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Adv. A&P - Summer Study - Basic Biochem.

For adv. a&p students who are required to review intro. chem., a pre-requisite, prior to testing the first week

Monica Bowman

on 6 August 2013

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Transcript of Adv. A&P - Summer Study - Basic Biochem.

Introduction to Biochemistry a.k.a. Basic Organic Chemistry
It is assumed that you have completed a full year of chemistry prior to taking the advanced anatomy and physiology course.
If this isn't the case, please see you counselor.
For our purposes, we will simply look at the organic molecules that we will discuss in this course.
Each one of these organic molecules contains C:H:O in certain ratios.
Carbohydrates contain a 1:2:1 CHO ratio.
They include sugars, starches, glycogen, cellulose, and dietary fibers.
They can account for 1% of your total body weight.
They are important energy sources and are usually catabolized instead of stored.
As with any other macromolecule, carbohydrates are composed of repeating units or monomers.
The monomers of carbohydrates are referred to as monosaccharides or single sugars.
Monosaccharides can be composed of 3 to 7 carbon atoms.
3 carbons = triose
4 carbons = tetrose
5 carbons = pentose
6 carbons = hexose
7 carbons = heptose
The hexose glucose is the most important metabolic sugar for your body.
See Figure 2-10 in your textbook for the two possible structural forms of glucose.
The ring structure for glucose is the most common.
Please note that they are isomers.
Another isomer of glucose is fructose.
See Figure 2-11 on page 47 of your textbook.
Glucose and fructose will have different enzymes that will react with them and different biochemical processes because of their isomerism.
However, both of these isomers readily dissolve in water/body fluids.
A disaccharide is made up of two monosaccharides.
Sucrose or table sugar is an example of a disaccharide.
Most disaccharides taste sweet and dissolve readily in water.
Dehydration synthesis or condensation reactions produce disaccharides and water.
While hydrolysis reactions use water as a reactant to break down disaccharides into two monosaccharides.
Polysaccharides are composed of 3 or more monosaccharides that are produced as a result of repeated condensation reactions.
Cellulose is a plant polysaccharide that cannot be digested.
Starches are also plant polysaccharides, but these can be digested to produce energy.
Glycogen is an animal polysaccharide composed of glucose chains made and stored by the muscles.
See Figure 2-12 on page 47 of your textbook.
Lipids or fats contain a CH ratio of 1:2 with varying amounts of oxygen.
Lipids may also contain P, N, or S.
Lipids include fats, oils, and waxes, but we will be focusing on fatty acids, eicosanoids, glycerides, steroids, phospholipids, and glycolipids.
Lipids act like structural components, energy reserves, protection, insulation, hormones,... within the human body.
As with any fat, lipids are insoluble in water and, therefore, require special transport mechanisms in order to move throughout the body.
Lipids can provide up to 2x the amount of energy that an equal amount of carbohydrates can supply.
If there is an excess of lipids and the energy demand is low, the lipids will be stored in the body.
Fatty acids are long chains containing a carboxylic group.
Fatty acids
The carbon chain of a fatty acid is referred to as a hydrophobic tail.
The carboxylic end is referred to as the hydrophilic head of the fatty acid.
Generally, the longer the tail of a fatty acid, the less soluble it will be in water.
Fatty acids can either be saturated, unsaturated, or super saturated depending on the number of hydrogens that are attached to the carbon chain/double bonds between the carbons.
See Fig. 2-13 on page 49 of your textbook.
Read the Clinical Note on page 49 of your textbook that discusses Fatty Acids and Health.
Eicosanoids are lipids derived from an acid that is absorbed into the body through your diet - arachidonic acid.
Two major classes of eicosanoids are leukotrines, which are involved when cells are damaged or infected, and prostaglandins.
Prostaglandins are synthesized throughout the body and are short-chains attached by a ring structure.
Prostaglandins are released by cells when coordinating cellular activities.
See Fig. 2-14 on page 50 of your textbook.
Fatty acids that are attached to glycerol by means of a dehydration synthesis reaciton are known as glycerides.
Monoglyceride = glycerol + 1 fatty acid
Diglyceride = glycerol + 2 fatty acids
Triglyceride = glycerol + 3 fatty acids
See Fig. 2-15 on page 50 of your textbook.
Triglycerides are energy sources, provide insulation, and provide internal tissue protection.
Lipid droplets within cells contain stored triglycerides, lipid-soluble vitamins (A, D, E, K), drugs, and toxins (DDT).
