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UGA / Biology / BCMB 3100 / What is the study of biochemistry all about?

What is the study of biochemistry all about?

What is the study of biochemistry all about?

Description

School: University of Georgia
Department: Biology
Course: Intro to Biochem and Molecular Bio
Professor: Wood sabatini
Term: Fall 2016
Tags: amino acids, Proteins, and biochemistry
Cost: 50
Name: BioChem 3100 Test One Study Guide
Description: Study guide from lecture notes for Dr. Rose Test 1
Uploaded: 01/29/2017
17 Pages 47 Views 3 Unlocks
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BioChem Test 1


What is the study of biochemistry all about?



∙ What is BioChem?

− Biochemical processes of life

− Biochemical generalizations for living things

♦ Life requires life

♦ Biochemical reactions require life

♦ The information for life is transmitted in the genome

♦ The central dogma of life information flow

⇒ DNA--RNA--Protein

∙ Biological Molecules

− Proteins: series of linked amino acids that can fold into functional structures − Carbohydrates: ring structure composed of C, O, and H

− Lipids: hydrocarbons that are nonpolar and make up the membrane bi-layer − Nucleic acids: DNA, RNA, ATP, and ADP


What are biological molecules made of?



∙ Energy

−∆ G=∆ H−T ∆ S

−∆ G<0 -- Spontaneous

−∆ G>0-- Nonspontaneous 

−∆ G=0 -- Equalibrium

− Le chateliers principle  

♦ A system strives for equilibrium

♦A+B ↔C+D [C] [ D] 

[ A] [B]=Keq Kforward


What does the weak interaction effect?



If you want to learn more check out What is the definition of disruptive selection in natural selection?

K reverse=Keq

♦ At equilibrium the concentration of all species remains constant over time. Both the forward and reverse reactions continue to occur at the same  

rate. Keq=1

∙ Weak Interactions

− Electrostatic interactions

♦ Salt bridges, ionic bonds

♦ Hydrogen bonds

⇒ Created by induced dipoles

⇒ Strength depends on distance and angle with closer and 180 degrees  

being the strongest  

♦ Vanderwaals interactions

⇒ Random fluctuations can produce a dipole If you want to learn more check out What are representational works of art?

r12−Br6 r=distance between atoms

A

⇒ U=

⇒ Vanderwaals contact curve

We also discuss several other topics like Why do we need to know norse mythology to understand norse poetry?

− Hydrophobic effect

♦ Water is a great acceptor when it is being deprotonated

♦ Driven by the entropy of water and is proportional to the decrease in  

surface area of the ordered water

♦ Clathrate= water cage

♦ Hydrophobic molecules, squeeze out water and will fold to avoid water ∙ Acids/bases

− Ionization of water--water dissociated into hydronum and hydroxyl −¿

+¿+O H¿ 

H2O↔ H¿ 

+¿

H¿ 

¿−¿

O H¿ 

¿

Keq=¿

+¿

H¿ 

pH=−log ?¿

− Weak acids

−¿A¿ 

¿¿¿

pH=pKa+log¿ We also discuss several other topics like What is the nature of light?

pKa=−log (ka)

+¿H¿ 

¿−¿A¿ If you want to learn more check out Does the constitution really need bill of rights?

¿¿

Ka=¿

♦ Pka tells how strongly an acids wants the proton

⇒ pH < pKa = protonated

⇒ pH > pKa = deprotonated

Example Question: The pKa of ascorbic acid is 4.2 at 24°C. What is the pH  when the unprotonated: portonated ratio is 1:1? At 1:10?

