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Unit 1 - Biochemistry

Atoms to building blocks of cells
by

Daniel Garvey

on 22 January 2013

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Transcript of Unit 1 - Biochemistry

Positively charged particle
Located in the NUCLEUS of the ATOM
Equals 1 Mass Unit Protons (+) Neutrally charged particle
Located in the NUCLEUS of the ATOM
Equals 1 Mass Unit Neutrons (o) Change the structure change the element Different Atoms have Different Particle configurations 3 subparticles What is an Atom? Every Element is unique and has a specific physical property Periodic Table of Elements Various elements can "link" together by having their electrons interact Combining Elements Sharing is caring with Covalent bonds Covalent Bonds I will steal your electron!!! Ionic Bonds You know a chemical reaction occurs when you see:
Color change
Temperature change (hotter or colder)
bubbles (gas created)
something new is formed that can't change back (precipitate) THE MOST UNIQUE SUBSTANCE
ON EARTH Water is AWESOME Polymer 2 Electrons (-) Located on VALENCE RINGS around the Nucleus Negatively charged NO MASS*** http://www.rsc.org/periodic-table This creation of a compound alters the atomic make-up of the atoms (electrons) and therefore changes the physical properties. Valence shells are stable when full
Shell What is matter? Anything that
takes up space
and volume Isotopes... fat or skinny atoms.... Ok so an atoms mass is calculated by adding up the protons and neutrons (both are equal to 1 a.m.u. each.) Carbon has 6 protons and 6 neutrons. Therefore it has a total mass of 12 atomic mass units (a.m.u) Isotopes are unique in that there are more neutrons in the nucleus that changes its mass... and sometimes makes them unstable and radioactive Uses....
-Medical screening
-Radioactive dating PROTEINS CARBOHYDRATES Nucleic Acids If two elements are near each other and have the ability to share electrons to fill up their valence (outermost) shell they will. This forms a Covalent Bond! Valence shells are stable when full
Shell Sometimes it is easier for elements to give up or steal an electron. By gaining an electron the element becomes -1 charged. by losing and electron the element becomes +1 charged. Now oppositely charged, they will stick like glue!!! and be in an Ionic bonded! POLAR! Density Universal Solvent SO necessary for life! Think of water as a small magnet. This small magnet is polar in that it has a positive and negative end. When water molecules are with water molecules, they stick together. This is called Cohesion. Water can form long chains too. The bonds (forces) that hold the water molecules to each other (cohesion) and to other things (adhesion) are called Hydrogen Bonds When water molecules are with other substances they can stick like a magnet to them sometimes too. This is called Adhesion. Lets Recap!! You can combine these elements by bonding them to each other to make new things The more atoms you stick together the bigger the molecule you form! Everything is made from atoms There are many different types of atoms Each has its own number of protons, neutrons, and electrons H2O CO2 NaCl Water is a unique element
that has awesome properties
we rely upon for life!! The most important elements we need are Carbon
Hydrogen
Oxygen
Nitrogen Because they make up 96% of our bodies Cancerous Cells Grow uncontrollably. Because of this they require and absorb much higher amounts of glucose (sugar) which they need for fuel to make more cells.

Scientists will "mark" glucose with a low level radioactive element and feed the glucose to the patient.

A PET scan which takes photos of your body and highlights where more energy is being released will pick up what part of the body has the most radioactive glucose.

Therefore is doctors see this pet scan above, what conclusion can they come to? A radioactive element will decay because it is an unstable element. for example Carbon 14 will actually decay into Nitrogen....

Ok here is how it works.

When a radioactive element decomposes it may give off beta particles which are electrons coming from the nucleus. Since there are no electrons in the nucleus, they have to come from someplace. It is thought that a neutron is really a proton with an electron. In beta decay, the electron is sent out of the nucleus and a proton remains. The atomic number goes up one but the mass does not change. So now it is N-14, 7 protons, the mass stays the same, it still has 7 neutrons.

