WEEK 4 AMINO ACIDS AND PROTEINS PART 2!!!!!!!

This week’s lecture was about the continuation of amino acids and proteins. I  learnt a lot of new things, well actually a more advanced study of proteins than I did in  at A-levels. The topics covered include the different structures of proteins, types of bonds in proteins ,impacts of changes in amino acid sequences in proteins and the denaturing of proteins. This is a lot so lets get started folks.

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The PRIMARY structure of the protein is quite straight forward but the SECONDARY may need a bit more elaborating on that is, features such as  the alpha helix and beta pleated sheet.

In the helix, hydrogen bonds form between the carbonyl oxygen from a  peptide bond and to a hydrogen of the amino group in the fourth amino  acid in the chain. The hydrogen bonds run somewhat parallel to the axis of the helix. Some things to note: there are approx. 3.6 A.A per turn of the helix which covers a length of 0.54 nm,the amino acids side chains are situated on the outside of the cylindrical helix. Some amino acids are rarely found in alpha-Helices for e.g proline which 1)lacks rotation around the nitrogen-carbon bond,2)cannot form hydrogen bonds due to a lack of hydrogen atom on its nitrogen atom. Proline often acts as a molecule which ends the helix.    Image
Glycine is another amino acids rarely found due to its high conformational flexibility.

Factors affecting  the stability of the Alpha Helix:
1)Interactions between A.A side chains- side groups with like charges causes repulsion which prevents the helix from forming
2)Steric Interference by bulky side groups can stop the formation of the helical structure-cannot fit and turn properly
3)Formation of ion  pairs and hydrophobic interactions (aromatic A.A’s)-  stabilize the helix
4)Peptide bonds contain miniature dipoles which ultimately form macrodipoles at the ends of the helix. Molecules close to each dipole contain opposite charge so as to stabilize the structure.

WHY DOES THE ALPHA HELIX FORM MORE READILY THAN MANY OTHER CONFORMATIONS?…this was a question posted on the lecture that need to be paid attention to and the answer is as follows:
It is formed  more readily due to the more efficient  use of hydrogen bonding as each peptide bond takes part except those close to the end of the chain.

Beta Pleated sheets:

In these, hydrogen bonds form between adjacent chains or sections of peptides and is positioned in such a way that the side chains protrude above and below the sheet. The bonds are planar. The sheets can be either parallel or antiparallel. The following link can give some insight into these types of sheets:
http://www.chem.wisc.edu/deptfiles/genchem/netorial/modules/biomolecules/modules/protein2/prot24.htm

TERTIARY STRUCTURE

The spatial arrangement of the polypeptide chain. It contain bonds such as disulphide,hydrogen,electrostatic and hydrophobic interactions.

QUATERNARY STRUCTURE

The way in which polypeptide chains are linked together. They contain the same forces as the tertiary structure mentioned above.

The following link explains the above information in detail:
http://themedicalbiochemistrypage.org/protein-structure.php

Denaturing of Proteins:

In denaturing of proteins, the primary structure always remain intact, it is mainly the tertiary and quaternary structure that is changed. Some proteins may or may not be able to return to its original state.  Factors which denature proteins include:
1)Heat- disrupts hydrogen bonds by vibrational and translational energy
2)UV radiation-same as heat
3)Strong acids and bases-disrupts hydrogen bonds
4)Urea-competes for H- bonds
5)Organic solvents
6)Agitation
7)Chemical denaturation- chaotropes and detergents

The following link should provide ample information about denaturing of proteins:

http://www.elmhurst.edu/~chm/vchembook/568denaturation.html

WELL THIS CONCLUDES THIS LECTURE ON PROTEINS BUT BEFORE YOU GO HERE’S SOME FOOD FOR THOUGHT FOR AL YOU GYM FREAKSSS

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INTRODUCTION TO AMINO ACIDS…….WEEK 3 OF BIOCHEMISTRY

Week 3 of biochem was basically an introduction to Amino Acids. The information learnt was nothing that I didn’t already know so in essence the word ‘learnt’ should really be replaced with something in similar meaning to  ‘review’ but for those ninjas out there I shall elaborate on this topic a bit so as to help spread some helpful knowledge.
First of all you must know the basic structure of an amino acid which is shown in *figure 1*. Which is basically a central carbon attached to an amino group, a hydrogen, a carboxyl group and an r-group…*note that the r-group can be variable thus leading to the formation of different types/categorisations  of amino acids..

These include :

1)Nonpolar (no charge)  aliphatic R-groups (e.g Glycine,Alanine a ‘special’ one with a ring structure, Proline)

2)Polar ,uncharged R-groups –the difference here is in the r-group where there is a charge difference.*note that in the basic structure of the amino acid,the charge on the molecule besiding the r-group cancels each other out..some examples are: Serin, Cysteine and Glutamine

3)Aromatic R-groups-these have a benzene ring present /double bonds in a conjugated form.e.g Phenylalanine, Tyrosine and Tryptophan.

