Notes PDF

Preview

Summary

All lecture notes for the semester...

Description

Sari Saint- Hilaire 1

09.06 Why do we have a sophomore seminar? ● So we have a community ● So we get to know the people who are leading the research ● Post undergrad so we know what we want ○ Career prep built into here ● How to get into an internship ○ Resume Bonafide experience in chemistry is important Incentive to really pay attention, to really get more! Resume prep is 30% When a question is asked, state name, then ask question Kevin Dagbay!!!! Sravanti Vaidya~ teacher in India Elih Velazquez~ rusn research lab in navy Impact of Neurodegeneration ● 50% of 85 year olds suffer neurodegenerative dementia ● Cost is huge and growing ○ 50% of GDP ● Alzeimer’s disease therapy ○ 6.4B/year market today ○ No drug to treat it Caspases are: ● A family of 12 human protein cutters or proteases involved in ○ Programmed cell death ○ Immune cell death Differences in brains ● Gaps in brain tissue ● Size is smaller ● No way to recover ● Need to be caught early Caspase-6 involvement in alzheimer's ● In healthy neuron, they contain microtubules, tau doesn’t stay and caspase 6 cut it ● If we can stop caspase 6 but none of the other, we can catch alzy early ○ Patient will get cancer, but more treatable than lazy Caspase-6 structure ● Same fold, 130 different with extended helix making unable to bind substrace ● In order to make a drug, we needed a populate state to exploit it therapeutically Hydrogen-Deuterium Exchange

Sari Saint- Hilaire 2 ● Helix and amid bond in water, but in deuterium ** 2H = D= blue ball, mass = 2 = more deuterium more deuterium binds to flexible regions than to inflexible regions Controls are most important part of science ● In this case, it is blue region, ● Caspace-6 became more blue on the end of the region Screen 360,000 compounds, founds 2 compounds that inhibited cap6 but none else ____ was unique to casp 6 KT 57 unmatched~ noiiiiccceeeeee

09.13 University of California Honorable mention

Sari Saint- Hilaire 3 Synthetic RNA Professor Martin First gen Chemists get Greedy: Tails of RNA Gone ad Martin Lab with Craig Martin In the beginning… → protein DNA → RNA A lot more complicated than that Enzyme replacement therapy ● Patient is deficient in or has a mutated protein ● Essentially we can clean proteins from donors to replace mutated DNA Tried before but there were some really bad side effects T7 RNA polymerase- the RNA Synthesis Catalyst! ● Essentially DNA will transcribe until it gets to the end then it will fall off Mechanism in transcription You can convert RNA into DNA and send it off into sequencing? RNA-Seq of in vitro reaction products Don’t just get the likes of the RNAs but also the sequence of the RNAs ● We can do a lot of DNA at once ● RNA → DNA Test the general hypothesis ● Supply the correct RNA, chemically synthesized, in the absence of promoter DNA Understand the heterogeneity ● Two major classes of primer initiation ○ Promoter driven reaction ■ 36% ■ 17% ■ 1.6% ○ Synthetic RNA extension ■ 25% ■ 36% ■ 4.4% ○ Possible mechanisms Test a specific hypothesis Upstream sequence matters! General indicators of viruses is double stranded RNA How can you do this synthesis better Lower concentrations Negatively charged Increase salt concentration, destabilize salt pairing

Sari Saint- Hilaire 4 Adding DNA to end of RNA will complete the reaction since it will fold over itself most important thing you learned from the lecture and the importance of that insight

The most important thing I learned from Professor Martin was that a first gen kid could make it. It’s cliché but it still is inspiring. It was difficult for me to follow along because I did not know or even understand what he was talking about, so it was hard to even take notes. You could tell he was very excited and eager to share and be proud of all that he had accomplished. Content wise, the enzyme replacement therapy is really what was intriguing. The concept of “cleaning” the protein and replacing mutated DNA with them, and possibly being able to get rid of the bad side effects is what was most interesting. With us being so early in our professional careers, it’s important to see how far we can go and be inspired both socially and intellectually in the field we are committing to. Professor Martin really woke that up within us.

09.20 Nessim Watson For chemistry majors Career & Resume Strategies Being noticed and making things noticeable Morrill II, Rm 321

Sari Saint- Hilaire 5 Faculty hires who they know Hey! What did you do this summer? Take 2-minute survey Folks that know at is going on are those that read their email Thursday 8 PM “Smart” bombs, programmed to targets Talk to Nessim by Appointment about ● Resume Handshake~ algorithms, tells you what you need at first ● Recommendations ● https://umass.joinhandshake.com LinkedIn ~ where the people are Winning the game of life 1. What you love 2. What you’re good at 3. What pays well What do Employers most want on your resume? ● Is this you trying to lift your GPA? ○ WHAT DID YOU DO WITH YOUR CLASSROOM SKILLS OUTSIDE YOUR CLASSROOM? ○ Internships! ○ Employment during college

