Biochem succinctly (finish Ledt5 actully im doing random things now

Anabolic rxns are ____-gonic, Catabolic rxns are ____-gonic

Endergonic, exergonic

Vital force was proposed by ____ and debunked by ____

Aristotle… Fredrich Wohler

Lysate

The components of a lysed (broken) cell

MATH Q: What happens to pH of acetic acid/acetate solution when 0.1 mol of NaOH is added? State how to solve, no numbers

The pH increases based on the new ratio of buffer solution. You can use molar amounts instead of concentrations.

H bond donor vs H bond acceptor

Donor supplies the Hydrogen (must be partially +ve aka -OH or -NH)

Acceptor accepts the Hydrogen (-OH, -NH, -COC-)

No, an H bond donor is not a lone pair donor

Where do you find pI on a titration curve?

Located at the steep slope after the buffer that turns +1 aa into 0 aa

Only the _ configuration of amino acids is found in living systems, and only _ is found in sugars

L in aa, D in sugar

Which amino acids are chiral?

All of them except Glycine

Be careful with the 3 letter abbrevs: Glu is for _ and Asp is for _

Glutamatic acid (not Glutamine), Aspartic acid (not Asparagine)

The 2 special amino acids

Cysteine - can make disulfide bond w another cysteine (a covalent called cystine)

Histidine - its imidazole ring makes it a zwitterion at physio pH

Smallest and biggest amino acids

Gly and Trp

Do enzymes change ∆G?

No, they change Ea not spontaneity

Proteins are built from … to … DNA is built from … to …

N to C, 5’ to 3’

Amino acids can freely rotate about their…

Alpha carbon

Ways of classifying proteins (hint 4º struct)

Monomeric protein: only 1 chain

Oligomeric protein: multiple subunits

Conjugated protein: a protein w/ a prosthetic group

Homotypic protein: all identical subunits

Heterotypic protein: different subunits

Fibrous protein key properties

Water insoluble, specifically made by a chain of hydroxy-P-G- and so on

HARD Q: Based on circular dichroism spectroscopy, how to tell an aa’s 2º structure?

If it has a beginning peak and ending bathtub, mostly alpha helices

If it has less steep beginning and ending, mostly beta sheets

If it has a beginning valley, it is likely denatured

Label the Ramachandran plot by stating which protein structure causes a blue region for: A, B, C, D

A: left-handed alpha helix (dont needa know)

B: right-handed alpha helix

C: antiparallel or parallele beta sheets, collagen triple helices and others (dont needa know)

D: nothing

Ball knowledge properties of alpha helices

• R groups are protruding out of the helix

• 3.6 residues to make 1 turn

• Bulky amino acids like Trp cannot form a helix

Ball knowledge properties of beta sheets

• R groups alternate btwn projecting above & below the sheet

• antiparallel sheets are more common

What are beta bends/turns made of?

Proline and Glycine

For the following (1º, 2º, 3º, 4º), describe what bonds are formed and if it occurs in the peptide backbone or the R groups

1º peptide bonds in backbone

2º H bonds in backbone

3º IMFs or disulfide in R groups

4º IMFs or disulfide btwn diff subunits

How does enthalpy and entropy increase and decrease In protein formation?

Entropy decreases as protein starts folding. Entropy increases as hydrophobic effect minimizes the # of ordered waters. Enthalpy decreases/ released when bonds/IMFs form.

Properties of chaperonins vs chaperones

Both consume ATP to function, but chaperonins surround the entire protein completely (Hint: ronin = W kidnapping)

Advantages and Disadvantages of SDS-PAGE

Cheaper, Simpler, Resolutioner, More reproducible than centrifugation; low resolution for very large molecules

Ingredients required for SDS-PAGE (and their purposes)

SDS - to give proteins a universal negative charge

beta-ME - to further denature proteins by breaking disullfide bonds

polyacrylamide gel

SDS-treated proteins go toward the ___ in SDS-PAGE

anode

3 (actually 4) types of chromatography (explain which protein elutes fastest too)

Anion exchange chromo: most POSITIVE protein elutes fast (becuase the resin has anions)

Cation exchange chromo: most NEGATIVE protein elutes fastest

Size exclusion/gel filtration chromo: largest protein elutes

Affinity chromo: protein that binds weakest to ligand elutes (lowest affinity)

Question: Predict which amino acids elute faster in anion exchange chromatography? Assume the pH thruout the solution is 7.

