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

Lecture 3: Protein Structure & Function

by: Olivia Sutton

Lecture 3: Protein Structure & Function 200001

Marketplace > Boston College > Biology > 200001 > Lecture 3 Protein Structure Function
Olivia Sutton
View Full Document for 0 Karma

View Full Document


Unlock These Notes for FREE

Enter your email below and we will instantly email you these Notes for Molecules and Cells

(Limited time offer)

Unlock Notes

Already have a StudySoup account? Login here

Unlock FREE Class Notes

Enter your email below to receive Molecules and Cells notes

Everyone needs better class notes. Enter your email and we will send you notes for this class for free.

Unlock FREE notes

About this Document

Covers the topic on Protein Structure and Function
Molecules and Cells
Danielle Taghian
Class Notes




Popular in Molecules and Cells

Popular in Biology

This 8 page Class Notes was uploaded by Olivia Sutton on Friday February 19, 2016. The Class Notes belongs to 200001 at Boston College taught by Danielle Taghian in Spring 2016. Since its upload, it has received 14 views. For similar materials see Molecules and Cells in Biology at Boston College.


Reviews for Lecture 3: Protein Structure & Function


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: 02/19/16
Lecture 3: Protein Structure and Function January 27, 2016 Structure of Amino Acids  Non ionized form is the most common form  H2N (amino group)  COOH (carboxyl group)  H – hydrogen atom  R – side chain In water (pH 7)  Amino groups ionize to NH3+ and Carboxyl group ionizes to COO­  The higher the pH, the more protons you lose o pKa increases; not good if it goes past 9.0  Some acids completely ionize completely in water  Carbon atoms are designated alpha and beta o Alpha carbon: C that always bonds to amino and carboxyl groups o Beta carbon: first carbon on attached R group  In pH 7, Lysine (NH3+ R group) could form a hydrogen bond or an ionic  bond (salt bridge) ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ Amino acid R­groups differ in electronegativity  When atoms of different electronegativity are bonded, they form polar, water soluble molecules  Nonpolar when electronegativity of Hydrogen and Carbon are the same  In organic chemistry, electrons can be spread past their electron cloud  Lysine is positively charged while Aspartate is negatively charged ­­­­­­­­­  The 20 major amino acids differ only in the variable side chain or R­group  attached to the central carbon o Groups differ in their size, shape, reactivity, and interactions with  water and other molecules ▯ ▯ ▯ ▯ ▯ The Nature of Side Chains  If given a structural formula for an amino acid, determine the amino acid type  by asking three questions 1. Does the side chain have a NEGATIVE charge? a. If yes, it has lost a proton, so its acidic 2. Does the side chain have a POSITIVE charge? a. If yes, it gains a proton, so its basic 3. If the side chain has no charge, does it have an OXYGEN atom? a. If yes, the highly electronegative oxygen or nitrogen will result in a polar covalent bond, so it ends up being uncharged and polar  If the answer to all 3 questions are no, then you’re looking for a nonpolar  amino acid! ▯ ▯ Why these 20 Amino Acids?  The set of 20 amino acids found within the standard genetic code is the result  of considerable natural selection.  May represent a largely global optimum, such that any aqueous biochemistry  would use a very similar set  20 is the minimum number that provides enough specificity in the R­groups  that we need ▯ ▯ Condensation/Hydrolysis Reactions  Monomers polymerize through condensation reactions, which releases a water molecule  Hydrolysis is when water reacts with a polymer to release a monomer   ▯ ▯ The Peptide Bond  Condensation reactions bond the carboxyl group of one amino acid to the amino  group of another  Has double bond characteristics where electrons can switch places (amide  bond) o Electrons shared between carbonyl group ad peptide bond offer some  char  The two groups that flank the amide bond can create hydrogen bonds  There is some rotation of bonds around alpha carbon:   Why alpha acids vs. beta acids? o Only alpha amino acids can form secondary structures o Must posses a hydrogen atom in the alpha position to avoid steric  hindrance when folding  Why amide bonds? o Amide bonds are planar, which allows intrastrand H­bonding o Are also chemically stable ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ (Carboxyl Group + Amino Group = Peptide Bond) ▯ ▯ ▯ ▯ Protein structure  Primarily built up based on domains  Has four levels of structures ▯ ▯ Primary Structure   Is the protein’s unique sequence  Essential to elucidating the protein’s function (e.g catalytic, structural)  Amino acid sequence is the link between the digital code within genes and the structure of the proteins  Polypeptide: flexible and has directionality, and its side chains extend from  peptide backbone ▯ ▯ ▯ ▯ The Power of One  Because amino acid R­groups affect a polypeptide’s size, shape, chemical  reactivity, and interactions with water, just ONE amino acid change can  radically alter protein function  Example: Sickle Cell o Hemoglobin tends to crystallize when Glutamate is changes to Valine ▯ ▯ Secondary Structure  The secondary structure is the local conformation of the polypeptide chain  Depends on the primary structure  Is formed by hydrogen bonds o Occurs between the carbonyl group of one amino acid and the amino  group of another  The most common location of the alpha helix is along side the outside of the  protein  In the alpha helix, the CO group of residue n forms a hydrogen bond with the  NH group of the residue n + 4  Each 360 turn = 3.6 aa. The peptide bond of every 4  aa interacts via H­bonds  The H­bonds are parallel to the axis of the alpha helix, whereas the aa side  chains are perpendicular ▯ ▯ Beta Turns  Allows the peptide chain to reverse direction  Carbonyl C of one residue is H­bonded to the amide proton of a residue three  residues away  Proline and Glycine are prevalent in beta turns Beta Turn Tertiary Structure  Results from between R­groups or R­groups and the peptide backbone o Caused the backbone to bend and fold o Bending and folding contributes to the distinctive three­dimensional shape of the polypeptide  R­group interactions include o Hydrogen bonds o Hydrophobic interactions o Van der Waals interactions o Covalent disulfide bonds  o Ionic bonds Quaternary Structure  Some proteins contain several polypeptide subunits   Bonding of two or more subunits produces the quaternary structure ▯ ▯


Buy Material

Are you sure you want to buy this material for

0 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

Bentley McCaw University of Florida

"I was shooting for a perfect 4.0 GPA this semester. Having StudySoup as a study aid was critical to helping me achieve my goal...and I nailed it!"

Anthony Lee UC Santa Barbara

"I bought an awesome study guide, which helped me get an A in my Math 34B class this quarter!"

Jim McGreen Ohio University

"Knowing I can count on the Elite Notetaker in my class allows me to focus on what the professor is saying instead of just scribbling notes the whole time and falling behind."

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.