Sari Saint- Hilaire 6

Umass does not “provide” an education Proactive vs Reactive Look around department website ● For student ● Faculty bios ● Research areas or centers Key to the heart of any professor ● A professionally written email or appointment request that: ○ Describe research experience and skills to date, include relevant courses taken and field or lab skills learned in relevant courses ○ Demonstrate you’ve worked to understand their research, reading their ■ Faculty bio online ■ Link to lab or project website Massachusetts Life Sciences Center Investing in the State of Innovation Identify your transferable skills ● Customer service ○ Communication skills ● Babysitting ○ Dependability, safety ● Food server ○ Prioritizing task, teamwork ● Custodian ○ Safety protocol, toxic chemical ● Office work ○ Procedures, systems, efficiency Scientific Method but Hyperfocusing on the verb- put those verbs in your resume Observing, identifying… Acknowledge your lack GO GET HARD COPY OF CAREER HANDBOOK Personal Brand~ what people say about you when you leave the room!!!! https://umass.biginterview.com Read This week in CNS Careers---- Thursday 8PM Download Career Handbook

Sari Saint- Hilaire 7 Complete Handshake profile and favorite jobs and events See a career advisor by appointment Career Fair Feb 19 10 A - 3 P Reflective Paragraph: Oh My Gosh he was a character! Nessim definitely gave us the most advice and then he presented that advice which is not only creative but impactful and memorable. That is what he asks us to be in the memory of people we interact with in the academic setting. His slides weren’t simple, there were colors, and rotations and sounds! So if you found yourself falling asleep, boom! TRUMPETS!!! It’s about being different, everything down to the suit. But what made the advice memorable was presentation. Even if all you’ve done is serve food- you have amazing teamwork skills. You present yourself better in order to climb and get more opportunities.

09.27 CV/Resume and LinkedIn Workshop Difference between a CV and a Resume ● The resume will be tailored to each position ● CV will stay put and any changes will be in the cover letter Differences ● A CV is that a CV is intended to be full of your career ● A resume is not Layout should be Balanced ● 50% white space on your resume ● 50% white space in each quadrant Resume Writing ● White or cream paper ● Cotton blend ● No perfume (you’re not Elle) ● Sans serif

Sari Saint- Hilaire 8 Customize resume for the position you’re applying for

10.04 Mingxy You Building nanoscale tools with nucleic acid DNA/RNA: self assemble and biocompatible and programmable Nucleic acid-based tools: precise spatial and temporal control Genetically encoded RNA sensors for cellular imaging lipid-DNA probes for cell membrane biophysics Conjugate DNA probes onto live cell membranes Studying lipid interactions in live cell membranes ● Cell signal transduction relies on membrane lipid interaction ● Temporal requirement ○ Interaction among lipids biochem -> Protein chemistry & structure Bio -> proteomics -> chemical Synthesis 37 T cells with the same genetic blueprint ● Red blood cell ● Cells in the inner lining of the intestine ● Bone cell ● Ovum ● Sperm cell DNA -> RNA -> Protein -> Degradation 3 roles of degradation ● Regulation ○ Cell cycle and the timing in which it happens ● Maintenance

Sari Saint- Hilaire 18 ○ Making sure it takes care of “trash” getting taken out ○ Misfolded protein are not doing their job and that can be toxic ● Recycling ○ mRNA ○ Degradation supplies Amino acids Rapid turnover is required for a fast response ● The longer the lifetime the slower the degradation ○ Need a fast degradation rate ○ Need a short half life Who is responsible? ● Practically this destruction chamber ● 26S Proteasome ○ 2.6 MDa, ATP-dependent protease Ubiquitin Tags Proteins for Degradation ● 76 proteins ● Tags on to other proteins and lets them know it must be destroyed ○ Chemistry based typed thing though ● Polymeric ubiquitin chain ● Tag that marks protein How is this related to human disease? ● Actually is imbalance by synthesis and degradation ● Cancer is more synthesis than degradation ● Cancer cells start to rely on protein proteasome for functioning ● As we age, Protasome loses function What controls the rate of Degradation? ● 8 amino groups that makes for great structural diversity ● Library of 92 UCHL5/UCH37 ● Essential for Growth and Development ● Overexpressed in various cancers ● A subunit of the proteasome and INO80 Chromatin Remodeling Complex ● This enzyme targets branch ubiquitin chain ● Trying to find out how it does that ○ UCH37 knows when ubiquitin has been modified only Hypothesis: Overexpression of UCH37 in Cancer Cells Fuels Proteasome Activity ● Cyclic peptide inhibits UCH37 in vitro *Concentration of drug and concentration on interaction of drug Reflective Paragraph: Professor Strieter is amongst the most passionate professors I’ve met at UMass who is really invested in students' success too. He gets really excited when he gets to talk about his research and that’s always a plus. He took my advice when talking about how he got there and

Sari Saint- Hilaire 19 sharing that with us because that was something not everyone had, and I really appreciated that. His research also made me think of Professor Farkas’s research except Professor Farkas’s research is a little more zoomed out whereas Prof. Farkas looks at cells and Prof. Strieter is looking at protein. I was very excited that I was getting the basic concept though. And that always gave me chills. I found my thing. And that’s really fantastic....