Biochemistry Final Exam Notes Dec 8 2025 day

Study as soon as possible

What is the applied operation of the pOH?

-log(OH) it equals to 14-pH ,it equals to 14 + log (H⁺) .Lastly it can be described as the pKa X 10¹⁴ and it eqauls to 55.5 M

Why does a buffer not work past its pKA +- ! ?

a) because the Weak Acid will be fully ran out

-A buffer is only deemed affected to the pH range that is its PKA+- 1. IF we go past this threshold there is no longer Significant Amounts of weak acids and conjugate base within the Buffers. 

What is an untrue Statements about aminos acids ?

That they all have a chargeable R-group.

An Amino Acid has a PI( Isoelectric point) Lower (smaller) than the pH of the solution it is in . How would it behave in an electric field.

A) it would move towards the Cathode (Positive End)

• When an environment pH is larger then Amino Acids isoelectric point it will emit a Negative charge And be attracted to the opposite Charge In

What is the purpose of the Henderson Hasselbalch Equation?

Known as a way to describe the Theoretical relationship between the pH of a Buffer solution and the Concentration  of weak acid (HA) or Conj Base (A^-) 

What are the 4 amino acids classification ??

Its deemed to be devided in 4 sections Through its R -group. Polar-Charged, Non-polar, Charged Acidic, And lastly Charged basic 

Define and briefly explain a basic amino acids?

Known as being Lysine Amino acid can be know to have polar qualities and For it to be a charged molecule.

Define a IEC (Ion exchanger column)??

Known to separate Amino acids/ Proteins Through there degree of charge. There are Two Main Types Cation Exchanger Like Dowexx-50 that binds to (+) Charged molecules. As well as An Anion exchnager that is DEAE that’s binds to (-) charged moleucles.

Briefly Explain the Anion Exchnager

Known as DEAE tends to have a much Higher Pka. Known to bind with Negative Charred molecules. Contains  (+) charged Resin Beads that will repel Same (+) charged molecules and force it to enter a Mobile Phase.

Explain the TLC ( Thin Layer Chromatography )

Known as A molecule Loaded into a stationary phase. The mobile phase will begin by capillarity Action. Movement starts Through the addition of a solvent such as a Paw Solvent.

Define a polyprotic amino Acid??

Known as a Molecule with at least 2 pKA and therefore at least having two buffering range

Types of movement within The TLC( Thin Layer Chromatography)??

Known as the more polar molecules moving from the point of origin in the Reverse Phase Chromatography. AN in the Normal Phase Chromatography  The least Polar molecules move

Describe A Catabolic Reaction ??

Known to consume energy to help  Build complicated molecules for Simpler one. The ΔG ( Gibbs Free energy) + Above 0

Provide an Biological example of the energy Coupling ??

Known as The an Exergonic Process ΔG =- . An example of this is the ATP through (Photon energy Transduction as well as Primary Active Transport

ΔH Enthalpy Relationship with bonds?

Known as ΔH relating to the bonds within a system Being Covalent, Ionic , Hydrogen bond and lastly hydrophobic interactions as well the kinetic energy 

Explaining the (ΔS) Entropy ??

Known to correspond to the idea of randomness, and the spreading of energy. The higher the (ΔS ) The more energy is being spread.

Evaluating a Folded/ Unfolded Protein ??

Known as an unfolded protein will have a larger ΔS The more energy is being spread 

Define a Spontaneous Reaction ??

Known as being an “Exergonic process” happens from a (-) ΔG. Known to released Energy to the surrounding. 

Effects of large clustering of Non Polar molecules ??

From this the Hydrophobic effect can lead to the reduction of the surface area with the saturation. The less hydrogen bonds lost less water molecules are contaminated which correlates less Reduction of surface area 

Movement of solutions from the perspective of non Polar to polar Ionic compounds ??

Due to the ability to form bonds . The water Molecules when mixed with polar molecules can move more in water molecules then the Non polar solvating molecules . which separate / Form a  barrier from the polar water molecules. 

Define the Metabolism??

Known as the sum of all chemical reactions that take place within an organisms 

Define Equilibrium and its function??

Appears through an exergonic reaction ΔG=- will occur to a point in which reactants that are converted products and products that are converted back to reactants  at equal parts.

Evaluating a Bond strength Through its angle??

The strength Of a hydrogen bond is seen as a portioned to its angle. Which is relevant to the covalent Bond of the hydrogen molecule . IF ΔH enthalpy is increased the H bond angles increased the weaker the bonds are. The larger the ΔS entropy the smaller the (ΔH) more  space from entropy will cause the hydrogen bonds to be more aligned eluting to it being stronger  

Where is the Most Disulfide Bridges founded ??

Known to be the most commonly founded in the Extracellular proteins. 

Importance of the Hydrogen & the Hydrophobic interactions??

Known as the main contributor to the formation of secondary structures. - The Solution layer helps to reduce both types of interactions compared to the unfolded protein.

