Enzymes and stuff.

Objs:
-What are enzymes
- Describe models to illustrate functions
-What do enzymes do?

Starch + Water = Amylase = Maltose

Lipid + Water = Lypase = Fatty Acid + Glycerol

Protein + Water = Protease = Amino Acids

Sucrose + Water = Sucrase = Fructose and Glucose

Maltose + Water = Maltase = Glucose

Big molecules being broken down into smaller ones = hydrolysis reaction, hydro: there should therefore, before the reactant should be water.

Substrate reacted with an enzyme = Products.

Enzyme = Biological Catalyst = speeds up reaction in living organisms

The body produces Hydrogen Peroxide. It is toxic for us, but we have an enzyme, catalayse, which breaks it down to make water and oxygen.

Molecules have more kinetic energy, collide more, but this is by heating. Can't heat up hydrogen peroxide, is in body, is why enzymes are handy.

An enzyme works by lowering the acitivation energy needed, which is a barrier to the rate of reation, therefore, the enzymes speed it up. (See catalyst.)

What do enzymes do?

Speed up reactions by lowering activation energy needed, which acts as a barrier.

Why are Enzymes Catalysts?

Substrate Energy is always higher then product energy. The barrier gets lowered with an enzyme. Enzymes are catalysts as they lower the activation energy required to drive a reaction.

The nature of Enzymes:

They are globular proteins. Globular proteins have a globular shape. If the shape is wrong, it won't function properly, if the tertiary structure is wrong. The tertiary fold relies on primary, as it is defined by the sequence of amino acids.

Enzymes are usually quite large, only a small area is important though. The active site: a specific shape due to the way it folds up. If something affects the active site, the enzyme will not be functional.

Enzyme + Substrate = Enzyme Substrate Complex + Products.

The substrate and enzyme have COMPLIMENTARY shapes. Like jigsaw pieces, they fit together, but they aren't identical.

At the end, the enzyme is unchanged and can be reused, whereas products diffuse away.

Enzyme + Substrate = Enzyme Substrate Complex, REACTION TAKES PLACE = Enzyme + Products.

Enzymes are:

• Proteins of high molecular weight.
  
• A bio-catalyst.
  
• Sensitive to temperature changes.
  
• Sensitive to pH
  

Enzyme and substrate have to hit at right force AND be of complimentary shape.

Models...

Lock and Key model, 1894, if there's not a specific key in the lock, the door won't open style metaphor. In an enzyme catalysed reaction the enzyme bonds to the substrate to form a complex.

Induced Fit Model, a glove is vaguely the same shape as a hand, when a hand is in the glove the fit 'induces' to fit it. Explains that the enzyme changes shape, and takes into account that they have some flexibility.

Once the substrate has bound to the enzyme, that bind tells the enzymes to change the shape to therefore become a perfect fit. Therefore, a reaction can't take place until the induced fit has happened.

Oh, and this was a side note, 'Saw chancges take place with x-ray defraction, therefore, better model.' Don't have a clue what I was on about. Suggestions?

-Nin.

A homework that I thought may be of use. Osmosis and that,

Active Transport - is energy requiring transport of molecules pr ions against a concentration gradient. It needs energy from respiration. An example is the resorption of Na in the kidney.

Exocytosis - is a process exporting large molecules from the cell. A secretory vessel is formed, and it is a type of bulk transport. An example of this is the secretion of digestive enzymes by cells in the pancreas.

Facilitated Diffusion- is diffusion through hydrophyllic protein channels. A protein carrier transports the molecules down a concentration gradient. It is a passive process. An example is the movement of glucose into cells.

Osmosis- is the net movement of water molecules down a water potential gradient through a partially permeable membrane. It is a passive process. An example of this is a red blood cell losing water when placed in a hypertonic solution.

Simple diffusion - is the net movement of molecules from a region of higher concentration to lower concentration down a concentration gradient. The molecules or ions move down a concentration gradient. Therefore it is a passive process. An example of this is the movement of respiratory gases between the alveoli and blood capillaries.

Phagocytosis- is the uptake of solid material into a cell. It is a type of bulk transport and a phagocytotic vessle is formed. An example of which is a white blood cell engulfing bacterium.

