What is a zwitterion?

Neutral ion w/ equal # of +/- charges

Ionization state of an AA is altered by _______

Change in pH

What does change in pH mean for AA's

Decrease pH = Protonate COO- Increase pH = Deprotonate NH3+

T/F: AA's are mostly achiral

False, they are chiral

What are the 3 types of classifications of AA's

- Nonpolar (hydrophobic) - Polar (uncharged) - Charged (very polar)

Hydrophobic AA's.... 2

- Lack reactive functional groups - Mainly hydrocarbon side chains

Which AA's are: Aliphatic R group, Hydrophobic R group? 4

- Ala - Val - Leu - Ile

Which AA is aromatic and hydrophobic R group?

Phe

Which AA is aromatic, hydrophobic and forms H bonds?

Trp

Is Trp a donor or acceptor?

Donor

What is the sulfur containing R group, aliphatic and hydrophobic?

Met

Which AA has a secondary amino group, aliphatic, and hydrophobic?

Pro

Polar AA's.... 2

- Reactive functional groups - Contain an electronegative atom

Which AA is achiral?

Gly

Which AA's are polar uncharged, have OH group, typically donor?

Ser, Thr, Tyr

Which polar AA's can be phosphorylated?

Tyr and Thr

Which R groups are neutral, polar? Charged?

Neu, polar: Tyr, Cys, His Charged: Asp, Glu, Lys, Arg

What AA can form disulphide bonds?

Cys

What happens to cysteine residues next to eachother?

Undergo oxidation to form disulfide bond

What is the pKa of His?

6.0

Which AA's contain amide/N, polar uncharged and can be donor or acceptor?

Asn, Gln, His

Which AA is often in enzyme catalyzed rxns?

His

What is the pKa of Asp?

4.0

Which AA's are polar charged, h bond acceptor?

Asp, Glu

Which AA's are polar charged, h bond donor?

Lys, Arg

What is a dipeptide?

Two AA's joined by 1 peptide bond

Explain the portions of a tetrapeptide

Only terminal amino/carboxylate in a peptide retain their charge

Why are the charges on the terminuses gone when forming a peptide?

Charges are eliminated by formation of peptide bonds

Explain primary structure

Sequence of AA's in a polypeptide

What joins AA's to the next?

Covalent peptide bonds

What is the geometry of peptide bonds?

Rigid, planar - No rotation around C-N bond

Where could there be rotation in a peptide bonds?

Alpha-Carbon and Nitrogen-alpha Carbon

Are the chemical groups in peptide bonds polar or nonpolar?

Polar

Carbonyl groups are H-bond _______, NH groups ______

- Acceptors - Donors

Explain secondary structure

Folding of the backbone - Allows for H-Bonding of groups in polypeptide backbone - Alpha and beta

Describe "regular" secondary structures

Every AA in a segment of polypeptide adopts the same geometry

What is an alpha helix

Carbonyl oxygen of each residue forms H-bond w/ backbone NH group

How many residues away do alpha helices form?

4 residues downstream C1 -> N5

What kind of forces exist in alpha helix?

Van der Waals

Alpha helix is same diameter as ________ groove

Major

What type of beta sheets are there? Describe them

Parallel and Anti-parallel - Parallel: same direction, alternating, evenly spaced

________ structures connect strands

Irregular

What forces stabilize alpha helices?

H-bonds between backbone CO and NH groups in SAME helices

What forces stabilize beta sheets?

H-bonds between backbone CO and NH groups of neighboring strands

Are alpha and beta sheets regular or irregular structures?

Regular - the peptide backbone has same configuration for every AA within secondary structure

Regular structures are linked together by ___________ of various sizes, what are these called?

Polypeptide loops - Irregular structures

Explain tertiary structure

Arrangement of all atoms in a single polypeptide - Position of AA sidechains

What types of tertiary structures are there?

- Fibrous - Globular

What are fibrous proteins? 3

- Insoluble in aqueous soln - Form long protein filaments - Usually structural or connective proteins

What are globular proteins? 2

- Soluble in aqueous soln - Fold into compact structures w/ nonpolar cores and polar structures

What is the geometry of fibrous proteins?

Linear, extended structures

Hydrophobic side chains are most likely to be found in the ________ of a globular protein

Interior

Hydrophilic side chains are most likely to be found on the _______ of a globular protein

Surface

Regular secondary structures are found in the __________ of folded proteins

Interior

Are loops on the surface or interior of proteins?

Surface

The shape of globular proteins depends on positions of hydrophobic AA's in the _________ structure

Primary

What is the hydrophobic effect?

Driving force via which soluble globular proteins adopt their tertiary structure

What are salt bridges (ion pairs)?

Electrostatic interactions between closely positioned formal charged groups - Fine tune secondary and tertiary structures

What Terminus is + charged?

N

What Terminus is - charged?

C

What are forces in disulfide bonds?

Covalent bonds between closely positioned cysteines

What is the purpose of disulfide brides?

Form stabilizing crosslinks for extracellular proteins

What kind of redox environment is the cytosol? Do cysteines oxidize?

- The cytosol is a reducing environment - The cysteines do not oxidize

What is a domain?

Polypeptide segment that has folded into a single structural unit w/ a hydrophobic core

What is a motif?

Short region of polypeptide w/ a 3D shape

Can prosthetic groups be apart of tertiary structure?

Yes

What is a prosthetic group?

Non-peptide component that is permanently incorporated into a protein

Which proteins are easily denatured? Globular or fibrous, why?

Globular - Stabilized by weak, noncovalent forced

What forces does heat affect? 2

- H Bonds - Hydrophobic interactions

What forces does pH affect? 2

- Salt bridges - H Bonds

What forces does salt affect? 2

- Salt bridges - Ion pairs

What force does detergents affect?

Hydrophobic interactions

What agent can disrupt disulphide bridges?

Reducing agents

Describe quaternary structure

Proteins composed of more than one polypeptide chain

What forces are quaternary structures stabilized by?

- Hydrophobic - H bonds - Ion pairs