Digestion videos

Protiens and nucleus acids:

http://youtu.be/bdUW82P4DUo

Carbohydrates and lipids :

http://youtu.be/4OYrBymOPaY

Protein Synthesis

 

Protein Synthesis video^

 

    Protein Synthesis has two main steps and they are transcription and translation. Transcription is where it makes a copy of one gene in DNA into mRNA. Translation takes the mRNA and translates it into a protein. We will take a closer look into these steps.
  TRANSRIPTION: 1. The enzyme helicase unwinds and unzips one gene of the DNA. 2. Complementary RNA base pairing attaches to form a mRNA 3. The enzyme RNA polymerase forms a sugar phosphate backbone and checks for mistakes. 4. The mRNA detaches and leaves the nucleus through the nuclear pores and the DNA winds back up.
TRANSLATION: 5. mRNA moves to join a ribosome in the cytoplasm 6. Initiation (the first codon on any mRNA molecule is called the initiator) 7. Elongation: ribosomes job is to position the tRNA with its corresponding amino acid onto the matching mRNA molecule. Then the amino acids bond together with a peptide bond and with the help of the enzyme peptidyl transferase. 8. Termination: the last codon on any mRNA chain. The last codon is the stop codon and it does not have a matching amino acid so that is the message to stop. The amino acid chain then detaches and is considered a protein.

 

      Below is the way that the sequence of DNA is transformed to mRNA and then to tRNA and then to amino acids. From DNA to mRNA they just pair up with their complementary base pairing and since it is turning into an RNA strand there is no Thymine, in its replace there is Uracil. From the mRNA to tRNA they do the came thing find their complementary base pairs. A short cut to this is just to look back at the DNA strand and change all the Thymine's to Uracil's. To find the matching amino acids to the tRNA you look at the mRNA strand and find them on the mRNA codon chart.

 

 

 MUTAGENS

    Some environmental mutagens are UV rays, gamma rays, ionizing radiation, caffeine, aflatoxin (from mold) and ISD. There are two types of mutations that can come from these mutations they are gene mutation or chromosome mutation. A gene mutation is the change of one or more nucleotides in a single gene. This affects the outcome of the protein and might affect the job that the protein does. A chromosome mutation is a mutation of all or part of a chromosome, which affect many genes. A chunk of the chromosome may be missing/or added. This affect many genes which will also affect the proteins being made. When a protein is made it is made to do a specific job, so when the protein gets messed up the job also gets messed up causing abnormalities. For example, extra limbs, downs syndrome or even making a person have male and female parts.

    A genetic disorder is an illness caused by one or more abnormalities in the genome, especially a condition that is present from birth. Two examples of these are Klinefelter syndrome and Turners Syndrome. Klinefelter syndrome is when there is an extra sex chromosome. For example, a persons sex chromosomes are XXY instead of XX or XY. This causes the person to have both female parts and male parts (breasts and testies). If one has this syndrome their IQ is usually impaired.  In the Turners syndrome the person is missing a sex chromosome. So their sex chromosome is usually just X. This causes women to be short and have a fold in the neck when they are young and they cannot have babies. Also, their breasts don't develop properly.

Biological molecules

DEHYDRATION SYNTHESIS AND HYDROLISIS

   Dehydration synthesis joins monomers together by taking H2O away, hence the dehydration part of the name. On the other hand, hydrolysis is the exact opposite of dehydration synthesis it is the breaking of polymers into units by adding H2O. Here is a link to a video that shows you a better understanding of these two concepts: http://youtu.be/_Ai5NyQ_ttE

This is dehydration synthesis. See how it is taking away the H2O and then the two monomers bond together with the oxygen and become a polymer.

     This is hydrolysis. See how they are ADDING H2O which causes the polymers to split apart and become monomers.

CARBOHYDRATES

The name comes from hydrated carbons. Carbohydrates empirical formula is (CH2O)n where n equals the number of times the chain is repeated. Carbs are made up of C,H and O and have a ratio of 1carbon:2hydrogen:1oxygen. 

