Solutions, osmosis and escape from the cell!

Solution: a solution contains solute (substance dissolved into a solvent to form a solution) and solvent: liquid that dissolves solute (to form a solution).

Diffusion is the net movement of particles from an area of high concentration to an area of lower concentration until all particles are evenly distributed. All particles diffuse independently of each other. Diffusion is a passive process and does NOT require an input of energy such as ATP. All particles in liquid and gaseous states can diffuse.

Factors that affect the rate of diffusion in a liquid or a gas:

Concentration gradient:

The greater the concentration gradient, the faster the rate of diffusion. Concentration

gradient is the difference in concentration between an area of high concentration and

an area of low concentration.

Temperature:

As temperature increases so does the rate of diffusion because particles move faster.

Diffusion occurs more quickly in a gas than in a liquid because the particles are moving

more quickly and there is more space between particles.

Particle size:

The smaller the particles the faster the rate of diffusion. Smaller particles can fit between

other particles more easily and they move more quickly at any given temperature because

it takes less energy for them to move than large particles.

Particle shape:

Some particles are more streamlined than others and can fit between other particles more

easily.

Electrical charge:

Non-polar molecules diffuse more readily in non-polar solutions and polar molecules

diffuse more readily in polar solutions. Polar and non-polar molecules do not mix well so

they do not diffuse readily in each other.

Factors that affect the rate of diffusion across a membrane:

All of the above factors plus:

Number of pores/carrier proteins/channel proteins:

Most cells can vary the number and type of pores, carrier proteins or channel proteins that are present at any one time. The more openings that are present for a particular ion or molecule, the more of that substance can cross the membrane.

Pressure:

The greater the difference in pressure the greater the rate of diffusion. For example the greater the osmotic pressure the more water will diffuse (osmose) across the membrane.

Pressure gradients act the same way as concentration gradients.

Hormonal effects:

Hormones such as insulin can affect whether or not a substance can access a carrier protein to cross a membrane. If insulin is present glucose can enter the cell.

Lipid solubility:

Small non-polar molecules can diffuse directly across the cell membrane because they are lipid soluble.

Cyclosis:

In some cells the cytoplasm moves in a cyclic path. This is called cyclosis or cytoplasmic streaming. Because the movement of the cytoplasm removes particles away from the membrane it serves to increase the concentration gradient across the membrane.

Membrane permeability:

One cell may be permeable to a particular molecule and another cell may not be permeable to that molecule. A cell may also vary its permeability to a substance depending upon need.

Describe osmosis and osmotic pressure.

Osmosis is the movement of water from an area of higher pressure to an area of lower pressure across a selectively [differentially] permeable membrane. 

Or, differently put-- it’s the diffusion of water -- into and out of cells.

Osmotic pressure is the pressure generated by the flow of water across a semi permeable membrane. This pressure is created by the solute of the solution.

We dunk a cell into a solution. 

The solution can be one of three types of solutions.

Isotonic solution: the concentration of solute and water is the same both inside and outside of the cell.

Hypotonic solution: lower concentration of solute, higher concentration of water than the cell. 

Hypertonic solution: this solution has a higher concentration of solute and lower concentration of water than the cell.

The solution can cause the following effects:

An isotonic solution causes neither a shrinking nor swelling of the cell because it is a balanced solution. 

Hypertonic and hypotonic solutions can have devastating effects to a cell.

Hypotonic environment causes Lysis:  Osmotic pressure builds up when the water surrounding the cell moves to the area of least resistance, which is inside the cell. The cell explodes from the pressure. 

Hypertonic environment causes Plasmolysis: when a plant cell is placed in a hypertonic solution, the plasma membrane pulls away from the cell wall because the large central vacuole loses water. Plasmolysis is the shrinking of the Plant cell's cytoplasm due to osmosis. 

 

Hypertonic environment causes Crenation: The cell’s water rushes out to the hypotonic solution because of osmotic pressure. The cell shrinks like a raisin.

