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

Week 2 Introduction to Biology Notes

by: Brittany Church

Week 2 Introduction to Biology Notes BIS 002A

Marketplace > University of California - Davis > Biological Sciences > BIS 002A > Week 2 Introduction to Biology Notes
Brittany Church

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

Notes for week 2 of Introduction to Biology with Michelle Igo. 13 Pages in length, includes lectures 3, 4, and 5, and Discussion 1.
introduction to biology
The staff
Class Notes
Biology, Pka, pH
25 ?




Popular in introduction to biology

Popular in Biological Sciences

This 12 page Class Notes was uploaded by Brittany Church on Sunday October 2, 2016. The Class Notes belongs to BIS 002A at University of California - Davis taught by The staff in Fall 2016. Since its upload, it has received 63 views. For similar materials see introduction to biology in Biological Sciences at University of California - Davis.


Reviews for Week 2 Introduction to Biology Notes


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: 10/02/16
BIS 002A Week 2 Notes Professor Igo Fall 2016 Lecture 3 “Spherical Cow”​: this simply means think critically about the situation presented. DISCUSSION SECTIONS START THIS WEEK. YOU MUST ATTEND YOUR DISCUSSION SECTION OR YOU WILL BE DROPPED FROM THE CLASS. BRING A COMPUTER. *Please make emails professional. Be concise. Include your student ID # and section. Pre and Post survey for extra credit! You must do both. Pre survey will be due Friday at 3 pm, find this on Smartsite. The workshops this week will focus on pH/the chemistry of biology. **Clicker questions are mostly old exam questions. Clicker Question​: A molecule is a vitamin called ascorbic acid. Based on it’s chemical structure you would expect this molecule to be ___________ because ___________: A. Be poorly soluble in water; of the many hydroxyl functional groups B. Highly soluble in water; of the many hydroxyl functional groups C. Be poorly soluble in water; of its ring structure D. Highly soluble in water; of its ring structure Design Challenge: What’s the big problem? Building a cell What does a cell need to do to accomplish this? ● Needs food ● To be able to extract energy ● To be able to extract building material What building blocks? ● Carbon ● Hydrogen ● Nitrogen ● Oxygen ● Phosphorus ● Sulfur **We will not be doing chemistry math in biology! The Structure of the Atom Atom​: Smallest unit of matter that retains the chemical properties of an element. Element​: Form of matter with specific chemical and physical properties that can’t be broken down into smaller substances by ordinary means. Composed of: Charge Mass (amu) Mass (kg) Location Proton +1 ~1 1.6726 x 10​-27 Nucleus -27 Neutron 0 ~1 1.6749 x 10​ Nucleus -31 Electron -1 ~0 9.1094 x 10​ Orbitals Orbital​: regions in space around the nucleus where an electron can be expected to be found. There are 5 elements common to all living things: 1) Oxygen ( O ) 2) Carbon ​( C ) 3) Hydrogen ( H ) 4) Phosphorous ( P ) 5) Nitrogen ( N ) Periodic Table:​ Table created by Mendeleev that organizes and displays the different elements. This has elements grouped by commonalities (atomic structure, chemical properties, physical state, and chemical reactivity). It is now organized and displayed according to atomic number and arranged in a series of rows and columns based on chemical and physical properties. Molecules​: two or more atoms chemically bonded together, causing the electrons to be shared between the two nuclei. Electronegativity​: The chemical concept that shows the tendency of an atom to attract electrons.Values for electronegativity are unitless and are relative to the standard reference--hydrogen. *The larger the electronegativity the greater tendency an atom has to attract electrons. **When electrons are not distributed evenly between two atoms and the electrical charge is not evenly distributed, the bond is polar. This creates two poles--or two dipole moments, one positive and one negative. ***We will focus primarily on three types of bonds: ionic, covalent, and hydrogen bonds. Periodic Table: Ionic Bonds:​ Electrostatic interactions between ions of opposite charges. Example​: Sodium Chloride (NaCl). Positively charged sodium ions and bound with negatively charged chloride ions to create a crystalline molecule with a net charge of zero. Electron Transfer​: The movement of electrons from one atom to another. *Electronegativity differences of ~2.2 are large enough to cause electron transfer between two atoms, and this is likely done through ionic bonds. Covalent Bonds:​ Bonds in which electrons are shared between two atoms. *Electronegativity differences will be approximately equal to 0. The atoms share the electrons, therefore the electrons are not being pulled further to one atom or the other. **When