Amino Acids and Primary Structure

primary protein structure

sequency of a chain of amino acids

secondary protein structure

local folding of the polypeptides chain into helices or sheets

tertiary-protein structure

3-dimensional folding patterns of a protein due to side chain interactions 

quaternary protein structure 

protein consisting of more than one amino acid chain

Explain knobs and holes

Amino acid sidechains create knobs and holes; the knobs must fit in holes to achieve tight chain packing during protein folding. this is a steric fit, no large empty spaces

list the three things that R groups affect in amino acids

1) size/shape

2) Hydrophobic character

3) non-covalent interactions

What configuration do amino acids take and what kind of carbon do they have

L, chiral alpha carbon

List the three key properties of amino acids and explain them

1) size/shape: knobs in holes, packing during folding

2) hydrophobicity: protein folding, interfaces, small molecule-protein interactions

3) non-covalent interaction: protein folding, interfaces, small molecule-protein interactions

How can DNA mutations that alter the amino acid sequence affect protein structure 

by changing one or more of the three key properties of amino acids

List the basic amino acids

Lysine, Arginine, and Histidine

List the acidic amino acids

Aspartate and Glutamate

What do basic and acidic amino acids participate in and where are they found

participate in charge-based non-covalent interactions between proteins/other molecules

often found in the active site of enzymes 

List the amino acids with polar R-groups

Serine, Threonine, Cysteine, Proline, Asparagine, Glutamine

Where are polar amino acids found and list the unique aspects of the individual amino acids

• found on the exterior of proteins

• proline can cause sharp bends in the polypeptide chain

• serine and threonine are often phosphorylated

• cysteines can form covalent disulfide bonds

List the amino acids with hydrophobic R-groups

Glycine, Alanine, Valine, Leucine, Methionine, and Isoleucine

What do amino acids that are hydrophobic help mediate, where are they found, and what is unique about glycine

• mediate the hydrophobic effect

• found packed together in the protein interior, especially ILV

• glycine imparts flexibility to proteins structures 

List the amino acids with aromatic R-groups

Phenylalanine, Tyrosine, and Tryptophan

Where are aromatic amino acids found? Are they hydrophobic/hydrophilic? List the unique qualities 

• hydrophobic

• buried in the protein

• Tyrosine and Tryptophan have H-bonding groups often near the surface

What three things are all important for amino acids and why

1) Chemical properties: determine the types of interactions the amino acids can participate in

2) Size and shape: determines how amino acids fit together as the protein folds

Why, since Glu and Asp have the same chemical functionality, do they still work differently

Glu forms a bigger knob than Asp

What are found at the end of the polypeptide chain that form ions

the backbone NH2 and COOH groups

is the amino acid protonated or deprotonated when pH is less than pKa

protonated

is the amino acid protonated or deprotonated when pH is greater than pKa

deprotonated

Amino acids undergo ____ ionization

ph-dependent

what is the basis for pH-dependent regulation of the cellular processes

amino acid ionization

changes in pH can also cause changes in the ___ of the side chains in certain amino acids

ionization  

What do post-translational modification do

change the chemical and/or steric properties of the original amino acid

what can changes in amino acid properties lead to

changes in the structure and function of the modified protein

what are eukaryotic genomes organized into

chromatin

What does chromatin fiber compaction regulate

transcription

why does chromatin compaction occur

due to interaction between positive and negative amino acid

Where are PTMs common on

histone proteins

explain Lysine acetylation

• side chain is longer

• 2 H-bond donors are lost then 2 H-bond donors are added

• moves from positive to polar

• regulated by HATs and HDACs

What does Lysine acetylation disrupt

chromatin compaction

what is permissive to transcription

unfolded, acetylated chromatin

What do post-translational modifications create more of

complexity in the proteome

What three things does the specific amino acid sequency dictate 

specific folding, structure, and function of a protein

What two things does the order of amino acids (sequence) dictate 

structure and function

What does a specific sequence determine

3D shape and specific cellular function

What two things does primary structure encode for

folding and function

What must the estrogen receptor amino acid sequence fold into

tertiary structure

what does estrogen receptor bind to, and what happens when it binds

binds to estradiol, changes its conformation once estradiol binds to expose a DNA interaction site on the protein surface

define peptide

a molecule that contains two or more amino acids

define polypeptides/proteins

peptides that contain many amino acids

what are amino acids in a polypeptide chain connected by

peptide bonds

What are on the ends of polypeptide chains

an unreacted amino group on one end (N-terminus) and an unreacted carboxyl at the other end (C-terminus)

what link amino acids into peptides

peptide bonds

how to peptide bonds form

through a dehydration reaction between the carboxyl group of one amino acid and the amino group of the next amino acid

where are peptide bonds formed

ribosomes