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GSU / Chemistry / CHEM 4600 / Hydrophobic interaction means what?

Hydrophobic interaction means what?

Hydrophobic interaction means what?

Description

School: Georgia State University
Department: Chemistry
Course: Biochemistry I
Professor: Gigi ray
Term: Fall 2015
Tags: biochemistry, amino acids, and equations
Cost: 50
Name: Study Guide For Biochemistry Exam 1
Description: These are important concepts to know for your first exam. It will behoove you to learn and study all of your Amino Acid structures
Uploaded: 01/18/2016
4 Pages 227 Views 3 Unlocks
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Biochemistry Study Guide: Exam 1 


Hydrophobic interaction means what?



In order to be successful in Biochemistry, the individual (you) must memorize all of the 20  Amino Acids (AAs) and their charges at different pH levels. This will guarantee success for the  first exam. This study guide will give out important tips and tricks and concepts that will help  you excel.  

Review from Basic and Organic Chemistry: 

Covalent bond: equal sharing of electrons

Polar Covalent bonds: An unequal distribution of electrons through the bond

IMFs (intermolecular forces) acts to Stabilize proteins and nucleic acids, Recognize different  biopolymers and to Bind substrates to proteins.  

Know the structures of a carboxyl, Ester, Ether, Alcohol, Ketone, Amine, and Thioester.  The Central Dogma is also important to know as well. Its process is DNA -> RNA???? PROTEINS!  


Amphophilic molecules mean what?



- Transcription happens between DNA and RNA; Translation happens between RNA  and Proteins.  

- Transcription happens in the Nucleus and Translation happens in the cytoplasm.  

Building Blocks of Biochemistry 

In this section an individual will know the main concepts that aids in Protein folding and the  different interactions that affects each.  

Hydrophobic Interaction: This interaction cause the protein to be stable in its environment. This interaction also plays a major role in protein folding- (hydrophobic effect). In hydrophobic  conditions the protein reaction has an increased entropy (+delta S) state. These molecules  dislikes water and are non-polar.  

- Amphophilic molecules: have hydrophobic chains and polar ends. (head is  hydrophilic and the tail is hydrophobic).  


Buffers refer to what?



If you want to learn more check out Contribution margin means what?

Buffers: Is a solution that can resist changes in pH. They are usually paired with a conjugate acid  and base. TO understand more about pH and pka the Henderson- Hasselbalch Equation is a  great example.  

Henderson- Hasselbalch Equation:

This equation is useful to determine the pH of the buffer solution and the pH quantities of the  acid and base reaction.  

- pH: Is the concentration of the H+ (protons)

- pka: Is the acid disassociation constant

- A- : Is the conjugate base

- HA: Is the initial acid

Tip: pKa concentration of HA & A- are similar. If HA is 50% the A- will also be 50%. It is also  written as pH=pKa [HA:A]. Also think of a protein as being an acid because of some of their R  side chain.  

Amino Acids 

There are 20 Amino Acids (AAs). Each AA contains a carboxylate group, Amino group and (R) a  side chain.  

Glycine does not have a chiral alpha carbon. However 19 of the Amino Acids do.  If you want to learn more check out In 2011 what is the percent of the population with access to safe water?

- Chiral means that the carbon has four distinctly different functional groups  - Glycine has two hydrogens off of the alpha carbon, therefore is ACHIRAL 

Amino acids have both L (levo) and D (dextro) pairs; however proteins are found in the L AMINO ACIDS STATE.  

- The configuration is ALWAYS (S) and not (R)

Amino Acids at neutral ph are considered zwitterions (dipolar with a protonated –NH3 group  and deprotonated carboxyl (-COO-) group.  

The 20 Amino Acids can fall into 4 groups:  

1. Hydrophobic with non-polar R groups

2. Polar AAs with neutral R groups but charge is not evenly distributed 3. Positively charged AAs with R groups that have a (+) charge at ph=7 4. Negatively charged AAs with R groups that have a (-) charge at ph=7

Hydrophobic AAs: CONTAINS 9/20 AMINO ACIDS  

Contains the simplest acid which is Glycine (achiral).  

Alanine is the second simplest acid with a methyl group as its (R)

Larger hydrocarbon side chain are Valine, Leucine, and Isoleucine.  

Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, methionine, tryptophan, phenylalanine

These amino acids participate in the Hydrophobic effect: Which will decrease free energy and  increase the number of hydrogen bonds. These amino acids will pack together enable them to  fold into themselves requiring little space.  We also discuss several other topics like What is the definition of government?

Polar Amino Acids: Contains 6/20  

Three AAs: Serine, Threonine, and Tyrosine all contains an –OH group attached to a  hydrophobic side chain.  

Asparagine and Glutamine are uncharged Amino acids that are derivatives of Aspartate and  Glutamate. Both contain a terminal carboxamide rather than a carboxylic acid.  

Lastly, Cysteine is similar to serine but contains a thiol (-SH) group instead of (-OH) group. The  thiol group is more reactive.  

Polar Amino Acids contains: Serine, Threonine, Tyrosine, Asparagine, Glutamine, and Cysteine Positively Charged Amino Acids: 3/ 20

Contains: Lysine, Arginine, and Histidine

These amino acids are highly hydrophilic. This will be best to know the structure of these amino  acids.  

Negatively Charged Amino Acids: 2/20

This set contains: Aspartic Acid and Glutamic Acid. Their side chains (R) usually lack a proton  thus giving them a negative charge.  

However they can accept protons which is functionally important as well.  

After memorizing the amino acids, this section will be beneficial to learn about the protein  structure.  We also discuss several other topics like Holism refers to what?

Primary Structure: is basically the sequence of the amino acids in a peptide. Secondary Structure: Is the H-bonding between atoms in the peptide Backbone.  Tertiary Structure: Is the actually 3D look of the protein.  

More relevant information:  

- Convalent bonds are stronger than hydrogen bonds which is stronger than VanDer  Waals

- Nitrogen bond to H and Oxygen bonded to H are considered hydrogen bond  donorsWe also discuss several other topics like What is the importance of microorganisms?
We also discuss several other topics like What are the antagonistic effectors?

- If pH=pka, the concentration of HA TO A- is always 1:1 ration

- Entropy is the measure of randomness of a system. (This is why the hydrophobic  effect is needed for our bodies)!  

- Lysine and Arginine are the only Amino Acids that are positively charged at ph=7 - Hydrophobic interactions between atoms help proteins achieve their tertiary  structure.  

I hope this information Helps.

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