Biochemistry Review animasi

Topics:

A. Chemistry of Life (7%)

  1. Water
  2. Organic molecules in organisms
  3. Free energy changes
  4. Enzymes

JMcL.Proteins are very important biomolecules whose ability to carry out their functions is often dependent upon their shape. Examples would include enzymes, protein receptors, hormones and antibodies. An understanding of their shape is therefore very important.
Proteins show four different levels of protein structure:

1. Primary: refers to the unique sequence of amino acids in the protein. All proteins have a special sequence of amino acids, this sequence is derived from the cell's DNA.

2. Secondary : the coiling or bending of the polypeptide into sheets is referred to the proteins secondary structure. alpha helix or a beta pleated sheet are the basic forms of this level. They can exist separately or jointly in a protein.

3. Tertiary: The folding back of a molecule upon itself and held together by disulfide bridges and hydrogen bonds. This adds to the proteins stability.

4. Quaternary: Complex structure formed by the interaction of 2 or more polypeptide chains.



external image 12641392801203977540Main_protein_structure_levels_en.svg.hi.png

MAP
Functional groups

Structure
Name of Compound
Functional Properties
Hydroxyl
– OH
Alcohols
Example: ethanol, methanol
  • Polar
  • Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars
  • Hydrophilic
Carbonyl
O
/
-- C
\
Ketones and Aldehydes
  • Ketones: carbonyl group within carbon skeleton. Example: Acetone
  • Aldehydes: carbonyl group at end of carbon skeleton. Example: Propanel
  • Both may be isomers
  • Both found in sugars
  • hydrophilic
Carboxyl
O
/
-- C
\
OH
Carboxylic acids
Example: acetic acid, fatty acids and sugars
  • has acidic properties
  • tends to ionize
  • has source of H+ ions
  • polar
  • hyrdophilic
Amino
H
/
– N
\
H
Amines
Example: glycine
*compunds with both a carboxyl and amino groups are called amino acids
  • acts as a base
  • hydrophilic
Sulfhydryl
– SH
Thiols
Example: cysteine
  • forms disulfide bridges in proteins
  • hydrophilic
Phosphate
O
l l
-- O -- P -- O¯
l

Organic Phosphates
Example: ATP, DNA and phospholipids
  • contributes negative charge to molecule
  • hydrophilic
Methyl
H
l
-- C -- Hl
H
Methylated compounds
  • not reactive
  • often acts as a recognizable tag on biological molecules
Functional groups was something i especially had trouble with. It's important to be able to recognize them, and also knowing certain properties about each is important.

WMWOODS:
Heres a picture out of my review book, "Cracking the AP Biology Exam", which shows the structures of the listed above, and other functional groups. Sadly my computer would not let me turn the image to be vertical.

photo-7.JPG

Happy Studying!

RP. Chemical Bonds are what hold atoms together to form molecules. They form from the interactions between the valence electrons of various atoms. Covalent bonds occur when the valence electrons are shared between the two atoms. Nonpolar covalent bonds involve an equal sharing of electrons between atoms, and they are usually the same atom (such as H-H). Polar covalent bonds occur when one atom has a greater electronegativity (meaning it tends to attract electrons to itself). A good example of this is water. Ionic bonds involve great electronegativity, to the point where one atom takes the valence electrons of another (sounds pretty mean, doesn't it?). Ionic bonds always form salts. Other types of bonds exist, but there are the main ones.