See Fig. 2-16 on page 51 of your textbook to see the characteristic structure of a steroid.
Steroids have a characteristic four-ring structure.
What is attached to this basic structure determines which steroid is being studied.
Cholesterol is a very important steroid that is necessary for normal cell function.
Cholesterol is a component of plasma membranes and, therefore is needed for normal cell maintenance, growth, and division.
Steroid sex hormones such as estrogen and testosterone are steroids necessary for normal body development.
Steroid hormones such as corticosteroids and calcitriol are needed for normal metabolic processes and mineral homeostasis.
Bile salts, which are steroid derivatives made by the liver and stored in the gallbladder, help to digest and absorb lipids.
Cholesterol can be absorbed via your diet and synthesized by the body, which is why dietary cholesterol levels should be monitored to offset potential health issues.
Phospholipids can be synthesized by the body from fatty acids.
Phospholipids and Glycolipids
A phosphate group links a non-lipid group to the glycerol of a fatty acid.
See Fig. 2-17 on page 52 of your textbook.
A carbohydrate is attached to a diglyceride in a glycolipid.
The long hydrocarbon chains of both the phospholipids and glycolipids are referred to as 'tails.'
The 'tails' are hydrophobic, or water repellant a.k.a. non-polar.
The other end of the phospholipid or glycolipid molecule is referred to as the 'head.'
The 'head' is hydrophilic, or attracts water a.k.a. polar.
This explains why large numbers of either phospholipids or glycolipids placed in water will form droplets or micelles.
The heads point towards the water since they are hydrophilic.
If the lipid droplet is large enough, a lipid membrane may form in which the heads face the water and the tails face each other.
Cholesterol, phospholipids, and glycolipids are, therefore, considered structural lipids since they can be utilized to form membranes.
They are the most abundant organic molecule in the human body accounting for approximately 20% of a human's total body weight.
While all proteins contain C, H, and O, they also may contain S and P.
Structural proteins can provide 3D structure, strength, organization, and support.
Some proteins aid in movement and are known as contractile proteins.
Transport proteins bind to insoluble lipids, gases, minerals, hormones, and other chemicals in order to distribute them throughout the human body.
Proteins can also play the role of a buffer.
Some proteins have enzymatic characteristics and are, therefore, involved in metabolic processes.
Some proteins act as hormones involved in coordinating and controlling cellular activities.
Some proteins are involved in non-specific defenses of the body such as skin, hair, and nails.
Other proteins can be involved in specific defenses of the body and are known as antibodies.
Some proteins are involved in the blood clotting system during an injury.
Proteins are composed of linked monomers called amino acids.
There are 20 different amino acids or a'a for short.
A typical protein contains around 1K a'a but many can have over 100K.
Each a'a is made up of:-
a central C, an H, an amino group, a carboxylic group, and an R group or side chain.
See Fig. 2-18 on page 53 of your textbook.
A'a are relatively small, polar, and, at a neutral pH, will release H+ causing them to become negatively charged (That is why you can use Pr- as an abbreviation for proteins.).
Dehydration synthesis reactions link two a'a in a peptide bond causing the resulting molecule to be called a peptide.
See Fig. 2-19 on page 54 of your textbook.
2 a'a = dipeptide
3+ a'a = polypeptide
100+ a'a = protein
In addition to the R group, the overall 'shape' and 'folding' of the protein is very important
Primary structure = a'a sequence
Secondary structure = H bonding
An alpha helix or a beta-pleated (flat) sheet can result from this H bonding.
While alpha helix folding is more common, sometimes a combination of both folding patterns can be seen.
Tertiary structure = more complex folding due to the polarity of the protein with water or the R groups
Sometimes disulfide bonds form, which can be very strong covalent bonds between cysteines.
Disulfide bonds can form loops and coils in the 3D structure of the protein.
Quaternary structure = interaction between different polypeptide chains
See Fig. 2-20 on page 55 of your textbook.
Given a protein's folding structure, you could have a fibrous or globular protein.
Fibrous proteins form strands or sheets of very tough, non-polar materials.
Globular proteins form round, polar proteins that work best when hydrated.
Understand that the protein's 2D and 3D structure determine its efficacy. One minute change could change its entire function.
In order, then, to work with proteins effectively, the local environmental conditions need to be at an optimum.