Answer: at 1:1 the protonated=the unprotonated, thus pKa=pH so the pH is  

4.2

At 1:10  

A

pH=pKa + log

pH= 4.2 + log  We also discuss several other topics like What is democritus theory about?

pH= 3.6

− Buffers

HA A=unprotonated HA=protonated

1

10

♦ A weak acid or base used to maintain a specific pH by absorbing or  

releasing protons according to le chateliers principle

♦ Leaving group will be the conjugate acid with the lowest pKa In this example, OH is a poor leaving group because the pKa is 15.7, the  

conjugate acid is water

♦ pKa determine the buffering range-- the pKa ± 1 pH

♦ pKa predicts the leaving group

♦ on a buffer curve, like the one above, the pKa= the point of maximum  

buffering

− Maintaining physiological pH

♦ Regulated by the CO2- carbonic acid- bicarbonate buffer system ♦ Body pH remains at 7.4

⇒ At a low pH, excess acid in the body is neutralized by HCO3- . This  

occurs in the tissues

⇒ At a high pH, excess base in the body is neutralized by H2CO3. This  

occurs in the lungs

∙ Amino Acids

− Basics building blocks of proteins

− α amino acids occur when the R group is bound to the α carbon

− Organized by charge, hydrophobicity, and structure

− Hydrophobic amino acids

♦ Alipathics--only hydrocarbon side chaines

⇒ Alanine, A, ALA

⇒ Valine, V, VAL

⇒ Leucine, L, LEU

⇒ Isoleucine, I, ILE

♦ Sulfur-containing

⇒ Methionine, M, MET

♦ Aromatic

⇒ Tryptophan, W, TRP

⇒ Phenylalanine, F, PHE

♦ Structural

⇒ Proline, P, PRO

⇒ Glycine, G, GLY

− Acidic Amino Acids

♦ Thiol

⇒ Cysteine, C, CYS

♦ Carboxylic Acids

⇒ Aspartic Acid, D, ASP

⇒ Glutamic Acid, E, GLU

♦ Aromatic--hydrophobic l  

⇒ Tyrosine, Y, TYR

− Basic Amino Acids

⇒ Lysine, K, LYS

⇒ Arginine, R, ARG

⇒ Histidine, H, HIS

− Polar Amino Acids

♦ Alcohols

⇒ Serine, S, SER

⇒ Threonine, T, THR

♦ Amides

⇒ Asparagine, N, ASN

⇒ Glutamine, Q, GLN

− Special Amino Acids

♦ Isoleucine--has 2 chiral carbons so it has 4 stereoisomers

♦ Cysteine-- plays a large functional and structural role due to its ability to  

form disulfide bonds

⇒ Formation of cysteine-- reduction/oxidation reaction

⇒ Redoxs with glutatnione  

♦ Proline-- attaches to itself and can have both cis- and trans- confirmations ⇒ Usually trans

− Essential vs. nonessential amino acids: essential amino acids cannot be  produced by the body

♦ Essential: Hisitidine, isoleucine, leucine, lysine, methionine,  

phenylalanine,threonine, tryptophan, valine

♦ Non-essential: alaning, arginine, asparagine, aspartic acid, cysteine,  

glutamic acid, glutamine, glycine, proline, serine, tyrosine

− Amino Acid Stereochemistry  

♦ Contain chiral carbons

♦ Neutral acids have a L confirmation

♦ "CORN" method

If goes counter-clockwise: D

If goes clockwise: L

− Example Question: Which is least likely to be on the surface of a water

soluble protein?

a. Leucine

b. Serine

c. Glutamate

d. Lysine

e. Theronine

Correct answer: a

Reasoning: Leucine is hydrophobic and thus would "hide" from the water  

by folding towards the center

− Charged amino acids

♦ All amino acids have at least 2 charged groups

♦ Some amino acids can be ionized  

⇒ If pH is less than the pKa then the amino acid will be protonated ⇒ If pH is greater than the pKa then the amino acid will de deprotonated ⇒ There are 7 amino acids that have R groups that are ionizable 1. Cysteine--8.4 (pKa values)

2. Tyrosine--10.5

3. Aspartic acid--3.9

4. Histidine--6.0

5. Lysine--10.8

6. Glutaminic acid--4.1

7. Arginine--12.5

Example Question: Which amino acid would be positively charged at a neutral

pH?