BUT EMITS ENERGY - AKA Radiation!!!! Organic vs. Inorganic... Organic Molecules contain
both carbon and hydrogen Inorganic compounds can contain carbon or hydrogen or neither. Water has an amazing ability to absorb and retain ALOT of energy. It takes much more energy to heat water to boiling temperatures then it does to heat say... oil. In order to for a substance to change from a liquid to a gas, the molecules of the substance must have enough energy to "break away" from the remaining molecules. Water, being polar, sticks to itself. Because of this, water molecules are harder to separate from each other and are hence harder to push from a liquid to a gas... water requires more energy then most substances to boil! Specific heat Water is a polar molecule because of the uneven sharing of electrons on the molecule. Oil is a non polar molecule because all of the electrons are shared equally and the overall charge is zero.

"like dissolves like"

Polar solvents (thing doing the dissolving) can dissolve polar solutes (thing being dissolved) only.

Non-polar solvents can dissolve non-polar solutes only. Liquid water Ice (solid water) Acids and Bases!!! Water you talking about?.... pH scale is short for "potential Hydrogen"

In other words its the the ability of a solution to attract Hydrogen. The pH scale is a numerical scale ranging from 1-14. 7 being the middle and labeled "neutral" 7 14 10 3 1 percent ions and type H+ OH- H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ H+ OH- OH- OH- OH- OH- OH- OH- OH- OH- OH- OH- OH- OH- OH- OH- OH- hmmm.... So essentially, acids are chalk full of hydronium (H+) ions which are highly reactive with other molecules, this makes them corrosive in a sense that they will reactive with and break up or change other things very easily Bases are chalk full of Hydroxide ions (OH-) that will attract easily any hydrogen ions. This makes them rip off hydrogen whenever they can. So strong acids are very hungry for Hydrogen and will thus tear them off whatever they can.... hence strong bases are ALSO corrosive. Buffers - chemicals that are capable of absorbing much of the acidic or basic ions. By absorbing these ions, buffers allow for solutions to become neutral or more neutral on the pH scale.
ex. Tums


Indicators are chemicals that will change color when in the presence of either an acid or a base. since their are already tons of H+ ions (hydrogen) do you think this solution will have a high or low ability to attract more? what pH is an acid? Since this solution has a lot of OH- ions, do you think it would be highly likely to go after Hydrogen? What pH is basic? Indicators! What can we use acids and bases for?
cleaners
paint thinners
soaps
cooking!
rotting your teeth (yodsel pay attention....) Polymer 4 Polymer 3 Lipids
Not really A POLYMER monomer 1 Lipids The more BONDS, the more energy is stored within the molecule!! There are 4 basic molecules made by these 4 elements that are the 4 basic "molecular building-blocks" of all cells. Monomer 2 Amino Acids monomer 3 monosaccarides Monomer 4 Nucleotides All Cells and LIFE Monomers and Polymers Fats, oils, and waxes.... Lipids just hanging out together! Lipids are NONPOLAR Do they mix well with water? Monomers are broken up into 4 major classes. Each of these classes will build a different class of polymers. Monomers are as their name implies.... a single unit polymers are as their name implies.... a group! a group of monomers in fact. Now here is where it gets confusing. Monomers are going to be called the "molecular building block". They will each act as a single lego block needed to build larger lego creations.... Yes atoms are the building blocks of all things. we are now in a larger class! atoms make each monomer.... NOW that we have established the monomers, we will use them as the base unit to build larger units... polymers. The 4 MONOMERS are classified as
1. Lipids
2. Mono-saccharides (glucose, simple sugars)
3. Amino Acids
4. Nucleotides
These 4 monomers build the POLYMERS
1. Larger Lipids (fats, oils, waxes)
2. Polysaccharides (starch, carbohydrates)
3. Proteins (SO MANY DIFFERENT KINDS)
4. Nucleic Acids (DNA and RNA) Lipids basic structure consisting of a glycerol head and a fatty acid tails. In order to build a polymer from several monomers, the monomers must be "glued" together in a chemical reaction.

