Biochem 1

What is biochemistry?

The emphasis on the four macromolecules of life and how your metabolism uses them

What are covalent bonds?

Approximate equal sharing of electron pairs between adjacent bonds

What are non covalent bonds?

Interactions between atoms that don’t involve the sharing of electrons

Where are covalent bonds typically found?

Within a molecule to hold the molecule together

Where are noncovalent bonds typically found?

Between different molecules to temporarily or weakly hold them together

What is an H bond?

A bond between electronegative atoms and a hydrogen bonded to another electronegative atom

What is an ionic bond?

Bonds between charged species

What is hydrophobia (in reference to chemistry)?

Where polar regions of compounds interact with themselves and water to make clusters of themselves within water

Why is hydrophobia important in biochemistry?

Hydrophobia is what helps proteins fold and makes membranes form

What is VDW?

Van Der Waals interactions which involves interactions between uncharged atoms when in close proximity

What is the strongest kind of bond?

Covalent bonds

What is the weakest kind of bond?

Van Der Waals

What are enzymatic reactions?

An enzyme converting a substrate into a product

What kind of bonds are typically in enzymatic reactions

H-bonds & ionic interactions

What is ligand-receptor binding?

A similar activity compared to enzymatic activity where the ligand binds to a molecule to turn it on or off

How are the folds in a protein maintained?

Through H-bonds & ionic interactions

What is a common polar molecule in Biochem?

Sugars like glucose, glycine, aspartate, lactate, & glycerol

What are examples of nonpolar molecules in Biochem?

Waxes

What is an amphipathic molecule?

A molecule that is not considered polar nor nonpolar since the molecule has both of those regions within the molecule

What are the main contributors to the polarity of a molecule?

H-bonding potential & net dipole

What is ionization?

When a molecule’s charge depends on the protonation (pH) of the environment

When pka is equal to pH, what is favored in the reaction (acid or base)?

The acid (HA) and base (A-) are in equilibrium

When pka is more than pH, what is favored (acid or base)?

The acid (HA) is favored in the reaction

When pH is more than pka, what is favored (acid or base)?

The base (A-) is favored

What is the Henderson hasselback equation?

pH = pka + log(base concentration/acid concentration)

What is a buffer?

A compound with the ability to resist changes in pH by donating or accepting protons

What is a buffering region?

The range of pka that the buffer controls which is +1 & -1 of the pka value that is ideal

What is the average pka of a carboxyl group?

2.0

What is the average pka value of an amino group?

9.5

What are the different sections of an amino acid?

Middle alpha carbon, carboxyl group, amino group, proton, and an R group

What is a zwitterionic state?

The net neutral state of molecule that is zero with often opposing charges

Which steroisomer of alanine is preferred?

The L (clockwise) form using the CORN rule (carboxyl, R group, amino group)

What are the five different groups of amino acids?

Nonpolar aliphatic R groups, polar uncharged R groups, aromatic R groups, positively charged R groups, & negatively charged R groups

What is a characteristic of the nonpolar, aliphatic R group amino acids?

The R groups aren’t ionizable so the R groups are never changing pka and aren’t relevant

What amino acids have the nonpolar, aliphatic R group?

Glycine, alanine, proline, valine, leucine, isoleucine, & methionine

What amino acids have the aromatic R group?

Phenylalanine, tyrosine, & tryptophan

Which amino acids have a polar, uncharged R group?

Serine, threonine, cysteine, asparagine, & glutamine

Which amino acids have a positively charged R group?

Lysine, histidine, & arginine

Which amino acids have a negatively charged R group?

Aspartate & glutamate

Gly is what amino acid

Glycine

G is what amino acid

Glycine

Ala is what amino acid

Alanine

A is what amino acid?

Alanine

Pro is what amino acid?

Proline

P is what amino acid

Proline

Val is what amino acid

Valine

V is what amino acid

Valine

Leu is what amino acid

Leucine

L is what amino acid

Leucine

Ile is what amino acid

Isoleucine

I is what amino acid

Isoleucine

Met is what amino acid

Methionine

M is what amino acid

Methionine

Phe is what amino acid

Phenylalanine

F is what amino acid

Phenylalanine

Tyr is what amino acid

Tyrosine

Y is what amino acid

Tyrosine

Trp is what amino acid

Tryptophan

W is what amino acid

Tryptophan

Ser is what amino acid

Serine

S is what amino acid

Serine

Thr is what amino acid

Threonine

T is what amino acid

Threonine

Cys is what amino acid

Cysteine

C is what amino acid

Cysteine

Asn is what amino acid

Asparagine

N is what amino acid

Asparagine

Gln is what amino acid

Glutamine

Q is what amino acid

Glutamine

Lys is what amino acid

Lysine

K is what amino acid

Lysine

His is what amino acid

Histidine

H is what amino acid

Histidine

Arg is what amino acid

Arginine

R is what amino acid

Arginine

Asp is what amino acid

Aspartate

D is what amino acid?

Aspartate

Glu is what amino acid

Glutamate

E is what amino acid

Glutamate

What is the R group of glycine

H

what is the R group of alanine?

CH3

What is the R group of valine

CH(CH3)2

What is the R group of leucine

CH2CH(CH3)2

What is the R group of methionine

CH2CH2SCH3

What is the R group of isoleucine

CH(CH3)CH2CH3

What is the R group of lysine

CH2CH2CH2CH2+NH3

What is the R group of histidine

CH2CNH+CHNCH in a five membered ring

What is the R group of aspartate

CH2COO-

What is the R group of arginine

CH2CH2CH2NHC(+NH2)NH2

What is the R group of glutamate

CH2CH2COO-

What is the R group of phenylalanine

CH2 connected to a benzene ring

What is the R group of tyrosine

CH2 benzene ring OH

What is the R group of tryptophan

CH2 (5 membered ring with NH) (benzene ring)

What is the R group of serine

CH2OH

What is the R group of threonine

CH(OH)CH3

What is the R group of cysteine

CH2SH

What is the R group of proline

3 methyl groups that are connected to the amino group to make a ring

What is the R group of asparagine

CH2C(O)NH2

What is the R group of glutamine

CH2CH2C(O)NH2

What is the pka of tyrosines R group

10.07