Answer: Lysine, Arginine, and Tyrosine

Reason: Lysine, Argine, and Tyrosine have pKa's that are greater than a

neutral pH of 7

∙ Proteins

− In 1838 Mulder discovered that amino acids work as building blocks − Primary structure of proteins

♦ In 1958 frederic sanger sequenced insulin and won the nobel prize  ♦ Sanger's work implied that there was template in the cell that contained  

the information for protein sequences--DNA

♦ Edman sequencing was used to sequence proteins, today we use Mass  

Spectroscopy  

♦ Average weight of amino acid is 110 daltons

− Disulfide bonds are super important

♦ Made by 2 cysteine residues, usually in the extracellular proteins  ♦ Made by condensation reactions and needs enzymes or else would never  

happen

− Proteins can be modified

♦ Enzymes cut and patch to finalize protein sequences

♦ Example: Insulin

⇒ Usually has 3 disulfide bonds but enzyme cleave and repatch to make  

the active form which only has 2 disulfide bonds

− Protein evolution

♦ Homologous proteins have a common ancestor  

♦ Structure is more conserved than sequence  

♦ Proteins with a similar function have a similar structure  

− Protein folding

♦ Levintal's paradox

⇒ That proteins try all confirmations and then pick the most energy  

effecient

⇒ But, given a polypeptide of 101 residues which each have 3 possible  

confirmations, sampling would produce 5x1047 confirmations ⇒ Not possible  

♦ Anifinsen's Dogma

⇒ Native structure is determined only by the proteins sequence ⇒ Native structure is unique, stable and kinetically accessible, minimum  

of the free energy for a given environment

⇒ Primary structure determines tertiary structure  

⇒ Disulfide bonds form after the protein forms

♦ Denaturing of proteins can occur when the native confirmation is  

disrupted and the biological activity is lossed

♦ Protein folding occurs by cumulative selection  

♦ Energy of protein folding

⇒ The polypeptide collapses into an intermediate moltengobule due to  the hydrophobic effect, thus the backbone rearranges to achieve a  stable molecule

⇒ Chaperones assist in protein folding by hydrolyzing ATP  

− How to fold proteins to solve "problems"

♦ Folded proteins must…

1. Bury the hydrophobic groups

2. Expose charged groups or satisfy these groups with salt bridges 3. Expose polar groups or satisfy these groups with salt bridges 4. Obey stereochemical restraints

♦ But there is a problem

⇒ How do you bury the hydrophobic side-chain in the core of a protein  and still satisfy the strong dipole and hydrogen bonding of the back  

bone?

⇒ Solution: Alpha Helixes and beta sheets

− Alpha Helixes

♦ Carbonyl of residue 1 accepts a proton from the amide

♦ There are 3.6 residue per turn of the helix

♦ Amphipathic helixes

⇒ Needs another hydrophobic structure to shield its hydrophobic surface ⇒ Usually found on the proteins surface or at a protein-protein  

interactions

Example question: If you extracted a 21 residue amphipathic helix from

a protein and placed it in a pH 7 buffer, what do you expect to happen? Answer: The helix would not form because the water in solution would  

satisfy the main chain hydrogen bonding more efficiently than the helix

would

♦ Proline is a helix killer

⇒ Had no amide proton so most helixes stop at proline in a proton − Beta Sheets

♦ Needs at least two strands

♦ Satisfies main chain-main chain hydrogen bonding

− Torsion angles

♦ Native confirmation is achieved by rotation of the main chain and side  

chain torsion angls

♦ You need 4 atoms to make a torsion angle

♦ In proteins there are 3 torsion angles in the main chain given the names φ,

ω, ψ

♦ Trans confirmations are the most common

⇒ The difference is in the ω angles

⇒ Trans ω=180°

⇒ Cis ω=0°

♦ Ramachandran plot is a method that maps out the torsion angles and the  

most abundant found in nature

− Beta turns

♦ The 1st and 4th amino acids are hydrogen bonded

♦ The 2nd and 3rd are hydrogen bonded to a water

♦ There are two types that is defined by the torsion angles

Example question: Which noncovalent interaction is responsible for stabilizing  

alpha helices and beta sheets?