There are a couple different types of carbohydrates. The first type is monomers which are monosaccharaides. Specific examples are glucose, fructose, ribose and deoxyribose. Another type of carbohydrates are disaccharides, this is when 2 monosaccharaides join together. Some examples are; glucose+glucose forms maltose, glucose+fructose form sucrose and galactose+glucose form lactose. The last type is polysaccharides. This is when many saccharides are joined together forming what looks like a chain. There are 4 different types of polysaccharides that i will go deeper on and explain them a bit more, which are cellulose, starch, glycogen and chitin. 

     Cellulose is a long chain without any side chains. One can remember this by thinking of celery and how celery is straight just like the chain of glucose molecules. Plants use cellulose as protection and structure, it is in the cell walls of plants. The linkage between the carbon atoms of sugars are different than the bonds in starch and glycogen, no mammal can break this bond. This is why we cannot digest cellulose(fiber). 

     Starch is made up of many glucose molecules linked together in a straight chain with a few side chains. Plants store their energy as starch. Below is a picture of a starch chain, notice how it only has one side chain.

  Glycogen is made up of many glucose molecules linked together with many side chains, unlike starch that only has a few. Glycogen is very important to us animals. We store our energy as glycogen in our liver and muscles.  Below is a picture of a glycogen chain. Again notice how it has more than just one side chain. If this picture was extended then you would be able to see how it has many side chains as suppose to starch. 

  

  The last polysaccharide is chitin. It is made by animal and fungi. Chitin is made of long glucose chains linked with covalent bonds, which are very strong. It makes structures like exo-skeleton, fingernails, claws and beaks. This is was chitin looks like structurally.

A main function if carbohydrates is energy. When the bonds between carbon atoms are broken, the energy is released and can be used by cells. Starch stores energy in plants, and glycogen stores energy in animals. Another function is structural. Cellulose is the major structural and protection compound in plants.

 

 

 

LIPIDS

     There are 4 main uses for lipids and they are long term storage for energy, insulation and protection, they make some hormones(ie. steroids) and they are the structure of the cell membrane. The structure of a lipid is made up of Carbon, Hydrogen and Oxygen, just like a carbohydrate. However, in a lipid there is no set ratio for these elements. There are three types of lipids and they are triglycerides(neutral fats), phospholipids and steroids.

     Triglycerides are composed of three fatty acids bonded to one glycerol. The fatty acids contain a long chain of carbons with an acid end. The glycerol is a small three carbon chain with three alcohol(OH) groups. The fatty acid and glycerol bond together via dehydration synthesis. There are two types of triglycerides which are saturated and unsaturated fats. The difference between these two types of triglycerides are that in a saturated fat there is no double bonds in the carbon chains of the fatty acids, where in a unsaturated fat there is one or more double bonds. Also, a saturated fat is solid at room temperature, come from animals and are considered unhealthy. A unsaturated fat is liquid at room temperature, come mostly from plants and are considered healthy.



 

     Phospholipids are used to make up the two layered cell membrane of all cells. They are similar to a triglyceride but the third fatty acid group of a triglyceride is replaced by an inorganic phosphate group (PO4 3-). A phospholipid has a polar head that is water soluble(hydrophilic) and the non-polar tail is not water soluble (hydrophobic). There are a couple different ways that they display phospholipids. Here are some of them:

 

 

 

   A steroid is the last type of lipid I will be talking about. Steroids look different than all the rest of the lipids. They are made up of four carbon ring and the molecules are fused together. They kind of look like four honeycombs stuck together. The use of steroids is to create some hormones, cholesterol and vitamin D. Some types of steroids are testosterone, estrogen, cholesterol and vitamin D.

 

 

PROTEIN

     The functions of a protein is structural because they help make up all structures in living things for example, actin and myosin are muscle proteins, keratin is found in like nails and hair, collagen is found in bones, teeth, cartilage etc. Another function of a protein is functional, they help our bodies functioning properly and to digest our food. This is done by enzymes, which are proteins that are catalysts which speed up reactions and control all cell activities. The final function of a protein is they can act as a food source, once we have used up all of our carbohydrates and fats, proteins will be used for energy. However, proteins are worth the least amount of energy that is why they are saved for the last resort.  Proteins are made up of carbon, hydrogen, oxygen, nitrogen and maybe sulfur but in no set ratio. Proteins are chains of amino acids that bond together via dehydration synthesis. An amino acid has three parts: Amine Group (NH2 or HH3+) which acts as a base(accepts H+), Carboxyl Group (COOH or COO-) and it acts as an acid (donates H+) and the R Group which have twenty different combinations. When amino acids bod together they bond with a peptide bond which is formed between carbon and hydrogen and one water molecule is lost. If only two amino acids are together it is called a dipeptide if the chain becomes three then it is called a tripeptide. After that, when the protein chain has more than three amino acids it is called a polypeptide. Every protein is different because the order of amino acids are different.

