Molecular Biology BIOL-4310-14

What are proteins made of?

Amino acids

What are amino acids made of?

-Central alpha carbon

-COOH

-NH2

-R Group

What does a primary protein structure consist of?

Linear sequence of amino acids

What type of reaction joins amino acids together?

Condensation reaction

What are some different categories of amino acids?

-Non-polar, aliphatic

-Non-polar, aromatic

-Polar, uncharged

-Polar, charged [Negative and Positive]

What is the most common type of amino acid conformation?

trans

Secondary Structure

Local spatial arrangement of the main-chain atoms in a segment of a polypeptide/polynucleotide chain

What kind of shapes can secondary structures form

alpha helices and beta-sheets

Alpha helix

helical confirmation of polypeptide chain, usually right handed

Are alpha helices usually right or left handed?

right-handed

How are alpha helices formed?

internal hydrogen bonding, setting up an electric dipole giving the N-terminus a partial + charge and C terminus partial -

Beta sheets

Polypeptide chain assumes an extended zigzag arrangement between adjacent strands

Parallel beta sheets

adjacent strands have the same polarity

Antiparallel beta sheets

adjacent strands have opposite polarity

How are beta sheets formed?

By hydrogen bonding either within polypeptide chain or between separate polypeptide chains

What types of amino acids do not fit well within alpha helices?

Bulky R groups and proline, polar groups

What amino acid groups can be seen in beta sheets?

Basically, any residue, including bulky aromatics and proline

How are secondary structural elements in a polypeptide connected?

Reverse turns:

-Long, unstructured stretches of amino acid residues

-Beta turns [consisting of 4 amino acids]

-Gamma turns [three amino acids]

How can protein structures be represented?

-Van der Waals radius

-Atoms as sticks

-alpha carbons only

-Ribbon diagram

-Electrostatic surface representation

Tertiary Structure

3D structure, consisting of all of its secondary structural elements and loops

Domain

Distinct structural unit of a polypeptide

What are characteristics of domains?

-Domains may have separate functions

-Domains may fold as independent units

What are common structural motifs containing beta-sheets?

-Greek key motif

-beta hairpin

-Antiparallel beta-sheet

-Beta-barrel

What are common structural motifs containing both alpha-helices and beta-sheets?

-beta-alpha-beta motif

-alpha/beta barrel domain

What are common structural motifs containing alpha-helices?

-Helix-turn-helix motif

-Four helix bundle motif

-Coiled-coil motif

-Heptad repeat, or leucine repeat

Quaternary structure

Structure consisting of two or more polypeptides, including all of their connections

In quaternary structures, what does each polypeptide represent?

A subunit of the protein

What kind of structures can quaternary proteins have and examples?

-simple structures [Homo- and heterodimers]

-Complex structures [multi-subunit ribosome]

How can evolutionary relationships be determined from primary sequence comparisons?

The more similar the primary sequence of the same protein between two species, the more recently the species diverged from a common ancestor

Protein Family

A group of evolutionarily related proteins with similar primary sequence and function

Superfamily

A structural classification that includes protein families with little sequence similarity but with the same super secondary structural motif and functional similarities

What can help determine a proteins function?

Its structure, specifically determining its 3D shape

Are all proteins structured?

No, some are unstructured [Intrinsically unstructured]