the sharing between two covalently bonded atoms is approximately equal, it is a nonpolar covalent bond​. **If the sharing between two covalently bonded atoms is not equal between the atoms, it is a polar covalent bond​. ​ δ+: Indicates a slightly positive pole. ​ δ–: Indicates a slightly negative pole. When a polar covalent bond is created, there is a ​dipole​ in the bond (two poles). Example Molecular Oxygen (O​ ) 2​ Non-polar Covalent Bond Methane (CH​ ) Non-polar Covalent Bond 4​ Water (H​ 2​ Polar Covalent Bond Hydrogen Bonds​: When hydrogen forms a polar covalent bond with an atom of higher electronegativity and the partial positive charge comes in contact with a partial negative charge from another electronegative atom in a suitable orientation that hydrogen is not bound to. *This is a common bond in biology within and between all types of biomolecules. **These are critical interactions between biomolecules and their solvent (water). Electronegativity of Bonds: Zero Electronegativity Medium Electronegativity Large Electronegativity Pure Covalent Polar Covalent Ionic Water​: A key substance comprised of polar molecules with special properties tied to life’s processes. In the liquid state it interacts with itself through a dynamic network of hydrogen bonds that are constantly forming and breaking. “We forget that the water cycle and the life cycle are one” - Jacques Cousteau Hydrophilic​: A substance with sufficient polar character the may dissolve in water. Hydrophobic​: Non-polar compounds that do not interact well with water and do not dissolve in it. Solvent​: A substance capable of dissolving polar molecules and ionic compounds. Sphere of Hydration​: When molecules form hydrogen bonds with water, surrounding the particle with water that serves to separate particles or disperse them in water. Dissociation​: When ionic bonds are disrupted in the process of ionic compounds being added to water (the individual ions interact with polar regions). pH (Hydrogen Ion Concentration):​ -log​ [H​10​ +​ ​[H​ ​ concentration * A measure of the concentration of hydrogen ions in a solution (or the number of hydronium ions). pH Scale​: A logarithmic scale that ranges from 0 to 14. pH 7.0 is neutral. Below 7.0 is acid and above 7.0 is alkaline (basic). Functional Groups:​ A specific group of atoms within a molecule, responsible for a characteristic of that molecule. How are functional groups influenced by electronegativity? Example Hydroxyl, Methyl, Carboxyl, Carbonyl, Amino, and Phosphate. **Methyl’s are the only non-polar functional group in this group. Discussion 1 Discussion TA: Ruth Lee Email: r​ LA: Alejandro CHan Email: ​ Six Elements Essential to Life​: Sulfur, Phosphorus, Oxygen, Nitrogen, Carbon, Hydrogen. **Interesting Fact: We have iron which causes our blood to have a rusty red color. If you were to cut open a deep sea organism, it’s blood would have a blue cool, due to it having copper instead of iron. +​ Hydronium is arguably very polar. Large amounts of it cause H​ (a very strong acid). In water, the bonds in a single molecule are covalent bonds (meaning they share electrons), and the bonds between molecules of water are hydrogen bonds (the do not share electrons, they just kind of touch). Determining Bond Polarity: Is the difference of electronegativities 0.4? Yes, > 0.4 = Polar Bond Yes, < 0.4 = Nonpolar Bond Amino Acids: Amino acids have a central Carbon. They should have an amine and an R-group. **To determine the polarity of an amino acid, look at the R-group. If the R-group is non polar, the amino acid is non polar. Proteins​: Will have a N-C-C-N-C-C-N… repeating chain for a backbone. Fatty Acids: Will have CH​ c2​ins. Carbohydrates: Will have a C chain backbone and OH groups. Nucleic Acids: Will have phosphate groups, nitrogenous base, and sugar. Lecture 4 pH​: ​Unicellular and multicellular organisms have developed means of protecting themselves + against pH changes. **Free hydrogens do not exist in water. It will create H​ O​3​ Buffers​: Usually small molecules that can reversibly bind and unbind protons in solutions. One mechanism for pH protection. **If pH of an environment is lower than the pKa of a functional group on the buffer, that group will tend to become protonated and remove a proton from solution. However, if the pH in an environment is higher than the pKa of of the same functional group on the buffer, then that group will tend to become deprotonated, lowering the pH. Humans​: Blood pH is very critical to survival. Without buffers, the body’s pH would fluctuate and put the body’s survival in jeopardy. -​ ● The buffer maintaining blood pH involves carbonic acid (H​ CO​ ), bicarbon2​e (3​O​ ), 3​ and carbon dioxide (CO​ ). 