B2.075 Protein Structure Function: Knowns and Unknowns

Question 1

compare the exome and transcriptome portions of the genome

Answer 1

exome: all protein coding regions, 2% of genome, constant over lifetime
transcriptome: all transcribed RNA, changes with age and environment

Question 2

how many differences exist between exomes of two unrelated people?

Answer 2

10000

Question 3

what are the classes of protein functions?

Answer 3

chemistry (enzymes), signaling, structure, transport, storage

Question 4

what are the structural classes of proteins?

Answer 4

soluble/globular, fibrillar, integral membrane proteins, intrinsically disordered proteins

Question 5

characterize globular/soluble proteins

Answer 5

hydrophobic inside, hydrophilic outside
2 or more polypeptides
contain alpha helices and beta sheets
1/3 of eukaryotic proteins

Question 6

characterize fibrillar proteins

Answer 6

repeating globular subunits

long twisted fibers

Question 7

what functions are associated with fibrillar proteins?

Answer 7

cytoskeleton and extracellular matrix

Question 8

what are some well known fibrillar proteins?

Answer 8

repeating subunits: actin, tubulin

long polypeptides: collagen

Question 9

characterize integral membrane proteins

Answer 9

hydrophobic on the outside, hydrophilic on inside

25-30% of human exome

Question 10

what is one way to predict membrane spanning regions of amino acid sequences?

Answer 10

hydropathy plots: show hydrophobic stretches in sequence

Question 11

what are functions commonly associated with integral membrane proteins?

Answer 11

receptors, transporters

Question 12

characterize intrinsically disordered proteins

Answer 12

discovered by genome sequencing
30% of proteins in eukaryotes
no core
long repetitive sequences
small sequence islands for binding w a range of partners

Question 13

what functions are commonly associated with intrinsically disordered proteins?

Answer 13

scaffolding, transcription factors, membrane-less organelles

ex: dynein microtubule cargo transport

Question 14

what is a post translational modification commonly associated with intrinsically disordered proteins?

Answer 14

phosphorylation

Question 15

can we predict structure of function of a protein from the sequence?

Answer 15

no lol

Question 16

what are themes apparent from protein families?

Answer 16

conservation, motif, modularity

Question 17

what are conserved residues?

Answer 17

impart common overall structure/function to a group of similar proteins

Question 18

how do missense mutations affect conserved residues?

Answer 18

catastrophic…these residues are important to a group

Question 19

what is a motif?

Answer 19

a conserved short sequence that is associated with a specific function (structure may or may not be known)

Question 20

what are 2 examples of motifs?

Answer 20

zinc finger motif: needed for Zn2+ binding
walker A motif: needed for ATP binding

all common motifs have same sequence pattern and the rest of the protein can vary widely

Question 21

what is protein modularity?

Answer 21

when you mix and match different structure/function classes on one polypeptide

Question 22

how are contiguous domains on a protein connected?

Answer 22

linkers

Question 23

what is the important of domains?

Answer 23

they often have discrete functions which can be identified by deleting other domains from the sequence