Protein Structure and Function II

The 20 amino acids can be classified into 4 groups based on the behavior of the side chain: 3 __, 2__, 5__, and 10__

bases : acids : polar : nonpolar

Proteins Fold into a conformation of lowest __

energy

-__ structure: Linear amino acid sequence 

-Secondary structure: Stable conformations in stretches of the proteins, e.g. alpha-helix and beta-sheet, or random coil

-Tertiary structure: The 3 dimensional conformation of the entire proteins

-__structure: Arrangement in space of the subunits of a multimeric protein

Primary : Quaternary

Primary Structure: First order of complexity: linear sequence of __. Of all the amino acids in a protein, only a relatively few are critical for function (concept: __). Most play a __ role so that the protein can be folded correctly

amino acids : functional residues : functional

The __ is a right-handed spiral confirmation and completes a full turn every 3.6 amino acids. The … is formed when a single polypeptide chain turns around itself to form a rigid __. For every 4th amino acid, the C=O and N-H on the peptide backbone form __ bonds with each other

alpha-helix : cylinder : hydrogen

A-Helix: Found in __, which typically have amino acids of non-polar side chains because the backbone is __, the __ side chains will shield backbone, and The protein can thereby be embedded in the hydrophobic lipid bilayer

Cell membranes : hydrophilic : nonpolar

Higher Levels of Organization of alpha-helices: Two alpha-helical proteins can come together to form a __ structure. The helices are attached to each other by the interaction of __

coiled-coil (2-7 alpha-helices are coiled together like the strands of a rope) : hydrophobic side chains

The beta-sheet is composed of laterally connected strands that form a twisted, pleated sheet. The interaction occur __ strands not __ a strand. The __ groups in the backbone of one strand establish hydrogen bonds with the C=O groups in the backbone of the __ strand

between : within : N-H : adjacent

Tertiary Structures: A protein contains different __ and domains. Overall structure can be composed of alpha-helix, beta-sheet, and __. Domain of a protein: Parts that contain different secondary structures. A protein may contain __ domains

structures : random loops and folds : multiple/dozens of

Proteins have organization units called __.Protein domains are polypeptide segments that seem to fold __ into a stable structure (although still part of the overall protein structure). Domains are typically __ amino acids in length and often have a specific role or function. For example, DNA polymerase has a __ domain, which aids in proofreading during DNA synthesis

domains : independently : 40–350 : proofreading/exonuclease

Tertiary Structures: One or more Domains are Linked by Unstructured Regions

1.) __: No specific conformation

2.) __: Right-handed spiral

3.) __: Laterally connected

Primary structure/ aa sequences : Alpha-Helix : Beta-Sheet

Quaternary structure are formed from separate polypeptides called __. Do not subunits with __; domains are attached covalently within polypeptides, while subunits are separate polypeptides (that may contain domains)

subunits : domains

Some protein complexes are simply a combination of two subunits, called __. Those four subunits are __, those with eight are octamers (recall the histone octamer), an so on. Adult human hemoglobin contains two copies of alpha-globin and two copies of beta-globin (therefore a …)

dimer : tetramers

Actin is an example of a __, which if formed when several actin subunits come together in the shape of a __

filament : helix

Extracellular Proteins Are Stabilized by ___: Proteins that are secreted from the cell often encounter adverse conditions (e.g. lysozyme in tears. To stabilize their 3-D structures, cross-linkages like __ (S-S bonds) form between two cysteine amino acids

Cross-Linkages : disulfide bonds

Proteins can be grouped into __ based on similar amino acid sequence and/or structure. An example family is the __ (trypsin-like is a sub-family). The sequences and structures of the proteins in this family are remarkably similar. They all perform slightly different functions (cleaving different amino acids) due to their slightly different 3-D structures

families : serine proteases