Pinocytosis- is the uptake of liquid into cell. It is a type of bulk transport, and small vacuoles or vesicles are formed. An example of this is a human egg taking up nutrients that surround it.

Proteins and Protein Structure. :D

Two types of proteins, Globular and Structural.

Enzymes are catalysts that specifically increase reaction rates by as much as 10 (to the power of) 6. They are proteins. Other examples are Regulatory Proteins, Contractile and Motile Proteins, which allow cell and tissue movement. Actin and Mysoin in muscles. Protective Proteins, like antibodies. The little sea creatures, muscles, have proteins that allow the to attach to rocks. Fish have proteins that allow them to swim if freezing temperatures. Hemoglobin is in red blood cells, it transports oxygen to tissues, and Fibrin aids in blood clotting.

Amino Acids are the building blocks of proteins. They are monomers. 'Mono' means 'Single'. 'Mer' means 'Unit'. (Can you kinda see how the name applies?)

A chain of these is a polypeptide. 'Poly' meaning many.

Some proteins can be more then one polypeptide. Like Hemoglobin which is four combined together.

Lipids aren't polymers, they are big, but aren't lots of repeating units.

Amino Acids...

• Carbon
• Nitrogen
• Oxygen
  
• Hydrogen.
  

All have those basic elements. Some many have different ones such as Sulfur or Phosphorus.

Approximately 20 naturally occurring amino acids exist, so there is huge variation in polypeptide chains.

The basica structure of a amino acid is as follows: On the left, an Amino group (Nitrogen, with 2 single bonded hydrogen.) This is singley bonded to a Carbon, which is single bonded to a hydrogen, the R Group, which I will desribe next, and on the right, singley bonded to a Carboxylic Acid group. (As said before this is a singley bonded carbon and 'OH' with a double bonded oxygen.

The R group is the variable. It vaires from one amino to the next to give the different function or proerties. It can be as simple as just 'H' (Glycine), or CH3 (Adenine). They give different, specific properties like size, shape, charge, etc.

They are joined in a condensation reation. (Read a few posts below for my comment about those.)

The way they bond is that a bond goes from the carbonto the nitrogen in the condensation reaction. This is called a peptide bond.

Two amino acids joining together is a Dipeptide.


So, comment and coreect me or whatever. Critism is welcomed, help is to. Aiming for an A in this overall so any useful info is good. D:
-Nin. ^__^

Homework Notes. :D Mito and such.

Mitochondria:

1. Site of respiration that produces ATP.
   
2. Epithelial Cells use a lot of respiration due to active transport.
   
3. They are for absorption and products of digestion, this is the purpose of the cell, mito aids this.
   

Bile: Neutralises stomach acid, making the conditions alkaline, This allows the enzymes in the small intestine to work properly ,as they one work in small pH ranges.

Conditions of Centrifugation:

1. Cold: Reduces the ezyme activity that could damage organelles. Also stops bacterial Growth.
   
2. Isotonic: Maintains same water potential inside and outside of cell to prevent it from bursting or shrinking.
3. Buffer: To maintain pH, as enzymes only work in a certain pH range.
   

You divide by 1000 to get um into mm

Stuff about osmosis, water potential and active transport, in a big bulk of notes. ^_^

Distilled water has a higher water potential. It would be less of a negative water potential then in say... potato cells. Therefore, it diffuses in by osmosis, and the potato cells would swell and become turgid.

Turgid is once again, another one of those happy words that examiners would seem to dote on. xP

Yay. (:

Sucrose has a lower water potential then in the same potato cells, therefore, water would diffuses out of the potato cells by osmosis, and the cells will shrink and become plasmolysed. (Yes, that is another of those 'words'.)

Anymore water diffusing in by osmosis on a cell that has reached maximum turgidity will be forced the opposing pressure of the cell wall.

In sucrose, little or no water would remain in these potato cells. The cell wall would not be able to shrink any further.

The rate of change would be determined from an initial part of a graph as the initial part is linear, so it will be constant, and as time goes on the water potential of the cell will change and therefore slow, so it would be easier to compare all from the beginning.