4)Positively charged r-groups-caused by a positive charge present on N-atoms on the r-groups . Remember when nitrogen forms four bonds, the fourth bond is a dative one (e.g with H) thus taking the positive charge of the H. E.gs are Lysine and Arginine.

5)Negatively charged r-groups-these simply have a negative charge on the r-group( r = CH2,CH2,COO- ) e.g Aspartate and Glutamate.

Amino acids join by peptide bonds (covalent) formed by the alpha amino group of one and alpha carboxyl group of another via a condensation reaction. Amino acids can be written in different ways /abbreviated that is by the 1st 3 letters of its name or by a single letter that may be difficult to remember so it is best to keep an A.A table around.
One thing though that I never came across was the involvement of OX-RED reactions in forming bonds in amino acids for e.g the disulphide bond formed between the two sulfur hydroxils groups in Cysteine. Cystine is formed from two cysteine molecules via an oxidation reaction by losing two hydrogen atoms along with 2 electrons.

Q :WHAT ARE ESSENTIAL AMINO ACIDS?
A  :Simply said,essential amino acids are those your body cannot synthesise on its own and must get from external sources e.g meat and beans e.g leucine,lysine and valine.
It is therefore obvious as to what non essential A.A are….? Isn’t it? Well some examples are glycine,proline and serine.

Q :WHAT IS A COMPLETE PROTEIN?
A  :A complete protein is onw which has all 10 essential amino acids. (*By the way..there are 10 essential amino acids and 10 non-essential amino acids.) guess what an incomplete protein is then….

HOW TO TEST FOR AMINO ACIDS??

The NINHYDRIN REACTION tests for amino acids by turning a colourless solution purple…*but not all amino acids would give this colour though* this reaction is elabourated on using the *following link *:

DO NOT MIX-UP NINHYDRIN TEST WITH BIURET TEST!

The Biuret reagent tests for PROTEINS! It turns purple if protein is present the following *link* describes the test in detail :

PROTEINS HAVE MANY FUNCTIONS!!!!

This is a relatively easy topic but the following *link* should help:

DIFFERENT TYPES OF PROTEINS
1-Globular proteins
2-fibrous proteins
3-Membraneous proteins
….these would elaborated on in the other post…

THANK YOU FOR READING AND I HOPE THIS INFORMATION HELPS AND PLEASE DO ADD WHATEVER INFO. YOU HAVE TO SHARE!

CARBOHYDRATES CONTINUED………

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For this part, we looked at the formation of glycosidic bonds, structure and functions of certain di saccharides ,lactose intolerance, structure and function of types polysaccharides.

TYPES OF DISACCHARIDES….
These include:
1) sucrose-glucose+fructose –   non red. sugar
2) maltose-glucose+glucose(both alpha)-   red. sugar
3) cellobiose-Bglucose+Bglucose
4) lactose-glucose+galactose (beta 1-4 linkage)-   red. Sugar

Their functions can be found in the following link/s –   http://www.livestrong.com/article/535273-the-function-of-disaccharides/

LACTOSE INTOLERENCE…….
Lactose intolerance is simply the inability of the body  to produce enough lactase to break down amounts of lactose and it is the excess lactose which causes the problem. The excess lactose attracts water and causes bloating and diarrhea. Also bacteria decompose lactose to give off gas and acid in the stomach…well we can just imagine what that gas is right…lol…

TYPES OF POLYSACCHARIDES……

1)Starch-an energy store in plants
-a polymer of alpha glucose
-stored in the form of grains
-compact and insoluble molecule
-minimises osmotic effects

Starch composes of a mixture of TWO types of chains formed by alpha glucose:
1)Amylose-
-long unbranched chains of glucose forming 1-4 glycosidic bonds
-chains take up a coiled /helical form as each monomer has a bulky side group which has to be accomodated
-forms 20% of starch
-the end of the chain where an anomeric C is not involved in a glycosidic bond is the reducing end

2)Amylopectin-
-these are branched chains formed from glucose condensed by 1-4 and 1-6 glycosidic bonds
-coiled chains may contain around 1500 monomers with branches every 24 units
-forms 80% starch

2)Glycogen-an energy store in animals and fungi
-branched chains of alpha glucose condensed to form 1-4 and 1-6 glycosidic bonds
-chains may consist of 10-15 units
-more branched than amylopectin
-insoluble
-seen as small granules suspended in the cytoplasm of cells
-found especially in liver and muscle cells
-since the chains are so short ,they can be hydrolysed rapidly for an animal’s urgent needs.