How Non-polar molecules Impact Entropy ((ΔS) in an aqueous solution 

Known to have a more drastic decrease in (ΔS entrophy then the charge of Ionic/ polar molecules that is deemed as a minor change .

From non Polar molecules

ΔG ↑↑ =ΔH↓↓ -TΔS↑↑

Evaluation of the secondary protein structure ??

Known to be The molecules like the α-Helix and the Beta-Please sheets That are caused by a repeated protein of Identical or very similar dihedral angels. In most secondary structures they tend to lower ΔH. Due to the lost of the H(Hydrogen Bonds) 

Key Description of a secondary Protein Structure ?

Are known to have a hydrogen bond Arrangement being the backbone of the protein or (Polypeptide Chain). The closer bonds are stronger within the 2nd Structures will contain more ↑↑ ΔH ( Enthalpy). A more spread out secondary structure will have a ΔH↓↓ (Lower Enthalpy) trough the structure creating more aligned Stronger Hydrogen bonds.

Rotations within the Polypeptide ??

The single Carbon structure provide for more rotation then the Double bonds. The Peptide bonds between C=O and the N-H will give the resonance structure of a peptide bond. Rotations of a polypeptide is linked to the rotations causes by the Cα-C Bond. Rotations of these bonds are refereed to the dihedral angle (PSI) . The N-C_α are known as the PHI (BOnds)

What type of Bonds can formed H- Bond within Water??

Known as the Nα-H bonds as well as the Cα=O can be able to form hydrogen bonds with a water molecule . 

Folding of hydrogen bonds & peptides?

Can effect a polypeptide by reducing the decrease ΔS (entropy) less drastic drop and less clustering of a hydrophobic Moleucle  within water .

Define a Tertiary structure ?

Known as a 3-dimensional arrangement of all the Atoms in a protein. In which extends to the side (R-chain) and the prostatic  groups can be known to lower enthalpy ( ΔH) have less energy forming 

Explain the Native confromation of a Protein ?

Known to be Achieved and envaulted through the Counteractions on many weak interactions caused by the hydrogen bonds, Ionic & Hydrophobic interactions.  

Evaluating the Charge on an amino Acid ?

If The PH > PI A Amino acid will be negatively (-) charged. If PI> pH The amino acid will be (+) Charged . 

Importance/ Describing the quaternary structure ?? 

Is deemed as an arrangement of multiple polypeptides chains (subunits). With respect to one another ( example is a hemoglobin molecule . The interactions surrounding the subunits are mostly non covalent. The Hydrogen bonds & hydrophobic interactions are the main reason those structures get formed.

Describe / Explain the Co factors ??

Known as a Non protein component that can assist in the function of a larger Quaternary protein. Can be known as A Vitamins, Hemo groups or a Hemogloblin. Can work to be a cofactor to a large protein structure. 

Entalphy is

Known to be proportionate to the type & numbers of bonds within a molecule.

Adding Non-polar molecules impact Entropy ΔS of an aqueous solution ??

Know to have a more Drastic decrease In ΔS (entropy) then the Change of polar Ionic molecules that is deemed as a minor change.

What is the Strongest bond within a protein?

Known to be a covalent bonds that ranges from 200-460 Kj/mol can make primary structure thats is very strong .

Importance/degree of change from the Hydrogen bond Perspective

Known as the Hydrogen bond As well as the folding of the polypeptides can assist to reduce the decrease of ΔS entropy when a molecule begins to cluster within the water molecule.

Which of the following interactions/ /bonds singular reduces the ΔH entropy of a polypeptide the most.

e) known as the Disulfide bridges Due to the ability to form a stronger Covalent bonds among the Molecules that will require the most energy to break them had a ΔH that’s is much lower

Which of the following is true about the anabolic pathways ??

the ΔG (Gibbs free energy ) may be negative or positive but the total ΔG is (+) positive.

Define & explain the Use of a Specific assay ?

Known as a Approach that measures The presence of a Protein . That different types causes to the affinity & the enzymatic Assay.

Define the process of The ammnunio sulfate Percuipation ??

Known as the first major step assingting with the concetration and the partical purifctaion sof the Porteins. When adding the Ammioni sulfate Wull caused the Compeption of the superifcial polaort and the ionice gorups of a aprotne. The water meolcules will effetc the resulting with the pericipation of a protein leading into a higher concetraion.

Reasoning of the different timing of the Protein perceptions from the ammonium sulfate approach.

Can alter and have a vastly different timing based on a protein superficial Polarity and charge . The difference in MW and lastly temperature and the PH of the protein sample , can help with the Assisting in the process of Fractionating proteins .

Describe what is the P.A.G.E ??

Known as the poly -acrylamide Gel- electrophoresis that is an approach of a protein isolation that separates the protein of a polyacrylamide gel matrix by applying it within an electric field. The important because it can help identify the purity and mW( Molecular weights of a protein in a sample )(.

Explain the Denaturing SDS -page ?? 

