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

CBE:205 Introduction to Biological Engineering Study Guide (Exam #1)

by: Raffasarru

CBE:205 Introduction to Biological Engineering Study Guide (Exam #1) CBE 205

Marketplace > Colorado State University > Chemical and Biological Engineering > CBE 205 > CBE 205 Introduction to Biological Engineering Study Guide Exam 1
GPA 3.65

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

This covers everything that is on the exam #1 study guide on Canvas. Good luck!
Introduction to Biological Engineering
Christie Peebles
Study Guide
Biology, Bioengineering
50 ?




Popular in Introduction to Biological Engineering

Popular in Chemical and Biological Engineering

This 6 page Study Guide was uploaded by Raffasarru on Sunday September 18, 2016. The Study Guide belongs to CBE 205 at Colorado State University taught by Christie Peebles in Fall 2016. Since its upload, it has received 52 views. For similar materials see Introduction to Biological Engineering in Chemical and Biological Engineering at Colorado State University.

Similar to CBE 205 at CSU

Popular in Chemical and Biological Engineering


Reviews for CBE:205 Introduction to Biological Engineering Study Guide (Exam #1)


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: 09/18/16
CBE:205 Introduction to Biological Engineering Study Guide for Exam #1  Viruses o Lytic cycle: virus replicates within cell, then lyses (basically kills) it so they can spread to other hosts o Lysogenic Cycle: incorporates into DNA and when host replicates, the virus replicates within the DNA o Cannot live without another organism  Three domains of life Archaea Bacteria Eukarya Cell Type Prokaryote Prokaryote Eukaryote Cell Wall Peptidoglycan No peptidoglycan If present, no peptidoglycan Plasma Ester between Ether Links Ester Links Membrane polar heads and Lipids fatty acid tails RNA One Several Three Polymerase  Major Classes of Compounds in a Cell and Percentage by Weight o Proteins: 70%  Catalytic: enzymes  Structures: collagen  Transport: hemoglobin  Regulatory: insulin  Protective: antibodies o Lipids (membranes and storage): 10% o RNA (makes proteins): 10% o DNA (has info to make proteins): 5% o Polysaccharides (energy): 5%  Definitions o Extremophiles: bacteria that live in extreme environments o Psychrophiles: bacteria that live at < 20℃ o Mesophiles: bacteria that live at 20℃ − 50℃ o Thermophiles: bacteria that live at > 50℃ o Aerobic: requires oxygen o Anaerobic: oxygen inhibits cell o Facultative: can live with or without oxygen o Heterotroph: organism that gains energy from other organisms o Autotroph: organism that gains energy from other sources (producers) o Mixotroph: energy produced and consumed from other organisms o Chemoautotroph: energy from oxidation of compounds o Photoautotrophs: energy from light o Minimal (defined) Media:  supplies only minimal requirements for specific organisms  Contains known amounts of known compositions o Rich (complex) Media:  Wide variety of nutrients, chemical compositions unknown  Wide growth of organisms  More expensive than minimal media o Reduced Medium: removed oxygen o Differential Medium: multiple organisms grow o Selective Medium: only specific organisms can grow; selective agents kill the rest  Central Dogma: ???????????? → ???????????? → ????????????????????????????????  Watson and Crick Base Pairing: ???? − ???? with two hydrogen bonds, ???? − ???? with three  Replication: (5’-3’) o DNA Polymerase: synthesizes complimentary strand but only works in 5’-3’ direction o Primer: starts strand (it’s a short strand of RNA that is complimentary to the DNA strand and ends in −???????? so the DNA Polymerase can work) o Helicase: unzips DNA o Ligase: fills in gaps that DNA Polymerase leaves on lagging strand o Okazaki Fragments: fragments of DNA on lagging strand o Replication Fork: unzipped DNA where replication is occurring  Transcription: o Uracil instead of thymine o Promoter (bacteria): beginner of transcription sequence o Sigma Factor (bacteria): must bind to promoter to start transcription o RNA Polymerase: makes RNA (bacteria and eukaryotes but eukaryotes have three)  I: makes rRNA precursor molecules  II: makes mRNA and snRNA  III: makes pre-tRNA, ssrRNA, other small RNA o Spliceosome: molecule that splices introns out of the RNA, leaving the exons o Terminator (bacteria): ending sequence o Operon (bacteria): system of linked genes regulatory protein synthesis  Translation: o Codon: set of three bases that code for amino acids, start, or stop proteins o Reading frame: frame in which codons are being read o 20 amino acids o Ribosome: works with other molecules to make proteins o Bacteria  Ribosome binding site: 3-9 nucleotides before start  Shine-Delgarno Sequence: when ribosome binding site is a conserved sequence  Can occur while being transcribed o Eukaryotic  Multiple ribosomes on one mRNA  Physically separated from transcription (replication and transcription happen in nucleus, translation in cytoplasm)  Gene Regulation o Transcription factor: protein that binds to DNA and controls rate of transcription o Activator: protein that increases rate of gene transcription o Repressor: protein that decreases or inhibits rate of gene transcription o Lac Operon (transcription regulator mechanism): contains promotor, operator, genes transcribed together under control of catabolite activator protein; no transcription if low glucose and no lactose  Enzymes o Enzyme catalyzed reactions: can be used over and over, more efficient than chemical synthesis, catalyze both forward and reverse reactions o Co-factor: molecules needed for active enzyme o Co-enzyme: organic molecule needed for reaction tend to be regenerated by cell (CoA, NAD, FAD) o Active Site: site substrate binds to on enzyme o Lock and Key Fit: enzyme is specific to substrate o Main assumptions for Michaelis-Menten:  Batch reaction with constant liquid volume  Initial substrate and enzyme concentrations known  Initial rate measured (little substrate/product produced)  Total concentration of active enzyme constant  Enzyme-substrate complex established rapidly o Michaelis-Menten  ???? = ???????? ???? ]where ???? is max reaction rate and ???? = ???? at ???? 