 

 

   The levels of Protein Structure:

       Primary structure is simply when the amino acids bond together with peptide bonds. The protein depends on the order of the amino acids, if they are not in the right order then the protein may not be able to do its job.

       Secondary structure is when hydrogen bonds form between the amino acids positive (amine group, NH3+) from one amino acid and negative(carboxyl group) from a different amino acid. This bond makes the chain twist into either an alpha helix or a beta pleated sheet.

       Tertiary structure happens between the R Groups. The interactions is between  + and - attractions and sulfur sulfur bridges. The positives and negatives will attract each other and the same charges will repel each other. That makes the structure to fold into a highly specific 3-dimentional shape. The shape determines the protein's job or role it will play in the body.

      Quaternary structure is not seen in all proteins, this is where two or more molecules join together with an ionic bond to form a functional protein. Some examples are Insulin with two subunits or Hemoglobin with four subunits.

 

 

NUCLEIC ACIDS

 

   Nucleic acids are acidic molecules that are found in the nucleus of cells. There are two type and they are deoxyribonucleic acid(DNA) and ribonucleic acid (RNA). All nucleic acids are made up of units called nucleotides which are made up of three sub-molecules: Pentose sugar(ribose or deoxyribose), Phosphate, Nitrogen base (purine or pyrimidine). Adenine and Guanine are purines, they have two rings and are both found in DNA and RNA. Cytosine, Thymine and Uracil are pyrimidine's, they have only one ring and Cytosine is found in both RNA and DNA, however, Thymine is found in DNA and Uracil is found in RNA. A purine always matches up with a pyrimidine in a nucleic acid. A memory trick for a purine is "Its got 2 be GAp". The 2 represents the two rings and the GA represent Guanine and Adenine. A memory trick for pyrimidine is that "CUT the pyramid". The CUT stands for Cytosine, Uracil and Thymine and the pyramid reminds one of the single blocks the Egyptians had to cut for the pyramids, therefore it has one ring.

 

  A DNA strand is composed of nucleotides and a sugar phosphate backbone. The nucleotides go together with their complementary base pair, which is A-T and G-C. Adenine and Thymine bond together with two hydrogen bonds and Cytosine and Guanine bond together with three hydrogen bonds. The sugar phosphate backbone is formed after all of the complementary bases are paired up then it twist into a double helix. The main function a DNA is to direct and control all cell activities by making proteins and enzymes. The also contain all of the genetic information necessary to make one complete organism.

 

   Some of the difference between RNA and DNA is that DNA is confined to the nucleus and RNA can move to the cytoplasm. RNA has ribose sugar instead of deoxyribose and RNA has Uracil instead of Thymine like DNA. DNA is a double helix as suppose to RNA is a single helix. There are three types of RNA (mRNA, tRNA, and rRNA) and there is only one type of DNA. RNA's function is mainly to assist DNA in making proteins.

 

    Adenosine Triphosphate:

ATP is also thought of as a nucleic acid because it has a similar structure as a nucleotide. The only difference is that it has three phosphate groups instead of one. In a ATP molecule there is three phosphates (Triphosphate) a sugar and an adenine (Adenosine). ATP is the energy source of the body. This is because it takes a lot of energy to put two phosphate molecules together so when they are broken apart a lot of energy is released.











DNA Replication

The purpose of DNA replication is so that the genetic material can be passed from the original cell to the daughter cell. New strands of DNA is needed to produce new cells. This is because cells in ones body are dying every second, however, new cells are being made as well, this is why we don't clearly notice them.

Steps:

1. Unzipping the hydrogen bonds with the enzyme helicase.

2.complementary base pairing with ATP energy to build new molecules. 

3. Form of a new sugar phosphate backbone and checks for mistakes with the enzyme DNA polymerase. 

4. Now you have two identical strands. The two strands are semiconservative which means it has a strand from the original DNA in each new DNA and a daughter strand in each new DNA.

