia

Examples of stem cell functions in our bodies:

- Blood cell production (red blood cells, immune system cells) - Tissue repair - Continued skin renewal - Etc.

Places stem cells are found in our bodies:

- Bone marrow - Skin - Liver - Hair - Brain (limited)

How does DNA sequence determine protein function? What happens when the DNA has a mutation in its sequence?

- DNA sequence determines RNA sequence - RNA sequence determines amino acid sequence - Amino acid sequence determine protein folding - Protein folding determines protein structure - Protein structure determines protein function - Mutations: if the DNA acquires a change in sequence (mutation), that can change the RNA sequence, which may change the amino acid sequence, which may change the protein's folding, structure, and function

Describe the structures and purposes of the nucleus. Eukaryote or Prokaryote?

- E only. Only exist in eukaryotic cells - Carries genetic information - The nucleolus are spherical bodies inside the nucleus. They make ribosomal subunits(who decodes the genetic message and/or catalyzes peptide bond formation).

Describe the structures and purposes of the cytosol. Eukaryote or Prokaryote?

- E+P - Cytosol versus Cytoplasm: - Cytosol is the fluid contained in the cell cytoplasm. - Cytoplasm is the entire content within the cell membrane. - The cytosol contains dissolved nutrients, helps break down waste products, and move material around the cell.

Describe the structures and purposes of the mitochondria. Eukaryote or Prokaryote?

- E. - Generates ATP - ATP is the primary energy source for most biochemical and physiological processes

What are Embryonic Stem Cells (ESCs)? How are they created>

- Embryonic stem cells are pluripotent stem cells derived from the inner cell mass of a blastocyst. - Controversial to use in a medical/research setting because if you extract the inner cell mass from the blastocyst, then you destroy the embryo.

Discuss where in the eukaryotic and prokaryotic cell transcription and translation occur. What strikes you about these differences?

- In eukaryotes, transcription and translation are separate in space and time (Transcription is in the nucleus; translation is in the cytoplasm). - In prokaryotes, transcription and translation are done in the same space and can be carried out simultaneously; as soon as enough of the mRNA is made for the ribosome to bind, the ribosome can carry out translation while the rest of the mRNA is being created by RNA polymerase.

P vs. E: Organelles found in only E cells

- Nucleus - Mitochondria - Vacuole - Chloroplasts

What are Pluripotent Stem Cells? Examples?

- Pluri- = many. Have the ability to differentiate into any cell in our body except extra-embryonic tissue. - Only able to turn into embryonic tissue (any cell in the body). - Ex: In the blastocyst, the inner cell mass is pluripotent and will eventually become the fetus. The cells surrounding the outside of the sphere will become extra embryonic tissue. - Ex: embryonic stem cells. - Ex: induced pluripotent stem cells (iPS)

What are Induced Pluripotent Stem Cells (iPS cells)?

- Pluripotent. De-differentiated stem cells. Adult cells that have been genetically reprogrammed to an embryonic stem cell-like state by being forced to express genes and factors important for maintaining the defined properties of embryonic stem cells.

Describe the structures and purposes of the chloroplast. Eukaryote or Prokaryote?

- Produce energy through photosynthesis. - Plant cell organelles

What are cells made of?

- Proteins (made up of amino acids) - Organelles (only eukaryotes) - Lipids (e.g. phospholipids make up phospholipid bilayer) - Carbohydrates (e.g. glucose and other sugars) - DNA/RNA (made up of nucleic acids)

P vs. E: Organelles found in both P & E cells

- Ribosomes - DNA - RNA - Some P&E have cell walls; some don't - Plasma membrane (cell membrane) made of a phospholipid bilayer

What is transcription?

- Step 1 of Gene Expression: TRANSCRIPTION: DNA --> RNA - DNA is made up of nucleotides that can be thought of as information, or a language of sorts. Transcription is the act of taking that information and transcribing it into a "message" made of RNA, which is also made of nucleotides, but with a slightly different structure.

What is translation?

- Step 2 of Gene Expression: TRANSLATION: RNA --> Protein - RNA is a message. The message tells the cell in what order to string amino acids.

What are Multipotent Stem Cells? Examples?