1 ????????+[????] ???? ???? 2 ????  ???? is affinity of enzyme for substrate ???? 1 1  Lineweaver-Burke Plot: plot of (y-axis vs. (x-axis) shown in ???? ???? ] Figure 1  ????????= ???? [2 ]0  ???? = ????−1+???? 2 ???? ????1 1 1 ???????? 1  ???? = ???????? + ???????? ([????]  Enzyme inhibition:  Competitive: inhibitor can bind to enzyme active site o ???? + ???? ⇄ ???????? → ???? or ???? + ???? ⇄ ???????? where first arrow is ????1on top ,???? (−1 bottom), the second is ???? 2nd the arrow between ???? + ???? and ???????? is ???????? ????????[????] [????] o ???? = ????????,????????????+ ????]where ???? ????,???????????? = ????????(1 + ???????? o Y-intercept will stay the same with or without a competitive inhibitor o In the graph below, A is the competitive inhibitor 1 1 ????????,???????????? 1 o ???? = ???? + ???? (???? ] ???? ???? Figure 1: Enzyme Kinetics with Various Inhibitors No inhibitor 0.35 0.3 A at 5 μM 0.25 B at 25 μM 0.2 C at 100μM 0.15 1/V (nM/min) No Inhibitor 0.1 y = 0.0589x + 0.0151 0.05 A at 5 μM y = 0.0181x + 0.0992 0 y = 0.0197x + 0.019 0 2 4 6 1/[S] (mM) C at 100 μM  y = 0.0425x + 0.0253  Non-competitive (Allosteric) Inhibition: inhibitor binds to enzyme on allosteric (not active) site and changes shape of enzyme, affecting its affinity for substrates o ???? + ???? ⇆ ???????? → ???? or ???????? + ???? ⇆ ???????????? or ???? + ???? ⇆ ???????? where all arrows are the same, the ones with the inhibitor is still ???? ???? o ???? = ????????,????????????????]where ???? = ???????? ????????+ ????] ????,???????????? 1+[????] ???????? o X-intercept remains the same, with this inhibitor or without o C is the non-competitive inhibitor in the graph above 1 1 ???????? 1 o ???? = ???? + ???? (???? ] ????,???????????? ????,????????????  Uncompetitive Inhibition: inhibitor binds only to ES complex and stops reaction o ???? + ???? ⇆ ???????? → ???? or ???????? + ???? ⇆ ???????????? where all arrows are the same, the ones with the inhibitor is sti????l ???? o Slope remains the same, with this inhibitor or without o B is the uncompetitive inhibitor in graph above 1 1 ????????,???????????? 1 o = + ( ) ???? ????????,???????????? ????????,???????????? [????]  Solving Problems:  Find ????????,???? ???????? ????,????????????,????????,???????????? first, most likely by using a graph (compare to no inhibitor)  Use equations above to find ???? , ???? , etc. ????  Protein Engineering o Goal: design protein from scratch o Beneficial for drugs, enzymes, inexpensive o Experimental methods (3)  X-ray Crystallography  Crystallize protein  Scatter x-rays  Gives patterns and computations can be done  NMR Spectroscopy  Solution of protein placed in magnetic field  Frequency pattern  Only when small and soluble  Electron Microscopy  Big proteins  Beam of electrons used to image  2D, embedded in membrane is useful o Computational Prediction  Prediction from first principles  Molecular dynamics  Simulated annealing  Protein sequence is > 30% similar to protein with known structure  If sequence similarity is high, structural similarity is probably high too  Sequence structure alignment → partial backbone modeling → loop modeling → side chain prediction → refinement o Directed Evolution  Generates variance  Mimics natural evolution  Use best (stable/active) variants for next round  Gene shuffling  PCR and gene assembly, simple gene-shuffling, family shuffling  Library creation  Targeted mutagenesis  Screening library o Rational Design  Stabilization  Mutations result in more favorable interactions with protein  Disulfide bridges, supercharging  Molecular dynamics vs, empirical or statistical force field  Use energy calculations to predict effects changes to protein  Preferred side chain positions  Beneficial amino acid changes  Stoichiometric Limiting Substrate: substrate that is completely exhausted  Growth Rate Limiting Substrate: substrate that limits growth  Yield Factor: ????????= mass A produced ???? mass B consumed  Elemental Material Balance for Growth o Empirical Cell Formula: ???????? ???????? ???? ???? o Carbon coefficient is one o Aerobic growth, no product (except ???? 2 and ???????? )2 o Example: ???????? ???? +???? ???? + ???????????? 2 ???????????? ???? 3 + ???????? ???????? ???????????????????? 2 2  Simple elemental balances:  C: 1 = ???? + ????  H: ???? + 3???? = ???????? + 2????  O: ???? + 2???? = ???????? + ???? + 2????  N: 3???? = ????????  Need one more piece of information: could use energy balance  Degree of reduction (????): number of available electrons per mol of Carbon  ???? = 4  ???? = 1  ???? = −3  ???? = −2  ???? = 5  ???? = 6  To find ???? of a compound ???????????? ???????? ???? ???? ???? then it is 4 + 1 ???? + −2 ???? + −3 ???? + 6 ???? + (5)????  Energy Balance: calculate degree of reductance of all compounds and put them in an equation leaving out those that are zero  ???? + ????????????2= ???????? ???? ???????? ???? where x is biomass and s is substrate


Buy Material

Are you sure you want to buy this material for

50 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!"

Janice Dongeun University of Washington

"I used the money I made selling my notes & study guides to pay for spring break in Olympia, Washington...which was Sweet!"

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.