Active Transport :

With diffusion, osmosis and facilitated diffusion, they are all passive, and it moves in/out of the cell. Active transport is different in that it is not passive, it requires ATP (see previous posts), it is definitively more complex, and it goes against a concentration gradient.

It is carrier assisted, which means protein carriers are present. It requires energy to move the molecules against their concentration gradient.

What whats to go through, fits on to the carrier with the specific gap/shape. The ATP comes along and splits into ADP + Pi + energy. The energy attaches and changes the shape, and then the thing that wants to go through goes through.

Endocytosis means going in ti the cell. If it is a solid it is called phagocytosis, and if it is a liquid/fine suspension, it is pinocytosis. Exocytosis means going out of the cell.

Transport Across the Membrane. ^__^

Diffusion and Facilitated Diffusion.

Hydrophobic small and uncharged could pass through a membrane, but larger ones has more difficulty.

Simple Diffusion: Where molecules diffuse across the lipid bilayer through channel proteins in the direction of their concentration gradient.

Facilitated Diffusion: Where protein carrier molecules within the membrane assist the passage of substances across the membrane in the direction of the concentration gradient.

All methods above are passive, which means no cellular energy is required.

Concentration Gradient means that stuff from areas where there a lot goes into the areas where there's more little. Kinda to even things out a bit.

The bigger the difference between one side of molecule, the bigger/ more dramatic the net movement. [AN: So, basically, if there's more to shift, it puts more into doing it and gets the job done quicker, right?]

Diffusion is continued until equilibrium is reached.

It is chance that it hits are protein channel in facilitated, so wit ha higher concentration/amount of ions/molecules, the higher the chance of hitting the channel.

If they can pass through the lipid bilayer they are lipid soluble.

The larger the surface area, the more diffusion that can take place.

If the temperature is higher there is more kinetic energy, so the particles move quicker and there is more collisions. (Link this to before paragraph.)

Steepness of concentration gradient also affects it. If it is lower, diffusion will be less strong/quicker.

The membrane thickness affects the rate of diffusion too. The thicker the membrane, the longer it takes, as there's more to travel through.

Fick's Law states that the Rate Of Diffusion = (Surface Area x Steepness of Concentration Gradient) / Thickness of Membrane.

In facilitated diffusion there are CARRIER MOLECULES involved. When carier molecules have reached their limit, they can't transport any more. Eg, like only being able to fit two kids in a double buggy. Unless you take one out, only then can another take it's place.


Thoughts & Additions?
-Nin. ^_^

Triglycerides and all that jazz.

Obj- To be able to draw and label the components of a Triglyceride.

Lipids - Biochem of Biological Molecules.

Lipids are a diverse collection of substances. They are an excellent energy store. Hibernating animals use them to store nutrients as fats. They are found in seeds/the fruit of a plant.

They are used for:

1. Energy Storage.
   
2. Insulation - useful, conducts heat slowly.
   
3. Source of metabolic water- fats oxidised in respiration and make water. Deserts animals such as camels store fats as a source of this.

Lipids are not soluble in water, they are in organic liquids though, like ethanol.

A triglyceride, is glycerol, with 3 fats attached.

The difference between an oil and a fat is that an oil is a liquid at room temperature whereas a fat is a solid.

Glyderol is usually called a hydrocarbon, thanks to it's structure:

H
-
H- C - OH
-
H- C - OH
-
H- C - OH
-
H

If there are 3 hydrogens attached to a carbon, this structure is called a Methyl group. The -OH is a Hydroxyl group, wihch is the one found in alcohols. Therefore, Glycerol is a three carbon, alcohol molecule.

Fatty acids are hydrocarbons chains of varying length with a methyl group at one end and a carboxylic acid group at the other.

Methyl is a carbon with three single bonded hydrogens. Carboxylic acids is an 'Oh' single bonded to a carbon, with a double bonded oxygen.

COOH, means something is an acid.

Saturated fatty acid = Get a fat in triglyceride. (Yea, I don't get this bit of my note. Kersplain, someones?)

Unsaturated: Got double bonds, less saturated with 'H' atoms. Not as many particles that can move betweens each other can't become more squished and rigid, so becomes liquid, not solid. Also has a far lower melting point.