a. Hydrophobic

b. Ion pairing

c. Hydrogen bonds

Answer: C, secondary structure is defined by the hydrogen bonds between

the strands of amino acids

− Peptides and PI

1. Depends on the sequence  

2. The pKa of N-terminal is around 10

3. pKa of C-terminal is around 2

4. Then must take into account the pKa of the ionizable side chain 5. As the pH of the buffer system changes so too does the pH of the protein − Protein misfolding

1. Occurs spontaneously

2. Prion= same sequence different fold

3. Unknown occurrence because sequence determines fold

− Protein folding overview

1. Motifs--folds--domains--structure

2. Motifs: a recognizable combination of secondary structure (alpha helices  

and beta sheets)

3. Fold: order of secondary structure elements in a domain

4. Domain: a section of a polypeptide that folds independently of the rest 5. Tertiary structure: Dimenstional confirmation of a natively folded  

polypeptide made up of one or more domain

6. Quaternary structure: the association of two or more folded polypeptide  

chains into oligomeric complex

⇒ Named by the type of protein (α,β,γ) and then by the number of each ⇒ Examples: α2 is a two of the same polypeptide chains, αβ is two  

different proteins, αβγ is three different proteins, α2β2 is four chains  

with two pairs of the same chains

− Protein classification  

1. Globular: water soluble, compact, spherical with a hydrophobic interior  

and hydrophilic exterior

2. Fibrous: used in mechanical support. Example: collagen, tendons, skin,  

and hair--there is a glycine every 3rd residue

3. Membrane: lay across the membranes and work in transport and signals  ∙ Biochemical techniques used to study proteins

− Steps to purifying  

1. Isolate protein of interest

2. Remove bulk protein  

3. Purify protein of interest  

⇒ Several methods of purifying by: size, charge, hydrophobicity, ligand  

specificity  

⇒ Size exclusion chromatography: biggest proteins come out first ⇒ Ion exchange chromatography: cation exchange and anion exchange ⇒ Affinity chromatography: separates based on how a protein fits on a  

ligand  

⇒ Hydrophobic interaction chromatography: proteins bind at high salt  

concentrations and elute at low salt concentration  

− SDS-PAGE electrophoresis

♦ Native protein is heated in SDS and denatured with uniform charge ♦ Loaded into gel between glass plates with a positive and negative pole ♦ The molecules of with the lightest weights move towards the bottom of  

the gel

∙ Hemoglobin

− The red protein found in red blood cells

− Carries oxygen and carbon dioxide

− It was the first protein whose 3D structure was determined  

− α2β2 tetramer

− Beta chain is slightly larger

− Heme groups bind oxygen

♦ Six oxygen are bound to an iron in a square-bipyramidal confirmation ♦ Fe2++ O2⇒ Fe3+ + O2-

♦ It’s a continuous redox reaction  

♦ Hemes binding cleft is hydrophobic

⇒ Prevents charged superoxide from leaving

⇒ O2- is more attracted to Fe3+ than atoms in the binding cleft

♦ When oxygen binds to iron it pulls the iron into a prophyrin plan ⇒ Pulls the proximal HIS toward the prophyrin plane

⇒ Helix with HIS 93 shifts positions

⇒ Disrupts the ion pair interaction between subunits

− Hemeglobin is dynamic  

♦ Moves between high affinity (R-state) for oxygen and low affinity (T-state)  

for oxygen

♦ R-state has a hyperbolic binding curve

♦ T-state has a hyperbolic binding curve

⇒ This state aides in oxygen delivery by not competing for the released  

oxygen

⇒ This causes allosteric activation: occurs when the binding of one ligand

enhances the binding to other sites

♦ R-state is favored after oxygen has bound to αβ tetramets

♦ T-state is favored after oxygen is released

♦ 2,B-BPG is an allosteric inhibitor of Hemoglobin-oxygen binding ⇒ Interacts with the β-chain to stabilize T-state and promote oxygen  

release

− Myoglobin is another molecule that binds O2 but does not exhibit cooperate  binding

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