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Biochemist interview questions and how to answer them

Biochemist interviews circle back to one thing: can you reason about a protein you can't see. You'll be asked to rescue a purification that went wrong, pick a binding method and defend it, and explain a kinetics plot someone slides across the table. Below are the questions panels use, what they're listening for, and what a weak answer sounds like.

12 questions8 minute read

Part 1

1.Walk me through how you'd express and purify a protein you've never worked with.

Why they ask

Purification is the backbone of most biochemist roles, and a plan from scratch shows whether you understand the reasons behind each step or just follow a protocol you inherited.

How to answer

  • Start from the sequence: size, pI, cysteines, predicted disordered regions and any known cofactors
  • Pick an expression system and tag to match, such as E. coli with a cleavable his-tag, or insect cells if it needs folding help
  • Run a small expression test before scaling, checking soluble versus insoluble fractions on a gel
  • Lay out capture, polish and a size exclusion step, and say how you'd judge purity and whether it's folded

2.Your protein looks clean after size exclusion, then crashes out when you concentrate it. What now?

Why they ask

Aggregation eats weeks in real labs, and they want to see whether you troubleshoot in a logical order or change everything at once.

How to answer

  • Check whether it's precipitating at a particular concentration, temperature or after freeze-thaw
  • Screen buffer conditions: pH away from the pI, salt, glycerol, arginine, a reducing agent if there are free cysteines
  • Use thermal shift or dynamic light scattering to compare conditions quickly instead of guessing
  • Consider construct changes, like trimming a floppy terminus, if buffer tweaks don't fix it

3.How would you measure Km and kcat for an enzyme, and what would make you distrust the result?

Why they ask

Kinetics is core biochemistry, and interviewers use it to separate people who've fit curves from people who understand the assumptions behind them.

How to answer

  • Pick a readout, continuous if possible, and confirm the signal is linear with time and enzyme amount
  • Measure initial rates across substrate concentrations that bracket the expected Km
  • Fit to Michaelis-Menten with nonlinear regression in Prism rather than a Lineweaver-Burk plot
  • Flag substrate depletion, inner filter effects, inhibition at high substrate and an enzyme that loses activity during the run
4.When would you use SPR, ITC or a plate-based binding assay to measure an interaction?

Why they ask

Choosing a method is a judgment call they'll trust you with on the job, so they want to hear trade-offs, not a list of acronyms.

How to answer

  • SPR for on and off rates and for ranking many binders, as long as immobilizing one partner doesn't break it
  • ITC when you need thermodynamics in solution and have enough protein to spare
  • A fluorescence or AlphaScreen style plate assay for throughput during screening
  • Mention confirming a key result with a second method that works differently
5.Tell me about an assay you developed or fixed. How did you decide it was ready to use?

Why they ask

Industry biochemists spend a lot of time building assays other people will run, so they need to know you think about reliability, not just a pretty first plate.

How to answer

  • Describe what the assay was for and what was wrong or missing before you started
  • Explain the variables you optimized, like enzyme amount, incubation time and DMSO tolerance
  • Say how you checked plate uniformity, controls, signal window and day-to-day reproducibility
  • Mention writing it up so someone else could run it without you

Part 2

6.A Western blot shows an extra band below your protein. How do you find out what it is?

Why they ask

Mystery bands are an everyday problem, and they want to see whether you reach for evidence or just crop the image.

How to answer

  • Check whether it's there in the input or appears over time, which points to degradation
  • Add protease inhibitors or change handling and see if it goes away
  • Probe with an antibody against the other terminus or the tag to map which end is missing
  • Send it for intact mass or in-gel digest mass spectrometry if you need a definite answer
7.How do you decide on controls and replicates for an experiment?

Why they ask

Bad controls are the most common reason a project gets fooled by its own data, and a panel will probe this in your seminar anyway.

How to answer

  • Name the question first, then the positive and negative controls that would prove the readout works
  • Separate technical repeats from true biological or independent preparations
  • Decide the analysis and what counts as a real difference before running it
  • Give an example where a control caught a problem
8.How do you keep your notebook and data in shape for someone else to use?

Why they ask

In regulated or partnered work, your records can end up in a filing or an audit, and sloppy notes create real risk for the company.

How to answer

  • Describe your electronic lab notebook habits: dates, lot numbers, instrument IDs and raw file locations
  • Explain how you link raw data to processed results so the analysis can be rebuilt
  • Mention GLP or GMP rules you've followed, like second-person review or controlled templates
  • Say how you record deviations instead of quietly fixing them
9.Tell me about a project that didn't work. What did you learn and what did you do next?

Why they ask

Failure is normal in biochemistry, and they want to hear honest reasoning, not a story polished into a success.

How to answer

  • Pick a real failure, such as a protein that never expressed solubly
  • Walk through what you tried and why each step made sense at the time
  • Explain when and how you decided to stop or change direction
  • Name the habit you changed afterward
10.How would you explain your binding data to a medicinal chemist who needs to pick the next compounds?

Why they ask

Your results only matter if the people downstream can act on them, and chemists and program leads won't read your raw sensorgrams.

How to answer

  • Lead with the decision the data supports, such as which series binds best
  • Show the confidence in each number and which values are near the assay's limit
  • Flag compounds that behaved oddly, like aggregators or ones that stuck to the chip
  • Offer the next experiment that would settle any open question

Part 3

11.Two projects need the same purification system this week. How do you handle it?

Why they ask

Shared instruments cause friction in every lab, and they're checking whether you plan ahead and talk to people before a conflict happens.

How to answer

  • Check the booking calendar early and look at which deadline actually drives the program
  • Talk to the other scientist directly rather than escalating first
  • Look for workarounds such as running overnight, using gravity columns for capture or splitting the run
  • Tell your manager about any delay before it happens
12.Why this role, and why industry rather than an academic lab?

Why they ask

They want to know you understand the trade: less freedom to chase your own questions in exchange for team goals and firmer timelines.

How to answer

  • Connect your past work to what this team actually does
  • Say what draws you to seeing your data feed a program decision
  • Be honest about what you'll miss and why you're fine with it
  • Ask a question that shows you've read about their pipeline or platform

Questions to ask them

Ask at least two. It shows you're picking them too.

  • Who makes the protein I'd be working with, and how often does the supply run short?
  • What does a scientist at my level decide alone, and what goes to the project team?
  • How is instrument time on the ÄKTA, SPR and plate readers shared across groups?
  • How are results from this group written up: notebooks only, formal reports, or regulatory documents?
  • What happened to the last person in this role?

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