~ JM
Unique Characteristics of water:
1. Cohesion: is the sticking together of similar molecules. Water is very cohesive. This allows water to be pulled along a pathway with relative ease.
2. Surface Tension: cohesion allows water to pull together and form droplets or form an interface between it and other surfaces. The measure of how hard it is to break this interface is its surface tension.
Water allows materials to rest upon it if the surface tension is not broken. Pollen, dust, water insects, and other biological materials are able to remain on the surface of the water because of this tension.
3. Adhesion: The sticking of one substance to another. Water is a good adhesive. It will cling on to many objects and act as a glue. Capillary Action is an example of cohesion and adhesion working together to move water up a thin tube.
4. Imbibition: The process of soaking into a hydrophilic substance. Water being taken into a sponge, into a seed, into paper towels.
5. High Specific Heat: Specific heat of a substance is the heat needed (gained or lost) to change the temperature of 1g. of a substance 1degree Celsius. Heat is the total quantity of kinetic energy due to molecular motion. Temperature measures the intensity of the average kinetic energy of the molecules.Heat and temperature are not the same thing. A Kilocalorie or large C equals 1,000 small calories.It takes 1,000 calories to raise 1,000g. of water 1 degree C. Nutritional Packaging has the calorie measurements in Kilocalories. One gram of Protein = 3 calories. This means 3,000 small calories or 3 Kilocalories.
This high specific heat allows water to act as a heat sink. Water will retain its temperature after absorbing large amounts of heat, and retain its temperature after losing equally large amounts of heat. The reason for this is that Hydrogen bonds must absorb heat to break. They must release heat when they form.The Ocean acts as a tremendous heat sink to moderate the earth's temperature.
6. High Heat of Vaporization: Water must absorb a certain amount of additional heat to change from a liquid into a gas. This extra heat is called heat of vaporization. In humans, this value is 576 cal/g. This results in evaporative cooling of the surface. Alcohol has a value of 237cal/g. and chloroform 59cal/g.
As one can see water removes much more heat from a surface upon evaporation than does either alcohol or chloroform.
7. Freezing and Expansion of Water: Water is most dense at 4 degrees C. At ) degrees C. it is 10% less dense. Ice floats because maximum Hydrogen bonding occurs at 0 degrees C.
8. Versatile Solvent: Water is a major solvent in nature. When water and another substance is mixed the resulting solution is called an aqueous solution


WJH
When I was going through my Biochemistry quizzes and tests I realized most of the questions I was getting wrong were ones about the effects of enzymes on chemical reactions.

http://www.youtube.com/watch?v=PILzvT3spCQ
This video does a pretty good job of explaining how an enzyme & it's substrate interact. It also explains competitive and noncompetitive inhibition.

I think it's important to know how different factors affect the catalytic activity of enzymes as well.

Temperature
Graph of enzyme activity verses temperature
Graph of enzyme activity verses temperature

As the temperature rises, this increases the chances of a successful collision between the reacting molecules. There is a certain temperature at which an enzyme's catalytic activity is at its greatest. Above this temperature the enzyme structure begins to break down (denature) since at higher temperatures intra- and intermolecular bonds are broken.

PH
Graph of enzyme activity verses pH
Graph of enzyme activity verses pH

Most enzymes work in a very small range of PH because PH can make or break the bonds of reacting molecules, changing the shape of the enzyme and it's effectiveness. Each enzyme has an optimal PH, where activity will be greatest.

Concentration of Enzyme and Substrate

Graph of enzyme activity verses enzyme concentration
Graph of enzyme activity verses enzyme concentration


Graph of enzyme activity verses substrate concentration
Graph of enzyme activity verses substrate concentration










http://www.rsc.org/Education/Teachers/Resources/cfb/enzymes.htm


JJS
I have always been confused with the difference between acids and bases.
Though part of this is just remembering the definitions, the concept is one that repeatedly arises in biology.
Acids are substances that increase the hydrogen ion (H+) concentration of a solution.
Bases are substances that reduce the hydrogen ion concentration of a solution.
In other words, a solution with a higher concentration of OH- than H+ is a basic solution.
A solution with equal concentrations of H+ and OH- is neutral.

ABM
Having just looked through my quizzes, tests, and lab reports, I've noticed that I really don't understand water potential, but I was able to find a video that does a pretty good job of explaining it.
http://www.youtube.com/watch?v=cd2H1sG0y1I

EGR
As I have been studying biochemistry more, my mind has really been refreshed as to just how important carbon is. First off, carbon molecules are in several functional groups (carboxyl and carbonyl) but are also important, in the sense that functional groups attach to carbon skeletons, to make larger and more complex molecules.

A few important facts to note about carbon:
- It has four valence electrons (6 electrons filled, 2 in first level then 4 in the next)
- It can form up to 4 covalent bonds
- Its bonds can be single, double, or triple covalent bonds
- Because of these many bonding possibilities, carbon can form large molecules
- The large molecules created can be branched, ring-shaped, or chains

This website provides some decent examples as to what different shapes of carbon can look like:
http://www.edinformatics.com/math_science/c_molecule.htm

JFMcL. It is also important to remember the tetrahedral shape of carbon. That is what causes the moleculkes made of carbon to have 3 dimensional shapes.
Tetrahedral structure
Tetrahedral structure