Figure out the net charge of the amino acids at pH 7. aa’s that are negative will be at top, neutral aa’s in the middle, positive aa’s in the bottom.

____ ____ is a measure of enzyme purity in a solution

Specific activity = activity units / protein mass in solution

Hemoglobin is made of

2 alpha + 2 beta, each subunit has a heme prosthetic group which is a porphyrin ring with Fe bound

Myoglobin is made of

1 protein which has 1 heme prosthetic group

Hemoglobin vs myoglobin

Hemoglobin for transport (loses affinity for O2 easily), Myoglobin for storage/ emergency (loses affinity at very low pressure)

Briefly state all molecules that Cooperativity in hemoglobin

O2 triggers the R state in hemoglobin, causing +ve coop. H+ and CO2 and BPG stabilizes the T state in hemoglobin, causing -ve coop.

Explain situations when hemoglobin has low affinity for O2

When partial pressure of O2 is low. When pH is low (aka lactic acid in excess), when CO2 is present, when BPG is present (a product of glycolysis)

How does O2 induce a conformation in hemoglobin?

O2 moves the porphyrin ring from bent to planar, causing R state.

How does H+ induce a conformation in hemoglobin?

H+ protonates a salt bridge (ionic interaction) specifically Histidine. Stabilizes the T state.

How does BPG induce a conformation in hemoglobin?

BPG binds to basic central cavity of hemoglobin, stabilizing the T state.

Examples of mutant hemoglobin

Sickle cell makes hemoglobin rupture blood cells, alpha thalassemia causes the complete lack of alpha subunits, beta thalassemia does it for beta

Cofactor vs coenzyme

cofactor = prosthetic group, coenzyme = cofactor that's organic

Holoenzyme vs apoenzyme

Apoenzyme = enzyme that's missing cofactor n doesn't work (hint apoptosis), holoenzyme = opposite

Enzymes vs synthetic catalysts

Enzymes are much more efficient, stereospecific and operate at physio temp & pH

The rate limiting step of an enzyme catalyzing reaction is…

the breakdown of ES -> E + P. This means the limiting reagent is [ES] which is proportional to [E] and [S].

Michaelis-Menten equation. There are 2 forms, 1 is on formula sheet

The bottom is the y=mx + b form found in formula sheet

What happens to V0 at 3 different levels of [S]? Look at Michaelis-Menten!

Extremely low [S]: V0 is close to 0 and dependent on [S]

When [S] = Km: V0 is exactly half of Vmax

Extremely high [S]: V0 is close to Vmax and dependent on [E]

What does a low Km mean?

It means the enzyme requires little [S] to reach Vmax. Because the formula is close to Kd, it also means the enzyme has a high affinity for substrate.

What does a low Kd mean?

Remember the formula

What does a low kcat mean?

It means little [E] is required to reach Vmax. This may mean the enzyme takes very long to do the rxn, and this means the reaction is easily saturated.

2 ways an enzyme can be efficient

An enzyme can weakly bind to substrate (high Km) but catalyzes fast (high kcat). Or an enzyme can strongly bind to substrate (low Km) but catalyzes slow (low kcat)

The best enzyme has a ___ kcat and a ___ Km

high kcat, low Km. However, the ratio kcat/Km cannot be greater than 10^9 (a limit like speed of light)

The ratio determining enzyme is called…

specificity constant = kcat/Km

Other names for Km, Kd, and kcat

Km = Michaelis constant

Kd = dissociation constant

kcat = turnover number

Characteristics of an enzyme's active site

Pretty small compared to rest of enzyme, must before noncovalent forces and not covalent bonds (important!)

Explain what variable in y =mx + b is changed per type of inhibition

For compet the slope changes. For uncompeti the y-int changes. For mixed both change (so two å's)

Explain if Km or Vmax changes per type of inhibition

Compet changes Km. Uncompet changes both Km and Vmax. Mixed changes both.

For which inhibition can adding an obscene amount of [S] nullify the inhibition?

Competitive