Carbs,lipids and proteins

A quick video that excitedly gives information of Carbohydrates,Lipids and Proteins. This vlog is extremely useful in cramming for any subject area. Enjoy 🙂 http://m.youtube.com/watch?v=H8WJ2KENlK0

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Amino acid and Proteins Quiz!

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1. About how many essential amino acids are there?

a) 21

b) 10

c) over 200

d) all the amino acids are essential

 

2. What does the ninhydrin reaction test for?

a) Reducing sugars

b) formation of peptide bonds

c) Amino acids

d) Proteins

3. How many amino acid residues does an oligopeptide have?

a) 25

b) 3.6

c) more than one, less than 10

d) 15

4. Which of the following is NOT a function of proteins?

a) Receptors

b) Channels

c) Storage

d) Warmth

5.  Which of the following is Not an example of fibrous proteins?

a) Enzymes

b) Bone

c) Skin

d) Cytoskeleton

6.  3.6aa per turn of alpha helix covers a distance of?

a) 50nm

b) 102nm

c) 54nm

d) 96nm

7. Bulky side chains causes what phenomenon?

a) Denaturation

b) Steric Hindrance

c) Destabilization

d) None of the above

8. Which amino acid has a cyclic R-group?

a) Proline

b) Cysteine

c) Glycine

d) Tyrosine

9. What bonds exists in secondary folding?

a) Disulphide Bonds

b) Hydrophobic Bonds

c) Hydrogen Bonds

d) All of the above

10. What chaotrope was used in Anfinsen’s Experiment?

a) Urea

b) GnHCL

c) H2SO4

d) Mercaptoethanol

Anfinsen’s Experiment..in a nutshell

…and by nutshell, i mean an  indian accent:

Anfinsen Expt:

  • He applied GnHCL and Mercaptoethanol to Ribonuclease enzyme and observed unfolding of the protein (denaturation)
  • GnHCL was used as a chaotrope
  • Mercaptoethanol was used to break disulphide bonds by reduction.
  • Dialysis was then used to remove the denaturing agents but not the unfolded enzyme
  • Once these agents were removed, re-folding occured.

Anfinsen showed that the evidence for protein folding resided in the amino acid sequence of the protein.

 

Get high off Proteins…

Now that i have your attention..Let’s start Proteins part 2!

We’re gonna discuss 5 simple but crucial things today:

  • Primary structure
  • Secondary structure
  • Tertiary structure
  • Quaternary structure
  • Denaturation

 

Primary structure:

the composition is a linear sequence of  amino acids joined by peptide bonds.

commons.wikimedia.org

prim

 

Secondary Structure:

regular folding of regions of polypeptide chains.

Alpha-helix and Beta-Pleated

Alpha-helix:

  • rod-like,aa arrange themselves in a regular helical conformation (telephone cord shape).
  • Carbonyl oxygen of each peptide bond is hydrogen bonded to the H on the amino group of the 4th aa away with hydrogen bond running nearly parallel to the axis of the helix.
  • 3.6 aa per turn of the helix, covering a distance of 0.54nm and each residue represents an advance of 0.15nm along axis of helix.
  • The R-groups of the aa are all positioned along the outside of the cylindrical helix.

www.chembio.uoguelph.ca

alp

 

 

5 factors affecting alpha-helix:

  1. Occurance of Pro and Gly residues
  2. Electrostatic repulsion/attraction between successive aa residues with charged R-groups.
  3. Steric Hindrance of adjacent R-groups
  4. Interactions between R-groups spaced 3 or 4 residues apart
  5. Interactions between aa residues at ends of helical segment and electric dipole inherent to the helix.

 

Beta-Pleated:

  • Hydrogen bonds form between the peptide bonds either in different polypeptide chains or in different sections of the same polypeptide chain.
  • the planarity of the peptide bond forces the polypeptide to be pleated with R-groups protruding above and below the sheet.

click4biology.info

betapleated

wiki.chemprime.chemeddl.org

Parallell_antiparallel_beta_sheet

 

Tertiary Structure:

Attraction between R-groups. Spatial arrangement of amino acids that are far apart in the linear sequence as well as those residues that are adjacent.

I would further explain, but the monotone, english voice in this video is much more simpler to understand:

alevelnotes.com

tert

 

Quaternary Structure:

Contains more than one polypeptide chains. e.g heamoglobin

Spatial arrangement of the polypeptide subunits and the nature of the interactions between them:

-Covalent links ( disulphide bonds)

-Electrostatic forces,Hydrogen bonding, hydrophobic interactions

I know i have a good bit of videos posted, that’s because besides JM, Youtube is my teacher!

biochemistryquestions.wordpress.com

quat

 

Doesn’t it look like all the polypeptide chains are having a party?! ..and i so wasnt invited.

bioinf.mpi-inf.mpg.de

333

 

Finally, we’re onto Denaturation!

Natural structures of proteins may be altered and activity destroyed by treatment that does not disrupt primary structure, but usually interferes with tertiary structure. Denaturation may be reversible under proper conditions or irreversible under extreme conditions.

 

Denaturing agents include: Heat, UV radiation, strong acids/bases, urea, some organic solvents and agitation.

Chemical denaturation may be: Chaotropic agents or Detergents

  • Chaotropic: high concentration of molecules denature proteins by allowing water molecules to solvate non-polar groups in the interior of the protein. Water molecules disrupt the hydrophobic interactions that normally stabilize the natural conformation.
  • Detergants: hydrophobic tails of detergants denature proteins by penetrating the protein interior and disrupting hydrophobic interactions.

chemistry.umeche.maine.edu

den

 

Now let’s all get high off Proteins!! No? Okay..