- The ONLY type of stem cells that adults can have. Much more limited as to what they can differentiate into. - No more pluripotent stem cells. As the body grows, the stem cells become more restricted. - Ex: Hematopoietic stem cells(HSC) - can develop into all kinds of blood cells. - Ex: Neural stem cells.

Why is the control of stem cells important?

- To prevent disruption of biological processes. Uncontrolled stem cells could turn into tumors. - Cell division takes a lot of energy, so the body doesn't want to expel more energy than necessary.

What are Totipotent Stem Cells? Examples?

- Toti- = all. Have the potential to differentiate into any cell required for fetal development. - Ex: Found in the early stages of the zygote(fertilized egg). Totipotent stem cells are present during morula stage of development (3-4 days after the fertilization of the egg)/before the blastocyst is formed - Can be embryonic - fetal, baby and human tissue - Can be extraembryonic - fetal support tissue like the placenta

What is a transcription factor? What is its function in transcriptional regulation?

- Transcription factors are proteins. Only in eukaryotic cells are transcription factors required. They bind to DNAs to turn on and off different genes in the DNA. They do so by binding to a certain sequence of DNA, which makes it more difficult or easier for RNA polymerase (the main enzyme responsible for transcription) to bind to the gene. - This way, these transcription factors help cells determine which gene they would like to express. If certain DNAs were never transcribed, they would never become useful proteins that function in our bodies. Cells have the genetic information to do multiple things. Different genes need to be turned on or off when making hair cells versus liver cells. Activating or repressing different genes guide cells in the process to becoming the cells they want to be.

To extract Dystrophin (a protein required for muscle function). - Which cells would you extract the Dystrophin gene? - Which cells would you extract Dystrophin mRNA?

- Which cells would you extract the Dystrophin gene? All cells will contain the genetic material for Dystrophin. Differential gene expression states that not all cells will use all of its genetic information. - Which cells would you extract Dystrophin mRNA? Muscle cells. Only muscle cells express the Dystrophin gene to create Dystrophin mRNAs.

Where in the cell would you find carbohydrates? What are they used for?

1. For structural purposes, carbohydrates can be found in cell walls. 2. For energy storage, carbohydrates can take the form of glucose.

How do RNAs determine a protein's function?

A sequence of the RNA codes for a sequence of amino acids which are the building blocks of proteins. Each amino acid has its own unique chemistry. Depending on each amino acid's chemistry, they drive the protein to fold into a 3-dimensional structure. That structure determines the protein's function.

Are there any cells that don't have a DNA genome? What about viruses?

All cellular organisms have a DNA genome. It's one of the defining characteristics of prokaryotic and eukaryotic cells. Viruses are not cells. They are microscopic particles that infect cells, but they do not metabolize, grow, or make their own protein.

Do RNAs stay around forever?

Because RNAs are a message, just like messages, RNAs don't stay around forever. That RNA can be degraded when needed, which is one way cells control gene expression.

How is it possible that your liver cell and your skin cell can have identical DNA content, and yet look different and perform different functions?

Because not every gene in the DNA is expressed. Depending on which genes are allowed to be expressed (turned into useful proteins), liver and skin cells get to have different genes expressed, which changes their look and functions.

P vs. E: Have DNA? Gene Expression?

Both have DNA genomes and carry out gene expression to make proteins.

Cells vs. Viruses: Cellular makeup?

Cells: Cell membrane, genetic information, E with membrane-bound organelles Viruses: Viruses have a genome wrapped up in either a protein coat or lipid bilayer. The genome could be a single stranded DNA, single stranded RNA, double stranded DNA, double stranded RNA.

Cells vs. Viruses: What is it?

Cells: Cells are the basic functional units of life; have the ability to grow, divide, and interact with other cells. Viruses: A virus is a microscopic particle that can infect cells of a biological organism.

Cells vs. Viruses: Considered living?

Cells: Yes Viruses: No because they don't grow, don't carry out metabolism, and don't have an energy source.

Cells vs. Viruses: Has genetic information?

Cells: Yes Viruses: Yes

Cells vs. Viruses: Does gene expression?

