New User Special Price Expires in

Let's log you in.

Sign in with Facebook


Don't have a StudySoup account? Create one here!


Create a StudySoup account

Be part of our community, it's free to join!

Sign up with Facebook


Create your account
By creating an account you agree to StudySoup's terms and conditions and privacy policy

Already have a StudySoup account? Login here


by: Udbluehen03

Lecture_5___Nucleic_acids.pdf BISC401

Marketplace > University of Delaware > Biology > BISC401 > Lecture_5___Nucleic_acids pdf

Preview These Notes for FREE

Get a free preview of these Notes, just enter your email below.

Unlock Preview
Unlock Preview

Preview these materials now for free

Why put in your email? Get access to more of this material and other relevant free materials for your school

View Preview

About this Document

We continued protein functions
Molecular Biology of the Cell
Class Notes
Biology, molecularbiology, cellandmolecularbio
25 ?




Popular in Molecular Biology of the Cell

Popular in Biology

This 5 page Class Notes was uploaded by Udbluehen03 on Saturday September 17, 2016. The Class Notes belongs to BISC401 at University of Delaware taught by Lachke,Salil in Fall 2016. Since its upload, it has received 10 views. For similar materials see Molecular Biology of the Cell in Biology at University of Delaware.


Reviews for Lecture_5___Nucleic_acids.pdf


Report this Material


What is Karma?


Karma is the currency of StudySoup.

You can buy or earn more Karma at anytime and redeem it for class notes, study guides, flashcards, and more!

Date Created: 09/17/16
Class 5 – 9/12/2016, Nucleic Acids Dr. Salil Lachke th Molecular Cell Biology, 8 edition – Lodish Proteins function depends on specific interactions with other molecules - Two proteins bind through interactions between their complementary surfaces Protein Binding and Enzyme Catalysis - The molecule in which a protein binds is called its ligand o The binding of a ligand to a protein is mediated by weak bonds o The binding site on a protein for a ligand consists of a number of amino acid residues brought together in the folded protein o A number of weak but specific interactions occur between the protein and ligand - Causes a change in the shape of a protein The properties of a protein that characterize it binds to a Ligand 1. Specificity o Ability of a protein to bind to molecules or a very small group of molecules in preference to all other molecules 2. Affinity o Refers to the tightness/strength of binding o Usually expressed as the dissociation constant (K ) d o K – dnverse of the equilibrium constant K . Theeqost common quantitative measure of affinity o The stronger the interaction between a protein and a ligand, the lower the valve of Kd Enzymes - Proteins that catalyze chemical reactions - The ligands of enzyme are called substrates - Most are located within the cells. Some are secreted and function at the extracellular sites such as blood. - Like all catalysts, enzymes increase the rate of a reaction, but they do not affect the extent of a reaction Class 5 – 9/12/2016, Nucleic Acids Dr. Salil Lachke Molecular Cell Biology, 8 edition – Lodish An Enzyme’s Active Site Binds Substrates and Carries out Catalysis - Active Site o Makes up only a small part of the total protein o Consists of the functionally important regions o 1. Substrate-binding site  Recognizes and binds the substrate(s)  Responsible for the remarkable specificity of enzymes  Alteration of the structure of an enzyme’s substrate can result in a variant molecule that is no longer a substrate of the enzyme  Only one or a few substrates can fit precisely into a binding site  The binding site for a substrate on an enzyme can be exposed by the action of a small molecule o 2. Catalytic site  Carries out the chemical reaction once the substrate has bound - The catalytic groups in the catalytic site are amino acid side chains and backbone carboxyl and amino groups - In some enzymes, the catalytic and substrate-binding sites overlap; in others, the two region are structurally distinct Serine Proteases - Large family of protein-cleaving - Used throughout the biological world; used to digest meal and control blood clothing - Trypsin, chymotrypsin, elastase How a Substrate Polypeptide Binds to the Substrate-binding site in the active site of Trypsin? - Two key binding interactions - 1. The substrate and enzyme form hydrogen bonds that resemble those of a β-sheet - 2. A Key side chain of the substrate that determines which peptide in the substrate is to be cleaved extends into the enzyme’s side-chain-specificity binding pocket, at the bottom of which resides the negatively charged side chai of trypsin’s Asp-189 Allostery - Refers to any change in a protein’s tertiary or quaternary structure, or in both, induced by the noncovalent bonding of a ligand Class 5 – 9/12/2016, Nucleic Acids Dr. Salil Lachke th Molecular Cell Biology, 8 edition – Lodish - When a ligand binds to one site (A) in a protein and induces a conformational change that alters the activity of a different side (B) o Ligand – allosteric effector/factor o Site A or site of ligand binding = allosteric binding site o The protein is called allosteric protein (target) - Important in feedback inhibition - Allosteric proteins have multiple binding sites, at least one for the allosteric effector and at least one for other molecules with which the protein interacts o The allosteric change in activity can be positive and negative o It can be an increase or decrease in protein activity Cooperativity - Often used synonymously with allostery - Refers to the influence that the binding of a ligand at one site has on the binding of another molecule of the same type of ligand at a different site - For example, hemoglobin o An example of positive cooperative binding o Binding of oxygen increases the affinity of hemoglobin for the next oxygen molecule o Four subunits in hemoglobin contains one heme molecule  Heme groups are the oxygen binding components of hemoglobin - Amplifies the sensitivity of a system to changes in the concentration of its ligands, providing in many cases a sensitive evolutionary advantage Noncovalent Binding of Calcium - Widely used as allosteric - The concentration of free Ca in the cytosol is kept very low (≈10 M) -7 - Many Ca - binding proteins bind Ca using the EF hand/helix-looping-helix structural motif Calmodulin - Found in all eukaryotic cells - May be individual monomeric protein or a subunit of a multimeric protein 2+ - Very sensitive to Ca concentrations and changes in structure and function in response to Ca levels>10 M -7 Class 5 – 9/12/2016, Nucleic Acids Dr. Salil Lachke th Molecular Cell Biology, 8 edition – Lodish - Contains four Ca - binding EF hands with K of abdst 10 M -6 - The binding of Ca to calmodulin causes a conformational change that permits 2+ Ca /calmodulin to bind to conserved sequences in various target proteins. Noncovalent Binding of GTP - GTPase superfamily - Used as allosteric switches to control protein activity - They are enzymes – GTPases – that can hydrolyze GTP (guanosine triphosphate) to GTP (guanosine diphosphate) o The GTP is obtained from the cytosol - Include the monomeric Ras protein - Both Ras and Gα can bind to the plasma membrane - Functions o Cell signaling o Cell proliferation and differentiation o Protein synthesis o Transport of proteins between the nucleus and the cytoplasm o Vesicles - Some GTPase proteins have a covalently attached lipid chain that meditates their binging to membranes - Exist in two forms o 1. Active (on) form with bound GTP  Influence the activity of specific target proteins to which they bind  Intrinsic activity of GTPase is low o 2. Inactive (off) form with bound GDP - The switch is turned on o when a GTP molecule replaces a bound GDP in the inactive form - The switch is turned off o when the relatively slow GTPase activity of the protein hydrolyzes bound GTP, converting it to GDP and leading the conformation to change to the inactive form - The amount of the time GTPase switch remains in the active, GTP-bound form depends on the rate of its GTPase activity - GTPase-activating proteins (GAPs) increases the rate of GTPase activity, thus reducing the time the GTPase is in the active form Class 5 – 9/12/2016, Nucleic Acids Dr. Salil Lachke Molecular Cell Biology, 8 edition – Lodish o Activates GTPase activity (Ras, G alpha protein). Activation of GTPase activity results in GTP conversion to GDP. GDP-associated Ras is now inactive - Guanine nucleotide exchange factors (GEFs) o Proteins whose function is to regulate the conversion of inactive GTPases to active ones o Mediates exchange of GDP for GTP Phosphorylation and dephosphorylation - Covalently regulate protein activity - Phosphorylation o The reversible addition of phosphate groups into hydroxyl groups on the side chains of serine, threonine and tyrosine residues - Phosphoproteins o Phosphorylated proteins - Phosphorylation is catalyzed by enzymes called kinases - Dephosphorylation is catalyzed by phosphatases o Removal of phosphates - Phosphorylation changes a protein’s charge o Sometimes its shape o Which can result in conformational changes - Phosphorylation/dephosphorylation o Can influence the location of a protein within the cells o Its intrinsic activity o Its ability to bind to other molecules o Its ability to undergo further covalently modification o Its stability - Phosphorylation sites can be masked by NAG (N-acetyl glucosamine) - Nearly 3% of all yeast proteins are protein kinases/phosphates - In human genome there are about 500 human proteins kinases