This reaction is facilitated by ENZYMES, which are a biological catalyst. To glue monomers together you must perform DEHYDRATION SYNTHESIS DEHYDRATION means to remove water SYNTHESIS means to put together conversely, in order to break down a polymer into a monomer, you must perform hydrolysis HYDROLYSIS - Using water (hydro) to split or cut (lysis) What are other words that have mono as a prefix? First things first, please take 5 minutes and write a well written paragraph with complete sentences that uses the following key words. Atoms Compounds Elements Energy Organic Inorganic Bonds smaller molecules your paragraph should answer this question:
"When I look into the mirror what do I see? If I could look closer, what would I find, How did I come to be?" NEW!!! Saturated fats are typically solids and are derived from animals, while unsaturated fats are liquids and usually extracted from plants. Fatty acid tails are either saturated with hydrogen atoms or not saturated with hydrogen atoms... Fatty acids are NONPOLAR glycerol heads are polar what happens when they are placed in water? Why would this occur? Dehydration Synthesis
Monomers to Polymers Hydrolysis (digestion) Polymers to Monomers What are fats oils and waxes needed for? - Cell membranes
- Messenger molecules - some hormones
- Energy storage
- Insulation
- Wax on leaves - waterproofing
- Protection - skin oils! Lipids have long hydrophobic (nonpolar water fearing) tails and hydrophilic (water loving) heads. When placed in water, the water fearing (hydrophobic tails) try and run away from the water and hang out with each other. The water loving heads will be drawn to water. When all is said and done, the lipids create little bundles or balls that have their tails all protected from the water and the heads on the outside acting like a barrier... This is how soap traps non-polar dirt and oil from your hands. This is why washing your hands alot can strip you of your natural oils and dry out your skin.... amino acids are the smallest unit of a protein. there are 21 amino acids... Essential amino acids
Humans can produce 10 of the 20 amino acids. The others must be supplied in the food. Failure to obtain enough of even 1 of the 10 essential amino acids, those that we cannot make, results in degradation of the body's proteins—muscle, enzymes, cell structures and so forth—to obtain the one amino acid that is needed. Unlike fat and starch, the human body does not store excess amino acids for later use—the amino acids must be in the food every day. If you have 26 letters in the English dictionary, how many words can you make? how do you make new words? are all words the same size? do all words mean the same? Every Amino Acid.... Amino Group (NH3) Base Carbon with Hydrogen Carboxyl Group All 21 amino acids differ in their
"R" or "random" group... this is how each has different properties. Enzymes! Protein Machines!!! Okay, enzymes are a major aspect of all living things. Enzymes are BIOLOGICAL CATALYSTS.
This means they are made by the cell, and speed up reactions in the cell. Catalysts - anything that lowers the activation energy for a reaction to take place -temperature
-pH
-Enzyme concentration
-Substrate concentration All of these effect how fast a reaction takes place Enzymes reduce the amount of energy needed to start a reaction.... If some enzymes are not produced in the body, what effect could this have? Each enzyme has a specific site, with a specific shape that will accept the substrate. this activation site is SHAPE SPECIFIC to its substrate. Catabolic enzymes will break down a substrate into 2 or more procucts.... Where would expect to find alot of this type of enzyme? Anabolic enzymes will produce a single product from 2 or more substrates.... Where would expect to find this type of enzyme? Other very important and well known proteins are.... Hemoglobin (O2 transport)


Cell receptors (communication)


Antibodies (immune system)


Muscle Fibers (movement)