Describe and be able to differentiate between facilitated transport and active transport.

Facilitated transport:  passive transfer of materials into or out of a cell along a concentration gradient by a process that requires a carrier.

Active transport: Transfer of a material into or out of a cell from a region of lower concentration to an area of higher concentration by a process that requires a carrier and an expenditure of energy.

Both processes require a carrier and both processes facilitate transport into or out of the cell. Both processes move material along a concentration gradient. However, Active transport requires an expenditure of energy and facilitated transport does not.

Describe endocytosis, including pinocytosis and phagocytosis, and contrast it with exocytosis.

Endocytosis: brings material INTO the cell. A portion of the plasma membrane invaginates to form a vesicle around the material. Then, the vesicle pinches off inside the cell.

Three kinds of endocytosis:

1. Phagocytosis: when the material coming into the cell is large- like a molecule of food or another cell (when old red blood cells are absorbed) this is common in unicellular organisms like amoebas that engulf their food.

2. Pinocytosis: happens when vesicles form around liquid or very small particles.

3. Receptor mediated endocytosis: makes use of receptor proteins in the plasma membrane. A specific substance binds to receptors that then gather in one location before endocytosis happens.

Exocytosis: brings material OUT of the cell. The [intracellular] vesicle fuses with the plasma membrane so the contents can be released outside of the cell.

CELL WALL

let's do cell walls all in ONE BIG FELL SWOOP, shall we? since the test is on Monday and there's lots of midterm review to do ;)
BTW, rocked the last test- 93%.



I'm loving this cell membrane unit. It makes sense to me, builds on what we've learned before. I find it fascinating how all the pieces work together and form a wall that holds all organelles in and anchors cytoskeleton.

In all things I love about biology, the plasma membrane really interests me. It's a true work of scientific engineering. It’s made of mostly of phospholipids and embedded proteins. These proteins can do a lot of things, like help channel things in and out of the cell, help with cell recognition or be enzymatic proteins. This is all covered later.

With all of this content, the structure of the fluid mosaic membrane is still fluid, with a texture similar to light oil. The proteins are scattered throughout the sea of phospholipids and create the mosaic texture that earns the phospholipid bilayer the term the ‘fluid mosaic membrane’.  

Remember our phospholipid. He has a polar head and nonpolar tails. He’s made from two fatty acids on one phosphate molecule. These nonpolar tails are hydrophobic while the head is hydrophilic. This is how the plasma membrane spontaneously arranges itself with the heads pointing to the outsides of the membrane and the tails facing each other.

Here is a generic picture that I take no credit for but really- I could have drawn it ;) 

Within this membrane of phospholipids, a molecule similar to a phospholipid resides. It’s a glycolipid. It is made of two hydrophobic tails with a head made of sugars joined into a straight or branching carbohydrate chain.  Even though it reduces the permeability of most biological molecules, cholesterol is also found in the plasma membranes of animals. Plants have similar steroid molecules in their membranes.   

The cell isn’t symmetrical on the outside and inside. While the phospholipid bilayer sounds like it would be symmetrical, the outside is coated with carbohydrates from glycolipids and glycoproteins. As well, the outside has proteins that anchor to an intracellular matrix. 

The inside has protein anchorings for the cytoskeletal filaments. 

 

Proteins are found throughout the membrane. 

Here are a few kinds.  

Integral proteins usually have a hydrophobic quality to them. Most of these integral proteins are also glycoproteins meaning they have an attached carbohydrate chain that floats out from the outside of the cell membrane.  

Peripheral proteins hang out on the outside of the membrane (either the cytoplasmic or external side) sometimes anchored by covalent bonds, other times, just resting on the surface of the cell lightly tethered with non-covalent interactions and are prone to shifting around when the cell moves or is shaken or even has a pH shift.