Cells: Yes Viruses: Yes but with the help of the host cell

Cells vs. Viruses: Replicate?

Cells: Yes Viruses: Yes, but viruses need a host cell to replicate

Cells vs. Viruses: Do cells evolve?

Cells: Yes Viruses: Yes. May evolve by natural selection. Viruses also evolve faster than their hosts (such as humans)

Discuss which macromolecule is the "information storage unit" in the cell. Discuss the properties of this macromolecule, try to explain the way in which this macromolecule stores information and how this information affects cell function.?

DNA is the information storage unity of the cell. DNA is made of long strands of nucleotides which are made up of four different nitrogenous bases, a 5-carbon sugar and a phosphate group. The sequence of the nitrogenous bases goes through gene expression. Each specific sequence forms different proteins that will take on different shapes due to the sequence's unique chemistry. Shape determines function of the protein. The macromolecule thus creates different proteins that will go on to perform different tasks or functions in the cell.

What is differential gene expression in the context of a multicellular organism? Why is it important for cells to do this?

Different cells in a multicellular organism express different sets of genes. This allows for cell specialization and makes it possible that a single zygote (totipotent) can become the specialized cells that are distributed throughout the body.

What processes do cells use to "express" genes? Make sure to use the correct terms in part (i) and name the enzymes used in each process in part (ii). ***

Gene expression is the mechanism by which "information" flows from DNA sequence to RNA sequence to amino acid sequence to make proteins. 1. Transcription: DNA to RNA; The process uses uses RNA polymerases to make a copy of a DNA sequence to make an RNA molecule. In eukaryotes, RNA processing occurs. This maturation process uses splicing to remove the introns in mRNAs (introns are sections of the DNA that are transcribed during transcription, but they shouldn't get into the Binal mRNA product). RNA molecules also get a 5' cap and a poly-A tail. 2. Translation: RNA to protein; catalyzed by ribosomes, assisted by tRNA. RNAs code for a sequence of amino acids, which are the monomers of proteins. Each gene will code for a different amino acid sequence (there are a total of 20 different amino acid sequences). Depending on the chemistry of each protein, proteins will fold in different shapes to make up different structures which determine the functions of the protein.

What does a ribosome look like?

Kind of like a hamburger bun, a top part and a bottom part. Each part of the ribosome is made of proteins and (ribosomal) RNA.

How are new cells created?

New cells can only be created through cell division.

True or False: Embryonic stem cells do not divide.

No. Embryonic stem cells are able to do cell division.

True or False: Embryonic stem cells are multipotent.

No. They are totipotent. Adult stem cells are multipoint.

True or False: Embryonic stem cells are exactly the same thing as iPS cells

No. iPS cells try to replicate an embryonic stem cell, but iPS is not the same as embryonic cells.

Where in the cell would you find nucleotides? What are they used for?

Nucleotides are the monomers of nucleic acids, which function as long- term and short-term information storage. When nucleotides are in the form of DNA, they are found in the nucleus of eukaryotic cells or the nucleoid of prokaryotic cells. During gene expression, nucleotides exist in the form of different RNAs that is produced in the nucleus(mRNA), moves into the cytoplasm(tRNA) to bind with proteins, and form ribosomes(rRNA).

Why is RNA processing needed?

Once an RNA message is transcribed, in eukaryotes, it is considered an immature message. So it has to go through a maturation process.

P vs. E: Discuss whether P/E cells can be part of single-celled or multi-cellular organisms.

P: - Are always single-celled organisms. - Prokaryotes can exist in communities called "biofilms", but biofilms are not considered a multicellular organism. E: - Can be single-celled organisms (amoeba, yeast). - Can be multi-celled organisms (plants, animals, microscopic worms).

P vs. E: Location of Genetic Information?

P: Bundle its DNA in a nucleoid E: Store genetic information in the nucleus

P vs. E: RNA Processing

P: Not all prokaryotes have RNA processing. Prokaryotes may have instantaneous transcription/translation E: Require RNA processing to transfer genetic message from the nucleus into the cytosol.

P vs. E: Membrane-bound Organelles

P: Prokaryotes do not have internal membrane-bound organelles, but there may be a loose organizational structure within the cell. E: Eukaryotes have a nucleus and other membrane-bound organelles (ER, Golgi apparatus, mitochondria, etc.) to organize cellular components and functions.