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These silly amino acids

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Nonpolar, aliphatic:

  • (G)lycine = gly
  • (A)lanine = ala
  • (P)roline = pro
  • (V)aline = val
  • (L)eucine = leu
  • (I)isoleucine = ile
  • (M)ethionine = met

Polar, aliphatic:

  • (S)erine = ser
  • (T)hreonine = thr
  • (C)ysteine = cys
  • (N) Asparagine = asn
  • (Q) Glutamine = gln

Negatively charged:

  • (D) Aspartic Acid/Aspartate = asp
  • (E) Glutmatic Acid/Glutamate = glu

Positively charged:

  • (K) Lysine = lys
  • (R) Arginine = arg
  • (H)istidine = his

Aromatic:

  • (F) Phenylalanine = phe
  • (Y) Tyrosine = try
  • (W) Tryptophan = trp

Unicorns and rainbows and proteins!

Ever realized how almost everything is made up of proteins?!! Your skin..your hair…a bunch of other stuff! and to think that there’s only 20 amino acids..what sorcery?! My first thought was magic..

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But after watching JM’s videos…my theory was disproved ):

Out of these 20 amino acids (aa)..only about 10 are essential..and by essential i mean that they cannot be synthesized by the body and must be acquired from food sources. Luckily for us..delicious animal meat are rich of these essential aa and for vegetarians, beans are also a good source of these aa. Animals and beans can therefore be termed Complete Proteins once they carry all 10 esstential aa. However, if a food source lack 1 or more of these essential aa, it is called Incomplete Proteins, such as vegetables. Great excuse for when mom tells you to eat all your vegetables huh?

Experiment time!

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Suppose you want to test for the presence of Amino Acids; firstly, get some Ninhydrin, and perform the Ninhydrin reaction, if amino acids a present, a purple colour would be produced because of the imino derivative.

However, if you want to test for the presence of Proteins; you must use Biuret reagent and perform a Biurets Test. Once again, a purple colour results if proteins are present because Copper ions (blue) react with peptide bonds of polypeptide chains to form a complex (purple).

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spsphil17.wordpress.com

I bet you didnt know there were different types of amino acids did you?

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Well there totally is!

First the basic structure of all aa:

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Then there’s Non-polar,aliphatic R groups:

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And..you guessed it, Polar,uncharged R groups: (glutamine)

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next is Aromatic R groups: (tyrosine)

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Also, positively charged R groups: (Lysine)

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And last but not least, Negatively charged R Groups:

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Let’s take a quick look at the formation of Cystine:

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please note the difference between spelling in CystEine and Cystine *jason matthews voice*…aaaaaaaaaaand we’re done! ..with that at least!

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OMG! Call your mom! Call your dad! Call the kids! cause you won’t want to miss this fine piece of proteins! How fine you ask? Summertime FINE!! I know what you’re thinking, and Yes! Yes!..i’m talking about Peptide Bonds!

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This is where a covalent bond is formed between the alpha amino group of one amino acid and the alpha carboxyl group of another. That magic theory seems legit now doesnt it? but sadly no, its due to loss of water, Condensation.

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Oligopeptides: up to 25aa residues

Polypeptides: >25aa residues

Protein: a biological macromolecule of molecular weight 5000g per mol or greater, consisting of one or more polypeptide chains.

Proteins have sooooooo many functions! like wow! these little buggers are SO diverse!

Proteins serve as: Receptors,Channels,Transport molecules,Storage,Enzyme,Structural and in Immune Response!

There are 3 ‘classes’ or ‘types’ of proteins:

Globular Proteins: e.g enzymes

  • Variety of secondary structures
  • Spherical Shape
  • Water soluble
  • Functions: catalysis,regulation,transport,gene processing

Fibrous (structural) Proteins: e.g collagen

  • ONE dominating secondary structure
  • Narrow rod-like shape
  • Poor water solubility
  • Functions: cytoskeleton,bone,skin

Membrane Proteins: e.g receptors,channels

  • Inserted through membranes
  • Multi-domain-membrane spanning, cytoplasmic, and extra-cellular domains
  • Poor water solubility
  • Functions in cell communication

I know your knowledge buds are tingling beyond control and you’re just craving more protein info! but fear not…part dos of proteins is up next!

References:

www.whitetigernaturalmedicine.com

biochem.pepperdine.edu

commons.wikimedia.org

medical-dictionary.thefreedictionary.com

commons.wikimedia.org

www.emeraldinsight.com

www.blc.arizona.edu

20 amino acids..song/rap/rhyme thingy!

A is for ALANINE, three carbons long; 
C is for CYSTEINE, with a sulfhydryl prong. 
D is ASPARTATE, a good proton source, 
And E, GLUTAMATE, is one also, of course. 

F, PHENYLALANINE, has benzene on board; 
GLYCINE, or G, wins the small-size award.
H is for HISTIDINE. What a great buffer! 
And water prompts I, ISOLEUCINE, to suffer. 

K: LYSINE’s high on the pKa scale; 
L is for LEUCINE, with its long Y-shaped tail.
M is METHIONINE, that sulfury lout, 
And N is ASPARAGINE, an amide, no doubt. 

P: PROLINE flaunts its odd ring like a bride; 
Q, GLUTAMINE, is another amide. 
R, ARGININE, has four nitrogens in all. 
And S is for SERINE, a petite alcohol. 

T is for THREONINE, similar to S; 
V is for VALINE. Aliphatic? Why, yes! 
W — that’s TRYPTOPHAN — has rings at the end, 
And Y, TYROSINE, is the kinases’ friendImage

References:http://www.tumblr.com/tagged/biochem