 Channel protein:

Shaped like a tube. It’s shaped to let particular kinds of ions pass at will across the plasma membrane.

Carrier protein:Selectively interacts with specific molecules or ions so they can cross the plasma membrane.

Cell recognition protein: The carbohydrate chains and glycolipids and glycoproteins are the cell’s fingerprints. These vary from person to person and species to species. These cells are why organ transplants are difficult to match since the body’s immune system can sense that the cells of the foreign organ do not have the same ‘fingerprint’ as the body’s original cells.

Receptor protein:

These are shaped in such a way that they can only bind to a certain substance i.e. growth hormones.

Enzymatic protein: Catalyzes specific reactions for example, the protein adenylate cyclase is involved in ATP metabolism.

The cell membrane is selectively [differentially] permeable. 

Some things can move across the membrane and others can’t. 

Ions and other charged molecules can’t cross because they can’t get through the hydrophobic layer. Macromolecules are just too big to pass through. 

Oxygen, Carbon Dioxide and Water can easily pass through because they are noncharged and small enough. 

Review: Unit 3. DNA, Mutations and rDNA

 What What What!? The end of this unit? Well, one more down, umm... 12 to go. Embarrassing, considering the amount of time I've been working on this,false starts and all.

Unit three test tomorrow, unit four test (aiming for a week from tomorrow) and then, a midterm. I'll be a third of the way through the course. It will be awesome. The pace needs to be picked up though, my scheduled college classes begin in May.

Of course, the rough endoplasmic reticulum is studded with ribosomes... and we all know the ribosomes are active in protein synthesis. ;) According to my biologist friend, the ribosomes on ER are for mRNA translation only.


Quick review:

Nucleotide: Biological building blocks for DNA and RNA. DNA: Made of a Phosphate, a 5-carbon deoxyribose sugar (a pentose sugar) and a base. One of Four bases (listed in the order they pair in)- Adenine, Thymine, Guanine and Cytosine. FOR RNA: Adenine, Thymine, Guanine and Uracil. Bases are either purines or pyrimidines. Purines are Adenine and Guanine. They have a double ring structure. Pyrimidines are Cytosine, Uracil and Thymine. These have a single ring structure. 


DNA: Deoxyribonucleic acid. Our genetic material. Looks like a twisted ladder but it is actually a Polymer of nucleotides joined in the middle (hydrogen bonds) with complementary base pairing. reproduces semi conservatively.The uprights of the ladder are sugar-phosphate-sugar-phospate pattern structure. DNA must replicate with a high degree of accuracy, be able to store information and undergo mutations to control both the development and metabolic activities of the cell and organism.

DNA replication: occurs in the nucleus of the cell. 3 steps: 1. Unwinding: DNA Helicase comes in and unzips [the bases] by breaking the hydrogen bonds that hold them together. 2. Complementary base pairing: Free floating nucleotides pair with the unzipped, now open bases. 3. Joining: DNA Polymerase joins the paired nucleotides and thus, two strands of DNA are born- one side of the DNA's ladder is from the old polymer and the other side of the ladder is new: this is known as semi conservative replication because part of the old strand is always preserved. DNA replicates in this way so that it can replicate with a high degree of accuracy.


RNA: Ribonucleic acid. Structurally the same as DNA with a phosphate, a pentose sugar (ribose) and a nitrogenous base. Adenine, Guanine, Uracil and Cytosine. SINGLE STRANDED IN STRUCTURE. Functions in the synthesis of proteins. Three different tyes of RNA: tRNA: escorts amino acids to mRNA during protein synthesis rRNA: has a structural role, forming most of the ribosome, along with protein. mRNA: messenger RNA carries a coded sequence of bases to the ribosomes for protein synthesis.


Triplet codes: During protein synthesis, amino acids are carried to mRNA dependent which bases are represented and in which order. If you were to supply a singular base at a time, there would not be enough bases to code for all 20 amino acids that must link together to make proteins. By having bases available in triplets, there are enough bases available to code for 64 different bases (this includes start and stop codons). Multiple triplets can code for one amino acid.