During DNA replication there is a chance of having a mutation. Not all mutations are bad, some may even improve your health and some may not even make a difference. There are three types of mutations that can happen; addition, deletion and substitution. Substitution mutation is the least dangerous mutation because if one letter gets switched it only would affect one amino acid and it may not even affect the amino acid because there are many codons for one amino acid. On the other hand, addition and deletion has more of a risk of messing up your health. Addition is when a letter is added and deletion is when a letter is deleted. You can think of the sequence of a DNA as a sentence.

Notice in the substitution sentence still makes sence even though there is a mutation. As suppose to the other two mutations. After the mutation in each sentence the sentence does not make sense at all. This proves how addition and deletion are way worse mutations and how they can seriously mess up your DNA.


This is our DNA replication video:

Cell presentations

My Favorite presentation was the one done by Trevor and Wynden because they made a very detailed/ professional looking movie. It made it easier to understand what they were saying when they had pictures in the background playing. I also liked how they recourded their voice over the movies so they didn't have any stuttering/errors when speaking. It flowed nicely. The video of how a baby grew was cool too. 

 I learned things about curtain cells during these presentations for example: motor neurons can undergo many action potentials used for one muscle twitch, the egg cell is the biggest cell in the female body and a sperm cell is the smallest cell in the male body, and a red blood cell has very little organelles they have some ribosomes and cytoplasm.

Me and Erika did our project on olfactory cells and neutrophil cells. Olfactory cells are in the nose and they are used to detect smell from the odor molecules and a neutrophil cell is a white blood cell and Its job is to kill bacteria. At first our project was just basic but after we did critical friends they had some good ideas to make our project better that we did not think of before. Some struggles we had in researching our project is finding out what organelles are prominent. They didn't have anything on the internet so we had to use our brains and go through each organelle and think if that cell would need it or not. I think our project turned out really good in the end and I am happy with the outcome. This is how our project turned out.

Acids, bases and buffers

An acid has a pH between 0 and 6.9. It turns litmus paper red, an easy way to think of this is by the stomach is red and the acid inside the stomach is very acidic. Acids are very corrosive. When you add an acid to water the acid adds more [H+] ions making the solution have a lower pH. For example, HCl--> H+ + Cl- 

A base has a pH between 7.1 and 14. It turns litmus paper blue. Bases are caustic and a way to tell it's a base is that they are slippery. When you add a base to a solution it will remove [H+] ions. This is because the base separates when it hits the solution and the OH pair up with an [H+] forming a water molecule, making the soliton have a higher pH level. An example is:    NaOH --> Na + OH then the OH connect with a H+ forming H2O.

 

A neutral solution is where the acids and bases are balenced (equal).

Buffers either absorb or give away an H+ ions until it is overloaded. Overloaded means that it can not take or give away any more H+ ions. When it is in an acidic solution, a buffer will absorb H+ ions. For example, H+ + CO3 2-  ---> HCO3 1- .

When it is in a basic solution, a buffer will donate H+ ions. For example, OH- + H2CO3 ----> H(OH) + HCO3 1-  

Usually a buffer has 3 or mot 'versions' of itself.

Why is water so unique?

The reason for water being different from many other cells is because water has a special type of bond called a polar covalent bond. This means that the electrons are shared throughout the molecule unequally.   

In addition, because the electrons spend more time surrounding the oxygen atom, the oxygen has a negative charge, and the hydrogenation have a net positive charge. That's why it is polar. Two polar molecules attract to each other and form a lattice. Water molecules are connected together by hydrogen bonds. Hydrogen bonds are weak in small numbers but lots of them together they are very strong, making water very stable. 

Another interesting fact is that a lot of energy is needed to break a water lattice, making it have a wide temperature range that water is stable at which is 0-100°C. The final unique thing that I know about is that is occurs naturally in three states of matter( liquid, solid and gas).

Some of the properties of water are surface tension. The water molecule are cohesive meaning they sick together. This is why you can fill a cup past the "full" point. Like in this picture.

Another property is capillary Action. This is where water is sucked up a small tube against the force of gravity because the water molecules are cohesive and adhesive so they sick to themselves as well as the outer surface.

Heat and vaporization is anothe property of water. This means that a lot of energy is needed to break water lattice apart making water stable over a wide range.