The proteins That are denatured WIth the SDS , and ONly Sperated based on theor size . Can help with the estiamting of the MW 

Describe the Western BLot ??

Known as a method To identify the presence of a protein in a sample separation that coccurs in the SDS not page are then moved to a Nitrocellulose sheet . The Charged proteins is then visualized on the sheet using a protein specific antibodies

Explain the polyacrylamide Gel

are used to separate proteins an the smaller DNA molecules .

Importance of the Affinity Chromatography ? 

Known as the method To give the largest old purification of any step that’s is used in a protein purification .

Explain the HPLC ? 

Known as the High performance Liquid chromatography. The elution buffer is used and pumped over the resin at a high pressure and speed. The Benefits extend to reduces the transit time of the proteins within the column. As well reduced the spreading if a protein band during elution . L:astly improves the resolution of the separation  

Explain the MSS ( Mass spectrophometry sequencing )??

Known to be an phsycial method . The prufied portein protein is first ionization. Then a selected peptide is fragmented and analyzed by the mass spectrometry . Separation based on the charge to ,ass ratio . Larger Peptide exit after the saller ones

Explain the Protein Consences seqeucing ?

Deemed as the sequence that are the highly conserves sequencing between the proteins/ DNA molecules molecules. The Importances of the Consensus sequence omplau on the eessmetail fuctiom with a portine (DNA opr ATP bdinding DOmain, as aeell as the intermembrande DOmain ).

What are the main Sources/ Tools to assist with the study for the tertiary/quaternary Structure ??

Known as the process of the X -ray Crystallography . NM|r ( nuclear magnetic resonance ). The cryo-em  (cyro-electron microscopy and lastly the computation Biology of the primary sequence 

Define and explain what are the enzymes ?? 

Know to be mostly proteins except For some RNA Exceptions known to co-operate within a protein native confirmation .

what are the key tools that’s help / assisting of mechanisms within the enzyme.

Known as the cofactor that appear as the inorganic ions such as mg²⁺(magneisum) and Fe²⁺ Iron. A coenzyme thats is an organic molecule such as NADH and FADH₂. And lastly a prosthetic group that appears when Cofactors bind highly 

Explain the overall rate of a Reaction ??

deemed to be associated with the Activation energy (ΔG⁺) of a molecule deemed as the energy necessary for the substrate in order to reach the transition state .

enzyme effect on an action ??

Known to promoted the environment through the active site of an reagent (S) Substrate to end up becoming more reactive and convert into the P Products

Evaluating the Enzyme activation energy ??

Are deemed to be formed by a non-covalent interactions. Known to be The same as the structural Interactions Such as the H-bonds. It leads to a major Releasse of energy. And through the non covalent interactions helps to lower the amount of activation energy

What are the two possible models of Enzyme Substrate biding ?

Known as the Lock and Key model along with the induced fit model 

Define the Lock & key model ??

Known as the active site and substrate that are completely Formed as used for the Immediate Optimal Binding 

Explain the Induced fit model?? 

Deemed as the Biding of the substrate induces a Conformational change with the enzyme as well as the substrate. Complementary that is reached at the transition state 

A reaction Overall Induced Fit model ??

will have a Energy released ( ΔG_B Binding energy) know to lower The activation energy of the reaction , Hench speeding up the reaction. Through this enzyme will try its best to orientate to cofactors within a placed that helps getting the Max of ΔG_b Binding energy. 

Evaluation of  ΔG_B and specificity with an enzyme molecule ? 

Changes in the enzyme’s or substrate functional groups
involved in weak interactions will result in lower ΔGB and
therefore lower specificity

Examination of the Entropy  ΔS reduction within a Enzyme ??

From the previous step of a biding of a substrate in an active site to the molecules included a more compact and constrained structures. The position of a Closer proximity  of a reacting group . This is offset by a binding energy. 

Describe the Electron Redistribution ??

Known as the electron molecules moving around through the impact of energy. This source us forming the binding energy.

What are the 3 types of Catalyst ?? 

Known as being the Acid-Base catalyze , covalent catalyzed and lastly metal Ion catalyst .

Assistance/ Impact on the covalent Bonds ??

Are important because it helps to decrease the activation energy of an enzyme. As well Promote the forming of the products. from the substrate from the metal - mediated Ionic bonds and covalent Bonds. 

Key Details of the Covalent Catalyst ??

Deemed as a transient Covalent Bonds that is formed between the enzyme and the substrate ,altering the pathway and lowers the activation energy with the Covalent (X), reaction becomes

1) A-B + X: —— A-X + B
2) A-X + H2O——- A + X:

A complex protein ?

Known as being an inorganic Ion or coenzyme labelled as the holoenzyme.

Other names of a Enzyme ??

Refereed as a apoprotein or a apoenzyme. 

The ΔG_b Contributes to the rate of reaction Through?

Offsetting the decrease with the ΔS entropy. Reducing the solvation effect. As well offsetting the energy required to redistribute electrons with the substrate. And lastly through the rearrangement from the enzyme substrates interactions