Transcription: a strand of DNA is copied to make a strand of mRNA. During Transcription, a segment of  the DNA unwinds and unzips (thank you, helicase) and ONE strand of the DNA is copied from the transcription bubble. Complementary nucleotides pair with the DNA bases using the following bases: Uracil, thymine, guanine and cytosine. A strand of mRNA results.  

Translation: Translation is the process where the sequence of codons formed during transcription becomes the order of amino acids in a polypeptide.Translation begins with rRNA, coming from the nucleus and joining with a protein to form a  ribosomal subunit. Then, the process of translation begins with 1.Initiation: mRNA bonds to two ribosomal subunits. 2. Elongation: tRNA brings amino acids to the ribosomal subunit/mRNA sandwich. These amino acids are the anticodons to the codons on the mRNA. The ribosomal unit has room for two tRNAs. One goes in, bearing an amino acid. That tRNA receives an amino acid chain from the tRNA just leaving the ribosome. That tRNA adds its amino acid and elongates the chain in this manner, passing the chain to the next tRNA to enter the ribosome 3. Termination: A stop codon is encountered on the mRNA. The protein drops off as the ribosome dissociates. Polyribosomes can sometimes form and they all work together along the same mRNA and create multiple copies of the same protein. 



Where transcription copies the sequence of bases from the DNA string to form mRNA, translation translates these base codons to become amino acid polypeptides (protein).


  
Mutation: A mutation is a change in the nucleotide sequence of a gene. 

Point mutation: A change in a specific nucleotide. When one base is substituted for another along the mRNA, different things can happen. There can be a silent mutation where, by luck of the draw, the nucleotide changed ends up coding for the amino acid that was needed in the first place. A Nonsense mutation happens where the codon is changed to become a Stop codon. This makes the resulting protein too short and useless. There is finally, a missense mutation. A missense mutation happens when the codon is a useful amino acid, but it is in the wrong place, affecting the shape of the resulting protein as well as the polarity. This missense mutation is what causes sickle cell disease.  Valine is substituted for glutamate along the protein chain. 

Frameshift mutation: An error on the reading frame or sequence of codons presented for protein synthesis occurs. A base is DELETED along the chain and shifts the codons all down one slot. This deletion changes the entire sequence of codons and confuses the entire meaning of the resulting protein. Frameshift mutations frequently result in severe genetic diseases such as Tay-Sachs disease.

Mutagens: Environmental factors that cause mutations. Mutagens cause cancer and birth defects. Radiation (Xrays) or Organic chemicals (pesticides and compounds in cigarette smoke) are mutagens. Mutations in the body cells will result in cancer. Mutations in the gametes will cause deformities in the offspring. 

Recombinant DNA: Recombinant DNA contains DNA from two or more different sources. rDNA is used to create products that would be difficult to obtain by natural harvesting in mass quantities. These products are things like insulin, hormones, lung surfactant and enzymes. 

To make rDNA: A vector is chosen. In the example here, we will use a bacterium. We remove the plasmid (small DNA molecule) from the bacterium and use resriction enzyme to cleave a space for the gene we want to replicate (insulin, for example) we then isolate the gene for insulin and remove it (again, using the restriction enzyme) the insulin gene is placed into the plasmid and is then sealed together as one unit using DNA ligase. The host cell (bacterium) takes up the recombined plasmid. As the host cell reproduces, the plasmid is reproduced as well, resulting in multiple copies for the rDNA. The resulting rDNA is inspected and if it is found suitable, the product [in this case insulin] is retrieved for use. 

Recombinant DNA

Recombinant DNA (rDNA)
 

Recombinant DNA contains DNA from 2 or more different sources. 