[AN: Surely with would mean Fats are saturated and Oils aren't? Yea? Comment and help???]

The more double bonds, the lower the melting point. [WHY?]

A triglyceride forms in a condensation reaction. If you're ever in doubt, write condensation reaction. Or at least, this is what my notes say. Lets go along with that one, shall we?

Anyway, it forms an 'o', or oxygen bond inbetween, which has a name, an esther bond.

To test for lipids, we use the Lipid Emulsion Test. To do this, we:

1. Take the material/sample, and put in the a test tube.
   
2. Add to this approx 2cm[cubed] of ethanol and shake. (Vigorously will do. xP)
   
3. Add 2cm[cubed] of water, and ...
   

If a MILKY EMULSION forms, this is a positive indictation of a lipid's presence.



Like usual, correct me, should I be wrong. I'm only an AS student, as I've said. (:
-Nin.

Magnification (Realllllly no notes whatsoever.)

Magnification = What you see/ Actual size.

The '/' represents divide, since, after like, 11 years around computers, I only just realised there's no divide sign on a keyboard.

Anyway, you can put it in a handy little triangle too. A bit the the distance speed time one at GCSE? It spells out IAM with the 'I' at the top, the 'A' on the left, bottom, and the 'M' on the right bottom. Cover up one letter to figure out which ever way round you need to put the equation for your question.

So yeah, short post.
-Nin

Cell fractionation and Ultracentrifugation.

Pg 41/42 in AQA Bio textbook. (They're the ones we use at QE, so if you're from there, that bit of info is for you.)

Obj- To describe the process and the resultant separation of cell components.

Cell fractionation is where cells are broken up and the organelles they contain are separated out.

1. HOMOGENATION: The cell is broken up by a homogeniser (big spinny thing, bit like a food liquidiser, only a little bit more high-tech. xP) The resultant fluid is called homogenate.
2. ULTRACENTRIFUGATION: Fragments of the homogenate are separated. rganelles get sedimented and seperated in order of density. (Not heaviness. Exam board people don't like heaviness. :D)

The three conditions of the whole thing are:

1. Temperature: Really low to prevent bacterial growth, but the main reason is to slow down any enzymes that may damage the organelles.
2. Isotonic Solution: Makes sure it has the same water protentail as the tissue to preven organelles from bursting or shrinking.
3. Buffered: Maintains a constant pH (Why???? )

The solid pellet at the bottom are centrifugation is called a supernatant.

It goes down a density gradient, For example: Nucleus, Mitochondria, Lysosomes, Membrane, Ribosomes.

The faster it is spun in centrifugation, the lighter the organelles that get separated/isolated, so it is spun with gradually increasing speed to get the denser ones first.

This is useful for finiding out the function, but not 100% perfect.

And remeber, correct me where I'm wrong. It helps. (:

-Nin.

The Electron Microscopeyyyy. ^_^

Obj- To describe the priciples and limitations of the Trasmission Electron Microscope, and the Scanning Electron Micrscope.

Cell surface membrane. Acts as a barrier (things go out and in). Smooth endoplasmic reticulum synthesises LIPIDS. (aka Fats.) [AN: See previous post, I asked about this part, yeah, probbem solved, will go back and correct in a bit.]

Magnification: Increases size, not deatil, only what you see increases in size.

Resolution: Allows you to see things close up, or closer together. Puts things into more detail.

The resolution depends on the wavelength of the illuminating source (i.e. the visible light from electrons.)

Resolution = 1/2 the Wavelength.

E.g. : A light has a wavelength of 500nm, the resolution would therefore be 250 nm.

Or: Electrons wavelength is 0.2nm, therefore, the resolution would be 0.1nm

Advantages of electron microscope:

• Greater resolution, see in more detail.
• Higher magnification (x500,000)

Disadvatages:

• Specimens are dead. *
• Artefacts (other things from outside, deposits, etc...) can be present.
• Preparation of the specimen is complex, and time consuming.
• Very expensive equiptment.
• Need a very specifically thin specimen.

*The tissue must be dead as it is in a vacuum. No oxygen, therefore, living organisms can't survive.

