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What is the van deer Waals attraction?
the optimal distance where electron clouds influence each other
What is the difference between alpha helices and beta sheets?
- alpha helices have intrachain hydrogen bonds
- beta sheets have interchain H bonds
evolution that occurs when two proteins with different ancestors develop similarities
What determines whether a group of proteins will be in a family?
the amino acid sequence, which gives a similar function and structure
What does the --- do?
1) SH3 domain
2) SH2 domain
- SH3 binds to strings of multiple prolines
- SH2 binds to strings of tyrosine
What do homeodomains do?
bind DNA and transcription factors
What is a modular system?
diffferent function of things--> take the gene and reconnect with other module or domain to compair characteristics
When does the active site form?
only if the amino acids are spread out
What is Ea?
the difference between the transition state and beginning energy
What are the three ways an enzyme can help a substrate reach the TS?
- 1) enzyme can act as a template to bring them together
- 2) amino acid side chains can influence the reaction, binding the substrate to rearrange electrons
- 3) the enzyme can apply stress so bonds are broken
What are ways proteins ensure they are not cast aside?
Having a multisubunit complex: can't get rid of one protein without messing up the whole system; needs all parts to function efficiently
Being a part of a pathway: if one is removed, the flow of the pathway is messed up. There is an increased importance if the protein is in the committed step
Combining functions: the more subunits, the better the regulation; increased amount of subunits allows less inhibitors to be present
What are the four modes of communication in cells?
1) kinase system: serine/threonine and tyrosine kinases
What is the advantage of kinase?
- 1) rapid
- 2) reusable
- 3) cascade effect
** kinases can add phosphates that turn it on or off**
What protein motif is needed for kinases?
What are Cdks?
involved in the cell cycle, which has checkpoints for controlling whether its good/ bad to go through with it
they are gathering points that determine what the status of the cell is
What are the steps of a Cdk?
- 1) cyclin must be produced only after certain events have occurred
- 2) An inhibitory phosphate group must be added resulting from activation of kinase
- 3) An activating phosphate must be added, activating another kinase.
- 4) The inhibitory phosphate must be removed, activating another phosphatase.
What is Src?
A member family of Src proteins
cytoplasmic tyrosine kinase usually linked to a receptor in the membrane; activation affects cell to cell adhesion, etc.
responds to outside signal
a meeting point in the cell; all things must meet in Src to become activated
Src protein structure
short N terminus
SH3 domain: binds to a string of proline
SH2 domain: binds to phosphorylated tyrosines
What must happen for Src to become activated?
In inactive orm, tyrosine near the C terminus is phosphorylated and bound to the SH2 domain; and the SH3 is bound to an internal peptide that causes distortion of the active site.
1) The C-terminal phosphate must be removed, loosening the structure
2) The SH3 domain must be bound by a specific activating protein called Nef, which has a proline region. The kinase then is able to phosphorylate tyrosine to self-activate.
This signals the completion of a set of separate upstream events.
When GTP proteins are active, what do they do?
they relay info by activating other proteins
to turn off, it is GTP hydrolysis
indepentn light detecting set of cells, each detecting a different wavelength of light--> compound eye
Which photoreceptor is the last to develop?
R7, which detects UV light
Which protein is responsible for formation of R7?
Sevenless, a receptor tyrosine kinase
bride of sevellness, which resides on R8 and inserts into the membrane, bidning to SEV, causing phosphorylation adn thus binding of the SH2 and SH3 domain.