MAP
So i have been going through my quizzes and such on biochemistry and one thing i keep getting confused with is dehydration synthesis and hydrolyisis. It is a very simple topic but for some reason my mind was having trouble picking up on it. I understand both of the terms in that dehydration is the removal of water and hydrolysis is the addition of water but what i was confused on is which reaction forms polymers and which one splits them.
Dehydration reactions create polymers from monomers. Two monomers are joined by removing one molecule of water.mail.jpg So this diagram is showing a dehydration reaction where two molecules are joining by removing a water molecule.
Hydrolysis occurs when water is added to split large molecules. In the above diagram if the arrow was going in the opposite direction then the diagram would show hydrolysis. Also something to help remember... "lysis" means to break down (destruct, decompose) thinking of this helps me

SMM
As I've been reviewing the biochem I've had a hard time keeping all of the functions of the organic molecules straight, and I find it easier to study them when they are organized into a chart.
external image 112415830.png
RMG
So i had trouble with remembering enzyme examples so i looked up the naming process of enzymes and found a few simple examples.
The names of enzymes often include the substrate or substance on which they act, joined with an -ase ending. For example, lactase acts upon lactose and maltase acts on maltose to produce glucose. Sometimes they are named for their reaction product, for example, sucrase is often called invertase, because invertase is the result of the reaction of sucrose. Enzymes can also bear a name that describes the reaction that is catalyzed. An example of this includes the use of the name oxidase, because oxidase is involved in an oxidation reaction.


MFT



Water potential = pressure potential + solute potential



Pressure potential : Basically, it is what it sounds like: pressure on a cell or solution. In plant cells, the presence of the water creates pressure on the cell wall. That pressure is turgor pressure, and it keeps the plant cell from bursting.



Solute potential (also called osmotic potential) : Simply, the tendency of water to move from an area of high concentration to low concentration (osmosis). The solute potential of pure water is 0. When there is more solute added, water potential is lowered due to the solute potential being negative. Solute potential is always proportional to the molarity of the solution



Combined, these make up water potential.



For some reason I never really understood this before. Most of this information came is in our textbook, but there is also an animation of it on Lab Bench:

http://www.phschool.com/science/biology_place/labbench/lab1/watpot.html

CCA
Energy was one of the first topics that we learned and I had forgotten many of the definitions for simple terms, especially the role of free energy. Got all the info from the review book

Energy is the capacity to do work and anything that is moving is said to have kinetic energy. If an object is at rest, it is said to have potential energy. Chemical energy is a form of potential energy that is stored in chemical bonds and released when they are broken.
The first law of thermodynamics states that energy can neither be created or destroyed, but rather it is transformed and transferred.
The second law of thermodynamics states that every transfer or transformation of energy increases the entropy, or amount of randomness and disorder in the universe.

Free energy is the part of a system's energy that is able to perform work when the temperature of a system is uniform. The free energy change of a reaction tells us whether the reaction occurs spontaneously. It includes exergonic reactions that occur spontaneously in which free energy is released into the system. It also includes endergonic reactions which require free energy that they absolrb from the system in order to proceed.

EJG
Just wanted to quickly draw the differences between the enzyme competitive inhibitors and the noncompetitive inhibitors. As I was reviewing, I came across this topic and felt the need to elaborate.
Competitive Inhibitors:
  • reversible - the binding of the competitive inhibitor with the active site of the enzyme produces no chemical result and the enzyme does not change shape
  • compete with the substrate for the active site
  • chemically similar to substrate
  • reduce enzyme efficiency
  • if one increases the concentration of the substrate, the substrate can out-compete the inhibitor
Non-Competitive Inhibitors:
  • do not compete with substrate for the active site
  • bind to any other part of the enzyme
  • the enzyme then changes shape and renders the active site useless
  • increasing the substrate to inhibitor ratio will not stop the inhibitor from acting on the enzymes
  • the shape changes is due to the inhibitor attaching to a side group of the protein (enzyme) which affects the tertiary structure of the protein
Summarized by Eva Golden

KGT
I always had trouble distinguishing between saturated fatty acids and unsaturated fatty acids. Here's a quick little summary to help:
Saturated Fatty Acids:
  • have no double bonds between carbons
  • tend to pack solidly at room temperature
  • are linked to cardiovascular disease
  • are commonly produced by animals
  • examples include butter and lard

Unsaturated Fatty Acids:
  • have some carbon double bonds which result in kinks
  • tend to be liquid at room temperature
  • are commonly produced by plants
  • examples include corn oil and olive oil

external image fatty_acids.jpg

ELB
This is a funny way to look at it, but the picture differentiates cohesion from adhesion clearly. Cohesion is when molecules of the same substance, such as water, stick together. Adhesion is when molecules of one substance stick to molecules of another, in this case water and the surface of a leaf.
external image adhesion-cohesion-2.gif
http://ga.water.usgs.gov/edu/adhesion.html