Buy Material

Are you sure you want to buy this material for

25 Karma

Buy Material

BOOM! Enjoy Your Free Notes!

We've added these Notes to your profile, click here to view them now.


You're already Subscribed!

Looks like you've already subscribed to StudySoup, you won't need to purchase another subscription to get this material. To access this material simply click 'View Full Document'

Why people love StudySoup

Steve Martinelli UC Los Angeles

"There's no way I would have passed my Organic Chemistry class this semester without the notes and study guides I got from StudySoup."

Jennifer McGill UCSF Med School

"Selling my MCAT study guides and notes has been a great source of side revenue while I'm in school. Some months I'm making over $500! Plus, it makes me happy knowing that I'm helping future med students with their MCAT."

Steve Martinelli UC Los Angeles

"There's no way I would have passed my Organic Chemistry class this semester without the notes and study guides I got from StudySoup."

Parker Thompson 500 Startups

"It's a great way for students to improve their educational experience and it seemed like a product that everybody wants, so all the people participating are winning."

Become an Elite Notetaker and start selling your notes online!

Refund Policy


All subscriptions to StudySoup are paid in full at the time of subscribing. To change your credit card information or to cancel your subscription, go to "Edit Settings". All credit card information will be available there. If you should decide to cancel your subscription, it will continue to be valid until the next payment period, as all payments for the current period were made in advance. For special circumstances, please email


StudySoup has more than 1 million course-specific study resources to help students study smarter. If you’re having trouble finding what you’re looking for, our customer support team can help you find what you need! Feel free to contact them here:

Recurring Subscriptions: If you have canceled your recurring subscription on the day of renewal and have not downloaded any documents, you may request a refund by submitting an email to

Satisfaction Guarantee: If you’re not satisfied with your subscription, you can contact us for further help. Contact must be made within 3 business days of your subscription purchase and your refund request will be subject for review.

Please Note: Refunds can never be provided more than 30 days after the initial purchase date regardless of your activity on the site.