• Organelle shapes can be distored by this vacuum.
• See it from different angles, as it is 2D

Transmission Electron Miscroscope: Electron beam passes through specimen onto fluorescent plate onto photographic paper. 2D, and has higher resolution.

Scanning Electron Microscope: Electrons atr reflected from surface to get a 360 degree/ 3D view. Specimens can be thicker so electrons don't need to pass through. Lower resolution, 20nm. Still 10x better then light/optical, not better resoltion then a transmission electron microscope, but gives a much better image.

In the bit above, I /think/ the advantages/disadvantages are for the TEM only, as the SEM doesn't need a thin specimen, so yeah, once again, correct if wrong, or give extra info if you like. REmember, I'm only typing this up from my notes taken in class. ^___^

-Nin.

Organelles and other such bits. (:

Organelles are the bits that make the cell more efficient and designed for it's purpose.

Epithelial cells, which we are focusing on, are speificated to secrete and absorb in the small intestine. They line the small intestine in an epithelial layer, about 1mm in thickness. They have microvilli (little flappy hair type bits on the top, a bit like the tassley bits on the end of a scarf, I guess?) are there top increase surface area, so more can be absorbed.

Part of the cell...

Nucleus; They control activity in the cell, direct protein synthesis, contain cromatin (which is DNA and proteins, diffused together.) Cromatin condenses and becomes thicker into the usual chromosome shape.

It also makes RNA, which makes ribosomes.

Nuclear Envelope; Is a double membrane with little gaps along it called nuclear pores, these allow the nucleus to communicate with the cytoplasm.

Endo-plasmic Reticulum; Comes in two varieties, Rough and Smooth. Rough is named so becuase it has ribosomes attached on it. It transports material throughout the cell. Used for the synthesis of proteins and can be used as a passway for proteins after.

There are no ribosomes on the smooth endoplasmic reticulum. They transport, produce and store lipids, and some carbohydrates. In the liver the smooth endoplasmic reticulum aids with detoxification.

Boths need to produce enzymes and absorb, in relation the an epithelial cell, that is, as it's purpose is the absorb and produce.

Ribosomes; Can exist on their own or in chains (polyribosome) in the cytoplasm. Made by nucleolous. Made my two units, RNA & Protein, in a cottage loaf type shape.

In relation the the epithelial cells, they have 80's ribosomes, they are bigger and sediment faster.

Golgi Apparatus; Have vesicles on the end, ready to bud off. Made of flattened sacs, called cisternae. It collects the products of the cell, which I believe are lysosomes, not 100% sure, someone correct me if I'm wrong, repackages them into vesicles to transport around & out of the cell. Modifies proteins produced by the endoplasmic reticulum. Collection, Modification, Packaging & Distribution. (:

Lysosome; A lot of enzymes in them. One membrane thick, can contain up to 50 different enzymes. Used for breaking other things down, like other cells and worn down organelles. Releasesthe content to the outsidde of the cell by fusing with it. Phagocites (they engulf and digest bad bacteria) can help them along.

Mitochondrion; 1-10mm in length, double membrane. Space between membrane is the inner membrane space, forms folds, folds are called Cristae. These are the site of ATP production, enzyemes that form it are situated there, in aerobic respiriation. Inbetween the folds is a called the matrix. This is the site of the krebs cycles. Has it's on DNA & ribosomes, /can/ produce own protein. Epithelial need lots of them as they use lots of ATP which is stored in mitochondria. More christae = more ATP. ATP = Energy ^_^

Cells (:

Revise GCSE, label and desribe a typical cell function.

Animal: Have nucleus, cell membrane, and cytoplasm. The nucleus has the nuclear membrance & envelope, and it contains DNA and chromatin. There is the cell surface membrane around the outside. In the cytoplasm there are enyzmes to catalyse reactions, and ribosomes to make protiens. The pores around the nucleus allow connection to the rest of the cell, and mRNA to pass through. Mitochondria also exist in animal cells, which aid in respiration (aerobic).

Plant: Has a cell membrance, vacuole, cytoplasm, mitochondria (or mitochondrion, singularly.) Chloroplasts, a nucleus, and a cell wall for stability.