3)Cellulose-structural compound in plants
-major component of lant cell walls
-formed from beta glucose chains
-alternate molecules rotate through 180 degrees to allow appropriate OH- groups to react forming straight chains
-bulky side groups have to be accommodated for thus leading to straight chains
-hydrogen bonds are formed from adjacent chains between OH groups and O
-parallel cellulose chains form microfibrils and macrofibrils with immense tensile strength and stability.

TO TEST FOR CARBOHYDRATES……

The following link will provide you with the relevant information on the most common tests required for carbohydrates:

http://www.esu.edu/~scady/Experiments/Carbohydrates(summer).pdf

WEEK 2 BIOCHEMISTRY-CARBOHYDRATES!!!

For this week we covered Carbohydrates and as one come across this word, immediately the words sugars and energy should come to mind. After all it is the source of BCninja’s energy and without it how else can I run this blog ???? What was learnt was very basic stuff as it is only level 1 biochemistry so here I go and I hope you understand what is going on….
Carbohydrates have a general formula of  (CH2O)n. Their  functions include transport ,storage,structural and as precursor molecules. We may think that sugars are always good for the body but it isn’t so….remember there are diabetics out there and the main culprit to their problems is glucose levels. So here’s a useful question,

QUESTION: How is this glucose affecting the diabetic??

ANSWER: Well according to http://www.news-medical.net/health/What-is-Diabetes.aspx  diabetes is said to be caused by an elevation in blood glucose levels due to the body not being able to convert excess glucose to glycogen stemming from a lack of the hormone insulin which is produced by the pancreas. there are two types of diabetes- 1 and 2. TYPE 1 diabetes a.k.a juvenile onset/insulin dependent disease (affects only 10% diabetics) is a chronic disease in which there are high levels of sugar in the blood. The affected needs insulin shots after meals to control glucose levels. It can occur at any age mostly in children or young adults. One cause of this is theorised to be an autoimmune disorder which destroys the insulin producing islet cells of the pancreas and being genetically caused, can be passed on to others. Type 2 diabetes is the more common one affecting the rest 90% diabetics.Due to lack or insufficiency of insulin there is high blood glucose in diabetes. Excess glucose in the blood can damage the blood vessels. This leads to several complications like heart disease, kidney damage, nerve damage, eye damage and blindness, impotence and stroke.Diabetes, when not controlled, may raise the propensity for infections.

For an informative video on Diabetes click the following link : https://www.youtube.com/watch?v=dZSnlo3W-3Y   ……… if that one is too good for you try this one (srsly, (-_-) )…….https://www.youtube.com/watch?v=jHRfDTqPzj4

SOME THINGS TO NOTE:
-Complex sugars also form dietary fibre.
-They form  sugars according to the amount of sugar molecules attached to each other giving rise to : 1)monosaccharides-single sugar molecule e.g trioses,tetroses,pentoses and hexoses, 2)Disaccharides-two covalently linkedmonosaccharides, 3)Oligosaccharides-a few linked and  4)Polysaccharides-chains of polysaccharides.

ALDOSES AND KETOSES

Monosaccharides can either be an aldose(-CHO) or ketose(-R-C-=O-R-) based on the presence of an aldehyde or keto group. An easy way to indentify them is when the carboxyl group is at the end of the molecule..it is an aldose but if the carboxyl group it between two other carbons (usually at carbon 2) it is a ketose.
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The Aldo- or Keto- prefix can govern the name of the sugar it is attached to according to the group attached to it for e.g Glyceraldehyde- a aldotriose or Dihydroxyacetone-a ketotriose.*Note-a very important definition that I learnt from my lecturer for carbohydrates is as follows-Carbohydrates are aldehyde or ketone derivatives of polyhydric alcohols classified as mono,di,oligo and polysaccharides.

More about aldoses and ketoses: http://www.chem.ucalgary.ca/courses/351/Carey5th/Ch25/ch25-2-4.html
D VS L DESIGNATIONS FOR THE ASYMMETRIC,ISOMERIC CARBONS

An assymetric/chiral carbon is one which has 4 different groups attached to a central carbon. The D and L designation just depends on which side the OH group is attached to on the chiral carbon. If on the left, it is an L designation and vice-versa. This D or L designation is for molecules of the same type such as glucose and for those with more than 1 assymetric carbon such as glucose (which has 4) ,the name is given according to the carbon furthest  from the aldehyde or keto group.
-D and L sugars are mirror images to each other
-the number of stereo isomers is given by 2^n where n=no. of assymetric carbons e.g if n=4 then 2^n=16

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AN EPIMER??

This is the first time I came across this term but it is pretty simple,it just means two sugars that are similar to each other except for the configuration around 1 carbon.