What is one "pro" and one "con" to using iPS cells instead of embryonic stem cells for the purposes of regenerative medicine?

PROS: - Can take differentiated cells (ex: skin cells) and differentiate them into other cells (ex: liver cells) using the right extracellular signals because all cells contain the genetic information to produce any cells. - Adult differentiated cells are relatively easy to obtain (ex: skin cells) - Useful for disorders - Not from embryos so not as controversial/no ethical implications - Less risk(no matching problems) when concerning transplants because they are your cells with your genetic code so your body is likely to reject them. CONS: - Difficult to control gene expression and induce differentiation properly (could cause tumor) - They're not quite like ESCs at the molecular level (especially chromatin) so it's not clear if they are as manipulatable as ESCs or if they will behave exactly as ESCs would.

Where in the cell would you find peptides (proteins)? What are they used for?

Peptides make up proteins, which are everywhere in the cell. Proteins can act as spores in the membrane to let small molecules through. They also make up RNA polymerase, exist in the nucleus, cytoplasm, ER and the mitochondria.

Where in the cell would you find phospholipids? What are they used for?

Phospholipids are the building blocks of cell membranes. They form a amphipathic bilayer, with their hydrophobic tails facing inside the membrane, and its polar hydrophilic (polar head) gets in contact with water. The cell membrane let in nutrients into the cell, and let out toxic chemicals out.

What is potency?

Potency is the potential stem cells have. Stem cells have different potency. Throughout development (baby -> adult), stem cells become more specialized.

What are the functions of the protein in the cell?

Proteins are everywhere in the cell, can sit on the cell membrane, as well as get secreted outside the cell.

What cellular "machinery" carries out transcription? What are each of the enzymes made of? (e.g. DNA, RNA, protein, multiple proteins, other macromolecules.) What other components are needed?

RNA polymerase (the main enzyme in transcription). They are made of nucleotides. It goes through a single-stranded DNA in a 5' to 3' direction to make a complementary strand. The created RNA message also replaces thymine(T) with the base uracil(U). To terminate the process of transcription, a shRNA hairpin exists the nucleus to signal the end of the process. Eukaryotes also need transcription factors to turn on and off different genes. When RNA processing is needed (in eukaryotes), a specialized nucleotide is put on the 5' end — called a 5' cap, and a poly-A tail is added.

Where in the cell would you find RNA polymers? What are they used for?

RNA polymers are essential in protein production. They transcribe genetic messages which codes for a sequence of amino acids -- the building blocks of protein. RNAs are also found in ribosomes and the cytoplasm.

Where does RNA processing occur?

RNA processing occurs in eukaryotes. RNA processing is not as universal in prokaryotes - only done for specific reasons. Prokaryotes don't have to process it. (Mainly bc transcription occurs in the nucleus in eukaryotes. The transcription has to travel outside of the nucleus into the cytosol. There's a much longer period of time). *In prokaryotes, the cells can translate as soon as the right parts of the RNA are made(simultaneous transcription-translation).

Differential gene expression is the result of different cells having different _____.

Regulatory proteins.

What is a sequence of an RNA made of?

Ribosomes and tRNAs.

What is ribosome made of?

Ribosomes live in the cytosol where translation happens. A ribosome is made of rRNA and proteins.

List two differences and two similarities between stem cells and differentiated cells.

Similarities: - They both go through the processes of transcription and translation. - They have the same DNA genome for the most part. (Difference is that different genes are expressed) Differences: - Stem cells can undergo cell division; differentiated cells are much less able to undergo cell division. Terminally differentiated cells cannot undergo further cell division. - Stem cells are unspecialized. Differentiated cells do perform specific functions in the body such as muscle cells and bone cells.

List three similarities and three differences between Prokaryotic cells and Eukaryotic cells.

