Biochemistry: Chapter 3 & 4

What is the difference between a Fischer projection and a stereochemical rendering?

Fischer projection:

• 2D convention

• uses vertical and horizontal lines

• standardizes orientation → makes comparison of molecules easy

Stereochemical rendering:

• 3D arrangement

• wedges show depth

What is an essential amino acid?

• 9 amino acids

• human body cannot produce it on its own

• need to be from diet

“it is essential to get this by food”

What is a non-essential amino acid?

• 11 amino acids

• human body can produce it

What is a conditionally non-essential amino acid?

• body can produce it, but sometimes not enough

• infants need more arginine as they grow

What is kwashiorkor?

• “the disease of the displaced child”

• protruding belly due to edema

• not enough protein distorts the normal distribution of water

• causes a fatty liver

What are stereoisomers? Do you find L or D isomer predominately in amino acid life?

• molecules with the same chemical formula and connectivity but differ in the three-dimensional arrangement of their atoms

• no plane of symmetry (mirror images)

• L isomers are more predominate

Why are amino acids usually found as a zwitterion in physiological conditions?

because they contain both an acidic carboxyl group (–COOH) and a basic amino group (–NH₂). This dual charge allows the amino acids to act as both acids and bases depending on the pH of their environmentBecause physiological pH (7.4) sits directly between the pKa values of its two backbones groups, carboxyl group and amino group.

• carboxyl group is deprotonated

• amino group is protonated

• more soluble in water, act as buffer, stability for structures

How does the R-group/side chain pKa value contribute to their function?

• pKa of the side chain determines if it is deprotonated or protonated

• important for protein stability

• ionizable side chain enhance reactivity and bonding

What is an isoelectric point?

• the point where a molecule has no net charge

Which amino acids contain a hydroxyl in their R-group?

STY

• serine

• threonine

• tyrosine

→ phosphorylated by kinases

→ dephosphorylated by phosphatases

What are the features of charged amino acids?

• either positive or negative

• highly polar

• found on protein surface

• participate in salt bridges

What are the features of hydrophilic amino acids?

• no net charge

• form hydrogen bonds with water

• short aliphatic side chains

• found outside of proteins

• involved in post translational modification

What are the features of hydrophobic amino acids?

• lack polar groups

• found in interior of proteins, clustered together

• mostly all hydrocarbon side chains

• stabilize protein via hydrophobic interactions

What are the features of aromatic amino acids?

• bulky (rings)

• absorb light between 250-280nm

• hydrophobic

• important in enzyme active sites

What are features of a peptide bond?

• covalent bond

• between carboxyl group and amino group

• forms backbone of proteins

How is a peptide bond formed?

• through condensation reaction, H2O is removed

What is the resonance (electrons being shared) of a peptide bond?

• partial double bond between C and N

What is the length of a peptide bond?

• it is shorter than a C-N single bond

• longer than a C-N double bond

What is the strength of a peptide bond?

• it is stronger than a C-N single bond

• but weaker than a C-N double bond

What is the planarity of a peptide bond?

• peptide bond atoms are planar

• no rotation due to double bond

• either cis or trans

What is the alpha carbon of a peptide bond?

• attached to R group, amino group, and carboxyl group

Why is a peptide bond chiral?

• because 4 different substituents are bound to it

What is a protein motif?

• combination of secondary structure

• present in many proteins

• exhibit similar functions

What is a protein domain?

• polypeptide chains folded into compact regions

• connected by flexible segment

• functional unit

What are the features of primary protein structure?

• amino acid sequence

• held by peptide bond

• covalent

• 1 polypeptide

What are the features of secondary protein structure?

• held by hydrogen bonds

• noncovalent

• 1 polypeptide

• alpha helix

• beta pleated sheet

• parallel or antiparallel strands

• turns and loops

What are the features of tertiary protein structure?

• 3D structure

• folding of polypeptide

• held by disulfide bond

• noncovalent and covalent

• 1 polypeptide

What are the features of quaternary protein structure?

• bonding between proteins

• noncovalent

• held together by all bonds

• more than 1 polypeptide

What are metalloproteins?

• proteins that contain a metal ion

• structural and functional effect

• covalently or ionically bonded

What is Levinthal’s paradox?

• if protein folding was completely random, it would take small proteins longer than the age of the universe to fold

• in reality, proteins fold in less than 1 second

• this is because protein folding is not random

• protein keeps the correct conformations and only tries the wrong ones again

→ chaperons help prevent misfolding

→ alpha helixes and beta sheets form fast, then guide the rest of folding

What are intrinsically disordered proteins?

• don’t have a fixed 3D structure

• they get structure upon interaction with another protein

• so different protein partners = different structure

What are metamorphic proteins?

• adopt 2 or more 3D structures, each with a different function

• difficult to predict secondary structures

What causes prion disease

• a normal cellular protein misfolds into pathogenic form

• this misfolded protein induces misfolding in other proteins (infects)

• causes growth of abnormal insoluble protein complex

• can happen without DNA or RNA

• infectious

What is amyloid disease?

• various unrelated proteins misfold and aggregate (cluster) into amyloid fibrils

• not infectious

• alzheimers, parkinsons, etc.

After a protein is translated from mRNA, is that the end?

• no, because there is post translational modification

• this is the chemical changes to a protein after it has been synthesized

• it alters the structure and function

What are examples of post translational modification?

• phosphorylation: addition of phosphate group

• glycosylation: addition of sugar molecule

• methylation: addition of methyl group