TWK
Purines vs. Pyrimidines -- on the tests I was never able to remember the difference between their structure.
Purines (Adenine and Guanine) have 2 carbon-nitrogen rings while pyrimidines (Cytosine, Thymine, and Uracil) have only 1
Below is a picture that shows this.
The Purines
Adenine

Guanine
external image Adenine.gif

external image Guanine.gif
The Pyrimidines
Cytosine
Thymine
Uracil
external image Cytosine.gif
external image Thymine.gif
external image Uracil.gif

SMM.
I always find it difficult to differentiate between the 3prime and 5prime ends of the DNA helix. This diagram shows how DNA strands fit together. It also shows nucleotide structure.
DNA Nucleotides are made up of:
-phosphate group
-pentose sugar: Deoxyribose (has one less Oxygen than Ribose)
-nitrogen base (Adenine/Thymine or Cytosine/Guanine)
RNA Nucleotides are composed of:
-phosphate group
-pentose sugar: Ribose
-nitrogen base (Adenine/Uracil or Cytosine/Guanine)
external image Image122.gif
<http://hshgp.genome.washington.edu/teacher_resources/Image122.gif>
&information taken from class notes

VBG
No matter how long I stare at a page explaining amino acids i can never understand them.

Amino acids play central roles both as building blocks of proteins and as intermediates in metabolism. The 20 amino acids that are found within proteins convey a vast array of chemical versatility.
Tertiary Structure of a protein
Tertiary Structure of a protein
The precise amino acid content, and the sequence of those amino acids, of a specific protein, is determined by the sequence of the bases in the gene that encodes that protein. The chemical properties of the amino acids of proteins determine the biological activity of the protein. Proteins not only catalyze all (or most) of the reactions in living cells, they control virtually all cellular process. In addition, proteins contain within their amino acid sequences the necessary information to determine how that protein will fold into a three dimensional structure, and the stability of the resulting structure. The field of protein folding and stability has been a critically important area of research for years, and remains today one of the great unsolved mysteries. It is, however, being actively investigated, and progress is being made every day.

As we learn about amino acids, it is important to keep in mind that one of the more important reasons to understand amino acid structure and properties is to be able to understand protein structure and properties. We will see that the vastly complex characteristics of even a small, relatively simple, protein are a composite of the properties of the amino acids which comprise the protein.

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 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.
The 10 amino acids that we can produce are alanine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine and tyrosine. Tyrosine is produced from phenylalanine, so if the diet is deficient in phenylalanine, tyrosine will be required as well. The essential amino acids are arginine (required for the young, but not for adults), histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. These amino acids are required in the diet. Plants, of course, must be able to make all the amino acids. Humans, on the other hand, do not have all the the enzymes required for the biosynthesis of all of the amino acids.
Why learn these structures and properties?

It is critical that all students of the life sciences know well the structure and chemistry of the amino acids and other building blocks of biological molecules. Otherwise, it is impossible to think or talk sensibly about proteins and enzymes, or the nucleic acids.
http://apbiologywiki.wikispaces.com/Biochemistry+Review

VBG
A diagram of glycolysis
To summarize, overall, in the process of glycolysis:
Glucose
Glucose

Glucose (C6H12O6)
arrow
arrow

Pyruvic Acid
Pyruvic Acid
Pyruvic Acid
Pyruvic Acid

2 Pyruvic Acid (written as either C3H4O3 or CH3COCOOH) molecules
+
Four Hydrogens
Four Hydrogens

4 H+ + 4 e
and then 2 of those electrons and one hydrogen ion combine with a NAD+ molecule to form NADH, leaving behind a hydrogen ion (H+), × 2 for the whole glucose molecule, so
NAD+ + 2 H
NAD+ + 2 H
+
NAD+ + 2 H
NAD+ + 2 H

arrow
arrow

NADH + H+
NADH + H+
+
NADH + H+
NADH + H+

4 H+ + 4 e + 2 NAD+ → 2 NADH + 2 H+
+ energy which is stored by making a net total of 2 ATP molecules, so:
ADP and Phosphate
ADP and Phosphate
ADP and Phosphate
ADP and Phosphate

arrow
arrow

ATP
ATP

H2O
H2O
H2O
H2O

(2 ADP + 2 → 2 ATP + 2 H2O)
So, overall:
C6H12O6 + 2 NAD+ + 2 AMP-PO3H2 + 2 H3PO4 → 2 C3H4O3 + 2 NADH + 2 H+ + 2 AMP-PO3H-PO3H2 + 2 H2O
(Note that, to make it easier to see what’s going on here, these molecules have all been shown with all of their hydrogens attached. However, for those of you who have had some chemistry, technically, in “real life,” just like HCl is really H+ + Cl, so also some of the hydrogen protons on the pyruvic acid, the lactic acid (below), and the ATP are really detached as H+ ions, leaving their electrons behind. If you haven’t had chemistry, don’t get stressed out over this technicality.)
http://biology.clc.uc.edu/courses/bio104/cellresp.htm