Channel Proteins (transport) Polar Charged (+ or -) Nonpolar Polar Uncharged What impact does the polarity of amino acids play? What is the importance of this? Proteins are looooooonnngggg chains of amino acids...every protein has a different sequence of amino acids. This is what allows each protein to have a different SHAPE and therefore a different FUNCTION ENVELOPE FUNCTIONAL PARTS GASOLINE INSTRUCTION MANUAL THE INSTRUCTION CODE FOR PROTEINS PROTEINS are the little machines and functional parts to a cell. They are what allow the cell to control reaction, have shape, receive signals and get needed materials.... Proteins, Shape Specific A protein's shape starts with its sequence of amino acids. This sequence can be 1000's of amino acids long in a single chain. Next because of the difference in charges of the "R" chains of each amino acid, the chain will begin to fold on itself. forming hydrogen bonds between the "R" chains of different amino acids The folding will continue until the entire chain of amino acids is folded into its "stable" form. This form resembles a blob.... The final stage of creating a functional protein is having multiple folded chains link together with each other to create the WHOLE protein with a VERY SPECIFIC SHAPE. Compared to CO2, H20, and even glucose, how big are proteins?

Support your answer with quantifiable data. ALL PROTEINS.... Why do temperature and pH affect enzymes rate? because they are proteins.... temperature and pH affect all proteins... Proteins, being long chains of amino acids are very shape specific.

their shape determines completely their function!

Change the shape.... change or lose the function! When a protein is heated or placed in too acidic or too basic a solution, the protein change can unfold!!! Unfolding of proteins occurs because either heat or ions are breaking the hydrogen bonds that are holding the chain of amino acids together in their specific folded shape. This is called DENATURING of proteins and its a one way street... once denatured the protein is done forever. can you un-fry an egg? There are a few forms of simple sugars... Glucose is the single unit that all your cells can use for energy!! (yaayyyyy glucose) Fructose can only be broken down by your liver.... and releases fats, acids, and radicals (bad, in large amounts....) Sucrose is the molecule formed when a glucose and a sucrose are linked together.... Sucrose is found in many fruits and veggies... lactose lactose is found in milk and dairies is a molecule made by linking two glucose molecules together. Homework: Please research sources of food that are high in fructose, sucrose, lactose and glucose. from this I want you to create a food chart that lists your food intake for the week. From this food chart, identify if you are eating a healthy diet or not. Write up your answer in a well written paragraph with complete sentences. Include:

- Food chart for the week (be honest!!)
- All your food choices listed out and labeled by what type of sugar they supply
- How healthy you think your diet is based on your knowledge of sugars
- what you can do to make it healthier
- site your sources Carbohydrates are loooong chains of simple sugars linked together. Starch is a long (100's) polymer of Glucose molecules, where all the sugars are oriented in the same direction. Starch is one of the primary sources of calories for humans.

Cellulose is a long (100's) polymer of Glucose molecules. However the orientation of the sugars is a little different. In Cellulose, every other sugar molecule is "upside-down". This small difference in structure makes a big difference in the way we use this molecule.

Glycogen is another Glucose polymer. Glycogen is a stored energy source, found in the Liver and muscles of Humans. Glycogen is different from both Starch and Cellulose in that the Glucose chain is branched or "forked". Starch is a great "slow burning" source of usable glucose molecules. Starchy foods are our main source of energy for our bodies. Cellulose is a source of STRUCTURE for plants!! it can also be used in all cells as part of the cell membrane. Cellulose is good in your diet because its very hard to break down. This "roughage" is an awesome food to help you poop.... glycogen is energy rich and usable stores of sugar in our muscles. When we run low on blood sugar we break this down into glucose and regain energy. this is often felt as a "second wind" Why do you think our body stores glycogen in our muscle tissue? Cytosine
Guanine
Adanine
Thymine Guanine
Cytosine
Uracil
Adanine Each nucleotide is made from a Sugar/Phosphate "backbone" and a Nitrogen Base The only variance between each of the nucleotides is the nitrogenous base.... RNA DNA More details in genetics..... Recap! With these four organic molecules combined You are able to build...
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