Vector: the means of by which rDNA is introduced into a host cell.
Plasmid: found in the cytoplasm of bacteria, a plasmid is beneficial to making rDNA since it acts as a vector. Plasmids are small accessory rings of DNA. They carry genes not present in bacterial chromosome.
Two enzymes are needed to make rDNA (Next part makes more sense if this here makes sense to you):

Restriction enzyme: cleaves both the plasmid and human DNA.
DNA Ligase: Seals foreign DNA into the opening created by restriction enzyme.


To make insulin:

1. Choose your Vector (host) We will use a plasmid from a bacterium for this.

2. Remove the plasmid from the bacterium.
3. With the help of restriction enzyme, isolate and remove the gene for insulin from the human DNA.
4. Again with the restriction enzyme, cleave a space for the insulin gene in the plasmid.
5. insert gene into vector and seal with DNA ligase.
*******now you have rDNA*************
6. Host cell takes up recombined plasmid.
7. Plasmid is cloned as host cell reproduces.
8. Multiple copies of the cloned gene are replicated and if this cloned insulin gene functions normally (as inspected by an investigator) the product (insulin)  may also be retrieved.


List three specific uses for recombinant DNA or transgenic organisms.
1. Vaccinations
2. Mass production of products to be used in the human body- insulin for example, that would be expensive and harder to achieve by harvesting it from other sources.
3. Growth hormones to produce leaner meat, for slaughter.

Mutagens

 Mutagens are environmental substances that cause mutations. 


Mutations can cause cancer or birth defects. 

Mutagens are factors like radiation (X-rays) or organic chemicals ( certain pesticides or compounds in cigarette smoke). 

Lots of mutagens are carcinogens. Mutations in the body cells will likely result in cancer. 

If the mutation occurs in the sex cells (gametes) then the mutation will occur in the offspring.

Mutation

In order for us to evolve, mutation of our genes is necessary. However, not all of these mutations are beneficial. 

 Define gene mutation.
 A gene mutation is a change in the nucleotide sequence of a gene. 
 Since each new strand of DNA is proofread for errors by DNA Polymerase, it's rare that there is an error in replication. Apparently, the chance that the DNA is repicated incorrectly is about one in 1 billion replicated nucleotides. 

There are two types of mutations that are relevant to this section of coursework: Frameshift and Point mutations. 

A frameshift mutation is an error on the  'reading frame' or sequence of codons that are presented for replication. Since replication begins at a specific point ,when one codon is deleted, the results can be devastating since it shifts the entire row codons down one slot and turns the result into something that doesn't make sense. Imagine you deleted the first letter out of a sentence but kept the spacing the same.
'When is dinner ready?' turns into 'heni sdinne rready?". Nonsensical and it has lost its intended meaning. This is how frameshift mutations occur- by deleting or adding a nucleotide into DNA, rendering it nonfunctional.

A point mutation  happens anywhere along the gene and does not involve a deletion or addition but a change in a specific nucleotide.  

Remember our chart of codons. Each three letters actually stand for a specific amino acid. 61 of them are amino acids, two are Stop codons (describes where termination of synthesis occurs) and one is a Start codon. 

In most instances, replacing one base with another does not have a drastic effect. It can change one codon to another and through luck of the draw, the change results in the same kind of amino acid and life goes on (called a silent mutation)  for instance, CGC is arginine. Substitute CGG and the result is still arginine.
 
In some cases, the codon can be changed to become a stop codon, prematurely ending synthesis and resulting in a too short protein that is non functional (nonsense mutation). 
 
Other times, a missense mutation happens. This is when the meaning of the codon is changed completely when one amino acid is substituted. if CAC is incorporated into the protein instead of UAC, then histidine is added instead of tyrosine. This is disastrous especially since the polarity of the two differ.


Sickle Cell disease is caused by a missense mutation. 
Along the chain, Valine is substituted for Glutamate long the hemoglobin chain. This results in the sickling of the red blood cells and among other things, their premature breakdown-- causing anemia and other complications.