2​ ● When bicarbonate combines with Hydrogen to form carbonic acid, hydrogen is removed from the outer environment, changing pH. ● Excess carbonic acid can be converted to carbon dioxide, preventing too many hydrogen ions from building up in the blood (and reducing the blood’s pH). ● If too much OH​ is in the system, carbonic acid will react to create bicarbonate, lowering the pH. ● At pHs between 1 and 3, a very small amount of bacteria can survive (however, in the stomach, the pH is about 1.5 and bacterial flora continue to survive). *Antacids are another buffer, used to control excess stomach acid and moderating the pH in the stomach. ​But​, the use of too much antacid can allow for salmonella poisoning. pK​ a​ ● -log​ of K​ OR -log​ [H​ ] where [H​ ] is the concentration 10​ a ​ 10​ ● **We almost never talk about pOH +​ ● Quantitative measure of how easily an acid gives up its proton [H​ ] in a solution ● Measures the “strength” of the acid (strong acid = small pKa, weak acids = large pKa) Common for BIS 2A:​ Carboxylic Acid functional group: acids that are typically weak, meaning they only partially dissociate (into H+cations and RCOO- anions) in neutral solution. HCL (hydrogen chloride) is a strong acid, meaning it will fully dissociate into H+ and Cl-. Clicker Question 1​: The following are a list of functional groups often seen in biology. 1. -CH3 2. -NH2 3. -OH 4. =O 5.-PO4 - If added to a molecule, which of these functional groups are likely to decrease the molecule‘s solubility in water? A. 2 & 3 B. 3 & 4 C. 5 only D. 1 only E. 4 & 5 **-CH3 is nonpolar, so it doesn’t interact with water. Clicker Question 2: ​The depicted molecules is best classifHint: I have underlined the word best for a reason. A. Nucleic Acid B. Protein C. Lipid D. Carbohydrate E. Biomolecule Functional Groups and Polarity: Clicker Question 3:​ There are two solutions: • One has a pH = 5 • One has a pH = 7 Which solution has the higher hydrogen ion (H+, proton) concentration? A. Thesolution at pH = 5 B. The solution at pH = 7 C. More information is needed to answer this question. **At a higher (more basic) pH, you have less H​ , at a lower pH (more acidic) you have many more H​ + Clicker Question 4: What happens if there is an increase in the H+ concentration? A. The concentration of the protonated form increases. B. The concentration of the protonated form decreases C. There is no change in the concentration of the protonated form. Lecture 5 **Don’t use the original like for NB anymore, use the link that Dr. Facciotti posted in the announcements. There are pre/post study guides and additional readings on Smartsite, use these to study for exams or making a study guide. Midterm 1: Monday 10/10 Review session: 10/7 8 pm - 10 pm in Sci Lec Group Question​: What are the chemical properties that distinguish saturated and unsaturated fatty acids? How do these differences influence their melting temperatures? The double covalent bond between Carbons in unsaturated fatty acids contributes to the shape of the fatty acid, causing it to bend into an L-shape. This L-shape makes it much more difficult to stack the molecules into a solid structure, this is why unsaturated fatty acids are usually oils. Saturated fatty acids have a much straighter shape, allowing them to bond together to create solid structures, such as butter. Amino Acid Structure: ● Monomers that make up proteins. ● Has the same core structure-- a central carbon atom (the alpha carbon), an amino group (NH​ 2​ a carboxyl group (COOH), a hydrogen atom, and the R group, variable group, or side-chain (these can be a single atom or a group of atoms). ● “Amino acid” is from the fact that all amino acids contain both an amino group and a carboxyl acid group in the backbone. **If carboxyl acid/group is in water, it will lose a +​ proton which associates with H​ O t2​form H​ O​ .3​ ● There are 20 very common amino acids in natural proteins (each has the same backbone [N-C-C] ).** Look for this pattern as an amino acid identifier. ● Sequence and the number (amount) of amino acids will determine a protein’s size, shape, and function. ● They are attached to each other by covalent bonds (otherwise known as peptide bonds--which form because carboxy group of one amino acid and the amino group of another amino acid combine and release water, creating the bond). ● The R group is different on all amino acids, which gives that amino acid specific chemical properties (polarity, acidity). ● Amino acids at pH ~7.0, each functional group will have it’s own pKa. ​ ​ ​ ​


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

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!"

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."

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."


"Their 'Elite Notetakers' are making over $1,200/month in sales by creating high quality content that helps their classmates in a time of need."

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.