Similarities: 1. Does gene expression. Goes through transcription and translation. 2. Both have ribosomes, DNA, RNA. Some P&E have cell walls, some don't. Their plasma membrane is made of a phospholipid bilayer. 3. Both metabolize on their own. Differences: 1. Ps are single cellular and Es are multicellular organisms. 2. Ps do not have membrane-bound organelles. Es do. 3. Ps(not all) go through RNA processing. All Es do. 4. Only Es have a nucleus, mitochondria, chloroplasts and a vacuole. 5. Location of genetic information - Ps in nucleoid, Es in nucleus.

Stem Cells vs. Differentiated Cells: Go through gene expression?

Stem Cells - Yes Differentiated Cells - Yes

Stem Cells vs. Differentiated Cells: Have the same DNA genome?

Stem Cells and Differentiated Cells: Yes for the most part. Different genes are expressed.

Stem Cells vs. Differentiated Cells: Specialization?

Stem Cells: - Unspecialized Differentiated Cells: - Perform specific functions in the body such as muscle cells and bone cells.

Stem Cells vs. Differentiated Cells: Undergo Cell Division?

Stem Cells: - Yes (called self-renewal) Differentiated Cells: - Much less able to undergo cell division. Terminally differentiated cells cannot undergo further cell division.

Where in the eukaryotic cell are proteins synthesized?

The cytosol.

Fertilized eggs (zygotes) contain all the genetic material required to make the complex human body. What changes during cell development?

The genes that are being expressed changes. A newly fertilized egg will be expressing a different subset of genes than an adult would be expressing.

What does rRNA in ribosome do?

The rRNA aka ribosomal RNA catalyzes peptide bond formation.

What cellular "machinery" carries out translation? What are each of the enzymes made of? (e.g. DNA, RNA, protein, multiple proteins, other macromolecules.) What other components are needed?

The ribosome organizes the structure of the Binal product. Ribosomes are made of rRNA and proteins. The rRNA catalyzes the forming of peptide bonds. A tRNA is also needed as a translator. The tRNA base pairs with the "message" — the mRNA, and then it attaches speciBic amino acids to them. The tRNA folds into a 3D shape based on its geometry.

What are the mechanisms for translation?

The ribosome. It plays a structural organization role.

Fill in the blank: The ______________ of a protein determines the _____________ of the protein.

The structure of a protein determines the function of the protein.

What is a tRNA?

The tRNAs serve as the adapter or translator by having a portion that base pairs with the mRNA and then carrying specific amino acids attached to them. It folds into a three-dimensional structure because it can fold with itself.

How are iPS cells derived? From what types of cells are they typically made?

They come from adult cells that have been "de-differentiated' into an embryonic stem cell. They are made of skin cells or blood cells.

What are stem cells?

Undifferentiated cell of a multicellular organism that can divide to more cells of the same type or differentiate into specific cell types.

Why are viruses host cell specific?

Viruses bind and infect cells by having protein on the outside surface of a coat that will bind to a specific surface protein on the host cell(the protein in question = protein receptors). Because cell surface proteins differ in structure in different types of organisms, viruses tend to be specific to one type of organism (although they can mutate and change their host)

Explain Asymmetric cell division:

When two daughter cells that do not look the same. It is not uncommon for one daughter cell to be a stem cell and for the other daughter cell to be a precursor cell that will eventually differentiate to have a specific function.

Why might iPS cells be so important to those that have ethical objections to using embryonic stem cells?

When we take embryonic stem cells from the blastocyst, it destroys the embryo which has some ethical implications. If we can do iPS cells perfectly, we can just scrape skin cells off, which do not have any ethical issues.

True or False: Embryonic stem cells can differentiate into extraembryonic cell types.

Yes. Embryonic stem cells are totipotent. They can differentiate into all kinds of cells in the body.

True or False: Embryonic stem cells have the potential to help cure cellular degenerative diseases

Yes. If there is a degenerating tissue, embryonic stem cells can go in and fix the problem.

True or False: Embryonic stem cells are derived from the zygote

Yes. The zygote divides forms the morula then becomes the blastocyst. The ESC comes from the inner cell mass of the blastocyst.

Identify the molecular structures of: 1. Carbohydrate 2. Nucleotide 3. Phospholipid 4. Peptide (part of a what?) 5. RNA polymer.

You got it.

What is an mRNA?

mRNA is a protein-coding RNA.