RAM: Adding on to ATP synthesis post, I found a step by step process that shows how the process of ATP synthesis and how exactly it works inside the mitochondria
http://vcell.ndsu.nodak.edu/animations/atpgradient/first.htm

LJ: I often get pH confused. I tend to forget that it is a logarithmic scale. The scale ranges from 0-14. Solutions with a pH of under seven are acidic, and ones with a pH of over seven are basic. If the solution has a pH of 7, its neutral (such as pure water).
An acid increases the hydrogen ion concentration of a solution. ( therefore, pH decreases as the hydrogen ion concentration increases)
A base is a substance that increases the number of OH- ions in a solution.
(Most biological fluids have a pH between 6 and 8)


phscale.gif.
YC
This is a picture on the energy pyramid. I am a little hesitant to post this, but maybe some people might find it useful. The picture nicely labels the steps of the pyramid and also show some examples.
external image Energy_Pyramid.jpg
http://www.biocab.org/energy_pyramid.html

As I was browsing my notes, I completely forgot that whole process of enzymatic reactions. I looked for a diagram because I am a visual learner. I found this one which seemed pretty clear on what happens during the reaction. The only exception that this diagram has is that it doesnt have an allosteric site or demonstrate the activity of inhibition.

external image enzyme5.gif
http://waynesword.palomar.edu/molecu1.htm

-MSL
CCB
I thought I would make a post on steroids, since they are extremely important type of lipid molecules and are often overlooked.

Cholesterol.gif
This is cholesterol, a type of steriod. Notice the ring structure, this makes steroids easilt identifiable and distinguishable from other molecules.

Steroids are separated into four groups:
- cholesterol: It is found on the cell membrane, and according to the fluid mosaic model, it keeps the membrane motile.It also aids in the permeability of the membrane.Also, it is involved in the production of sex hormones (androgens and estrogens), it is essential for the production of hormones released by the adrenal glands (cortisol, corticosterone, aldosterone, and others), it aids in the production of bile,
it converts sunshine to [[/articles/161618.php|vitamin D]], it is important for the metabolism of fat soluble vitamins, including vitamins A, D, E, and K, and it insulates nerve fibers However, too much bad cholesterol (LDL) in a person's diet is unhealthy and can buildup in the arteries and cause a blockage. Good cholesterol (HDL) does the reverse of bad cholesterol and works against the negative buildup of LDL.
- adrenocorticoid hormones (ADH): This hormone is found in the kidney and regulates water retention. If the animal has a higher salt-to-water ratio in their bloodsteam, the body conserves it. If it has a lower ratio, the water is removed from the body
- sex hormones: Some include testosterone which gives secondary male characteristics. There are various female hormones that control the menstruation cycle and give secondary female characteristics.
- bile acids: Bile acids emulsify fats in the intestines. Bile acids can also dissolve cholesterol.
http://www.queenoflub.com/biochem/waxster.html
http://www.medicalnewstoday.com/articles/9152.php


SRF
I struggled when trying to molecular structures on tests (not just functional groups) so I put together a few ones that I thought we might need to be able to identify.
http://course1.winona.edu/sberg/ChemStructures/Rib-drib.gif
http://www.micro.siu.edu/micr201/chapter2n.html
http://www.raw-milk-facts.com/fat_primer_T3.html
http://telstar.ote.cmu.edu/biology/MembranePage/index2.html -This last site also has some good diagrams.



1.gif3.gif
4.jpg

[SK] Molecules or knowing the different classifications of biological molecules is important. As are enzymes- "allosteric enzymes.... a, b, c, d." And "competitive and noncompetitive." Knowing that insulin is a protein helped me understand it could not pass through the cell membrane easily. Protein organization and denaturation, and basic enzyme definitions and concepts are crucial and probably amount to the majority of questions that might be on the multiple choice. Energy pyramids are also important.