Protein: Structure + Function (lec 14 not on midterm 2) Flashcards
(T/F) Human genome has around 20k to 23k protein encoding genes that through alternative splicing of mRNAs and post-translational modifications generate hundreds of thousands of distinct protein activity.
True!
What are proteins?
Polymers composed of the 20 amino acids with different R group side chains.
Amino acid side chains determine the distinct properties of individual proteins.
Match the following protein structures to their definition:
1) Primary
2) Secondary
3) Tertiary
4) Quaternary
5) Supramolecular complexes
A) large-scale assembly - consisting of tens to hundreds of subunits and other biopolymers such as nucleic acids (big power house engines; RIBOSOME)
B) association between multipeptide complexes (multimeric structure)
C) local folding of the chain into alpha helices and b sheets with lots of H-bonds.
D) overall 3D conformation - composed of 2° structural elements and loops + turns. May form distinct, independently stable domain.
E) linear sequence of amino acids linked by peptide bonds
Primary: linear sequence of amino acids linked by peptide bonds
Secondary: local folding of the chain into alpha helices and b sheets with lots of H-bonds.
Tertiary: overall 3D conformation - composed of 2° structural elements and loops + turns. May form distinct, independently stable domain.
Quaternary: association between multipeptide complexes (multimeric structure)
Supramolecular: large-scale assembly - consisting of tens to hundreds of subunits and other biopolymers such as nucleic acids (big power house engines; RIBOSOME)
What does protein function depend on?
Specific binding interactions and conformation changes in the structure of a properly folded protein
What are the 6 main functions of proteins? Briefly describe them.
1) Structure - they organize the genome, organelles, cytoplasm, protein complexes, and membranes in 3D space
2) Regulation - control protein activity (e.g. post translation modification)
3) Signalling - monitoring the environment and transmitting information
4) Transport - moving small molecules and ions across membranes
5) Enzyme activity - catalyzing chemical reactions
6) Motors - generating force for movement (flagella, actin filaments, etc)
How is a peptide bond formed?
Formed by a DEHYDRATION reaction linking one amino acid C-terminus to another amino acid N-terminus.
(T/F) In a linear polymer (polypeptide), there is a free amino end (N-terminus) and a free carboxyl end (C-terminus).
True!
Fill in the blank:
Protein function is derived from the ____ structure, which is determined by the aa sequence and ________ reactions.
3d; intramolecular
Define secondary structures.
Stable spatial arrangements of polypeptide chain segments held together by H bonds between backbone amine and carbonyl groups.
Alpha helix and beta sheets.
Which one of the statements regarding alpha helix is false?
1) They occur when the polypeptide backbone (ribbon) folds into a spiral/helix
2) Helix is stabilized by hydrogen bonds between backbone oxygen and hydrogen atoms (more bonds, more stable)
3) R groups project outward from the surface of the helix and determine the chemical nature of helix faces
4) Prolines are a major component of the alpha helix
4! Prolines cannot participate in H bonding and are usually excluded from alpha helix because they form kinks. Kinks constraints alpha helix from spiral.
What is a beta sheet? How is it stabilized?
LATERALLY packed beta strands, each of which is a nearly fully extended polypeptide segment.
Stabilized by H bonds between backbone oxygen and hydrogen atoms in amino acids on DIFFERENT STRANDS.
What is the difference between Antiparallel and Parallel beta sheets?
In parallel beta-sheets the strands all run in one direction (N-to-C), whereas in antiparallel sheets they all run in opposite directions.
What produces a pleated polypeptide backbone contour?
Alpha carbon bond angles
(T/F) In β sheets, alternate R groups project above and below the plane of the sheet.
True!
Fill in the blanks regarding a β turn.
A β turn is composed of _____ residues.
It ______ the direction of a polypeptide chain ( ____ U-turn)
Cα carbons of the first and the fourth residues are usually less than ____ nm apart and linked by a ______ bond.
four
reverses; 180°
0.7; hydrogen
What does the β turn facilitate?
β turns facilitate the folding of long polypeptides into compact structures.
Which amino acids are commonly found in β turns?
Glycine (smallest R group) and Proline (built in bend)
What are structural motifs? What can they be encoded by?
Structural motifs are regular combinations of secondary structures usually with a specific type of function.
They can be encoded by highly conserved sequence motif.
What are the three types of structural motifs?
- Coiled-coil motif
- EF hand/helix-loop-helix motif
- Zinc-finger motif