In your first year biology course, you may recall that enzymatic proteins also reacted to their local environment.
Many biology teachers like to refer to the action of enzymes with a their substrates as the 'lock and key mechanism.'
Well, not exactly.
See Fig. 2-21 on page 56 of your textbook.
The active site or sites of the enzyme are the locations of interest.
If the active site on the enzyme is blocked or altered, enzyme activity is changed.
One or more substrates can interact with an active site.
When a substrate interacts with an enzyme at its active site, an enzyme-substrate complex is formed.
As a result, a chemical reaction occurs.
You'll notice that enzymes show specificity regarding which chemical reaction they will catalyze.
That is why there are probably thousands upon thousands of different enzymes in the human body in order to handle of the different necessary chemical reactions that require a catalyst.
It should be noted that there are enzymes, isozymes, that do catalyze similar reactions in similar ways, but they may be found in different tissues.
Enzymes may have a saturation limit or must reach a certain concentration ( of either the enzyme and/or substrate) before it can act.
Therefore, in some cases, it is important to study the saturation limit of an enzyme in order to understand how it functions.
Enzymatic regulation, or what turns 'on' or 'off' an enzyme is also an important factor to consider.
These can be environmental factors such as pH, temperature, or the presence of cofactors.
Cofactors can be either ions or molecules that must bind to an enzyme in order to activate enzymatic activity.
Conenzymes, potentially derived from vitamins, are organic molecules that act like cofactors.
It is possible to denature enzymes, sometimes even permanently, by placing it in 'harsh' environment, such as an extreme fever or extreme pH.
Glycoproteins and proteoglycans
These molecules are a combination between proteins and carbohydrates that produce a sticky, syrupy material ex. mucus.
These molecules are nucleic acids composed of C, H, O, N, and P that store and process information in the body.
DNA is larger, double-stranded, helical, and located either in the nucleus or in the mitochondria of a human's cells.
DNA, or deoxyribonucleic acid, carries the inherited information of the cell.
See Fig. 2-22 on page 58 of your textbook.
As you learned in biology, any change in the DNA may result in changes in cellular function.
See Fig. 2-23 on page 59 of your textbook.
See Table 2-7 on page 59 of your textbook.
We will go in greater depth on the biology review, but the last Figure should have 'tweaked a few neurons.'
Nucleotides are connected together to form these macromolecules through dehydration syntehsis reactions.
Nucleotides are made up of a pentose (ribose or deoxyribose), a phosphate group, and a nitrogenous base.
The nitrogenous bases can either be adenine (A), guanine (G), cytosine (C), thymine (T), or uracil (U).
Adenine and guanine are larger molecules classified as purines.
Cytosine, thymine, and uracil are classified as pyrimidines.
On the DNA double-helix, the complimentary nucleotide chains are bonded together with hydrogen bonds.
The single-stranded RNA comes in several types including messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).
We will discuss their use in more detail in our biology review.
High Energy Compounds
Molecules containing covalent bonds that, when broken, release a lot of energy are referred to as high energy compounds.
The most common molecule of this type in your body contains a phosphate group attached to an organic molecule.
Multiple phosphates can be joined together in a phosphorylation reaction, but that does not guarantee that it will generate a high energy compound.
A high energy compound requires a phosphate group, a catalyzing enzyme, and an organic substrate that can have a phosphate group added to it.
One common substrate is adenosine monophosphate or AMP.
Adding another phosphate to AMP generates the molecule adenosine diphosphate or ADP.
Adding another phosphate to ADP generates the molecule adenosine triphosphate or ATP.
The most common form of storing energy in our body is the ADP to ATP reaction while the reverse reaction is the most common form of releasing energy.
See Fig. 2-24 on page 60 of your textbook.
ATP to ADP does require the enzyme adenosine triphosphatase or ATPase.
There are other chemicals that can also undergo phosphorylation.
These are guanosine triphosphate (GTP) and uridine triphosphate (UTP).
See Table 2-8 on page 61 for a quick summary.
Metabolic turnover can be defined as the constant replacement and removal of chemicals utilized by the body's cells.
See Table 2-9 on page 61 of your textbook for turnover times.
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