Ionization of water is a property of water. When the attraction is greater for something else, the hydrogen bonds will break and tear water molecules apart. This causes oxygen and hydrogen to dissociate into ions. H2O ---> H+ +  OH-

Finally the last property is the solvent properties, it can dissolve any ionic compound.  The polarity of water molecules will break the bonds between ionic compounds and the slightly positive hydrogen attract the negative ions and vise versa. 

Cell structure

   

There are lots of different parts in a cell. The cell is surrounded by a duel layer called the plasma membrane or phospholipid bilayer. Inside the cell there is a nucleus, its job is to store genetic information like chromosomes and it also controls the cell activity through protein synthesis. The nucleus is like a brain. Inside the nucleus there is the nucleolus which is the dark centre of the nucleus made up of RNA. Its rRNA's make ribosomes and send them out through the nuclear envelope. Ribosomes are where protein are made and they also make sure the amino acids are in the correct order. The role of the nuclear envelope is to let RNA and protein in and out of the nucleus through its pores. The last thing in the nucleus is the nucleoplasm. This is pretty much the same as cytoplasm but inside the nucleus, it is a jelly like substances that supports and suspends the contents of the nucleus. Next thing in a cell is the mitochondria. It acts like the furnace of the cell, converts the chemical energy in food to ATP, cellular respiration. Next is the endoplasmic reticulum, which is the rough ER and the smooth ER. The rough ER transports proteins and sometimes modifies them, it packages the protein up in a vesicles and sends it to the Golgi body.  The smooth ER transports hormones and fats and makes lipids and steroids, it detoxifies harmful material or waste products. The Golgi  body receives, modifies and temporarily stores the proteins and fats from the smooth and rough ER. It also makes lysosomes. Lysosomes are sometimes known as "suicide sacs", they attach to food vacuoles and digest their contents. They can also destroy old or malfunctioning cell parts. Vesicles and vacuoles are storage sacs of the cell membrane it transports substances around the cell that needs to be separate form the cytoplasm. They cans stir food, water and/or waste. The difference between a vacuole and a vesicles is that a vacuole is just bigger. The thing that makes the cell have its shape is the cytoskeleton. It acts as a frame work. Microfilaments are long and externally thin protein fibres that occur in bundles made up of two proteins called Actin and Myosin. The microfilaments help organelles move around the cytoplasm. The other structure you might confuse this with is the microtubules. They are pretty much the same thing but bigger and cylinder shaped made up of coiled protein called tubulin. Microtubules are used to make cilia, flagella and centrioles. Cilia are tiny little hairs and are used to produce locomotion. Flagella is found in sperm cells. Centrioles attach to and move chromosomes during mitosis. Finally, those are all the organelles of the cell that I know and what they do.

You may ask how does a cell make a protein.. Well your in luck cause I am here to tell you how! First,it all starts of with the nucleus. The nucleus makes ribosomes and sends them out the nuclear pore. Some ribosomes attach to the rough ER and makes the protein, sometimes it modifies the protein then it stores the protein. When the protein is ready it sends it to the Golgi body in a vesicle. In the Golgi body the protein is modified and the enzymes are activated and sends it to the plasma membrane, released via exocytosis. The end. 

This is the plasma membrane model I made.

This is the Golgi body you can tell because if the flattened pancake shapes that are all together and the vesicles (round dots) around it

Homeostasis

One thing i now know that i probably wont forget is the differences between positive and negative feedback loops. A positive feedback loop only stops when something occurs and a negative feedback loop shuts itself. 

Homeostasis keeps the body on track. Sensitive receptors monitor each condition under the homeostatic control. It monitors temperature, blood pressure, surcharge levels, osmolarity, PH and etc. If these are not in  the balanced range then the feedback loops kick in, called the corrective mechanism, which reverses the original change and brings the system back to normal. How this all works is the first thing is the stimuli, for example the body temperature rises above 37.5 degrees Celsius. Then the receptor detects it and sends a signal to the regulatory centre. Then the regulatory centre send that message to the effector, which is usually a muscle or a gland. Finally the response happens, for example sweat if its too hot. The body becomes normal again and if the feedback loop was a negative one it would shut off. This all happens continuously as we live our lives. An example of a positive feedback loop is labour. 

There is our poster we made...