DL-Glucose.svg

CYCLISATION IN SUGARS…

Hexoses and Pentoses tend to form cycle ring structuresby forming hemiacetals and hemiketals. These in turn can be either alpha or beta.
-6 membered ring-pyranose
-5 membered ring-furanose

Video on cyclisation :  https://www.youtube.com/watch?v=F2QDNRcd3E0

As I said…easy stuff nothing to figure out. Well I hope this post was of good use to any of you and I assure you people the links posted here are very helpful and I use them to aid in my studies…keep training my fellow NINJAS!!! -.-

WEEK 1 OF BIOCHEMISTRY : THE CELL!!!

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This post may be a bit late but it was due to difficulties in setting up and organising the blog…so I am sorry for the delay in providing this piece of information on the cell. It is a relatively easy topic with nothing to really figure out but more of a memory type of task and since I am one for relying mostly on memory I found this topic to be very easy J

ROBERT HOOKE DISCOVERED THE CELL!
So what is a cell ? you may ask…well a cell can be described as the smallest unit that is capable of surviving on its own.

This lecture contained some important bits of information that I did not know anything of and as I said nothing to figure out..just memory stuff..First time I ever came across the words Dialister Pneumosintes which is a tpe of bacteria that stands for a representation of the smallest limit to which a cell can be to exist on its own (.5*.5*1.6micrometers). It is said that any cell smaller than this size would not be able to make enough DNA to survive .
BUT….viruses are much much smaller than these bacteria so how can they survive??what would allow them to be smaller??
ANSWER:

CELL SIZE :

Surface to volume ratio limits the size of a cell. As cell size doubles there is 8 times as much volume but only 4 times as much surface area. This is sown in the following link :

The rate of diffusion slows down which ultimately kills the cell L either by being poisoned by wastes of starvation.

All living cells fall into two broad categories i.e Prokaryotes and Eukaryotes and as university level students the distinction between the two should be already known. Well the difference is mainly due to the presence of a nucleus or not. Other differences are :

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Now here are common structures found in Prokaryotic cells and Eukaryotic cells :

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Basically the rest of this lecture consisted of descriptions of cell organelles so to save time here are links leading to feasible definitions for each one:

1)cell wall-  http://library.thinkquest.org/C004535/cell_wall.html  and http://library.thinkquest.org/12413/structures.html
2)cell membrane- http://library.thinkquest.org/12413/structures.html
3)cytoplasm- http://biology.about.com/od/biologydictionary/g/cytoplasm.htm
4)nucleus- http://biology.about.com/od/geneticsglossary/g/Nucleus.htm
5)E.R- http://library.thinkquest.org/12413/structures.html

6)ribosomes- http://library.thinkquest.org/12413/structures.html
7)S.E.R- http://biology.about.com/b/2011/06/03/what-is-the-endoplasmic-reticulum.htm
8)golgi apparatus- http://library.thinkquest.org/12413/structures.html
9)lysosomes- http://library.thinkquest.org/12413/structures.html

10)nucleoid- http://en.wikipedia.org/wiki/Nucleoid

11)proteasome- http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Proteasome.html
12)peroxysome- http://www.ncbi.nlm.nih.gov/books/NBK26858/?redirect-on-error=__HOME__
13)mitochandria- http://library.thinkquest.org/12413/structures.html
14)cytoskeleton- http://library.thinkquest.org/12413/structures.html
SOMETHING TO NOTE ABOUT RIBOSOMES!!!

*NOTE-S refers to sedimentation coefficient i.e. how fast the ribosome move in a centrifuge. This gives the difference between ribosomes

FOR 70S RIBOSOMES-        

– found in prokaryotes
-divided into 2 subunits  that is.. a larger 50S + smaller 20S subunit.
-70s ribosomes move slower than 80s ribosomes in a centrifuge

 

FOR 80S RIBOSOMES-

– found in eukaryotes
divided into a larger 60S + smaller 40S subunits
-moves faster than 70s ribosomes in a centrifuge

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LASTLY, we touched a bit on the ENDOSYMBIOTIC THEORY. This theory in a nutshell describes the origin of chloroplasts and mitochondria in cells as a result of endocytosis.
The following link completely describes this theory as well as gives examples of evidence for the validity of this theory..

http://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter4/animation_-_endosymbiosis.html

Thank you for viewing and please do add whatever relevant info. you may have in the comments section….*ninjaman disappearrr……..lol

ABOUT YOUR BIONINJA!

Hello my name is Roger Harkissoon , i am currently enrolled at the University of the West Indies where i am pursuing a biochemistry major. My hobbies include playing cards, pool, cricket, computer games and girls…I love doing Biology and Chemistry and with their help emanates the hope of one day working in the oil industry, in laboratories or as a teacher. I enjoy helping people and hope this blog would be of great importance to many of you so do follow and help add to the wealth of information so we can create a most successful archive for all biochemists out there. ImageWELCOME!