Biology IA · B · Form and function · topic 6 of 25
Do heat-loving proteins have more charged residues? · IB Biology IA idea: guide, sample graph and step-by-step plan
stretch topic. rewarding if you're carefulEnzymes from hot springs survive where yours would unravel. Is there something different on the inside that you can actually count?
- ✓ you like protein structure
- ✓ you're happy to learn a free viewer
- ✓ you want a question with a clear mechanism to test
The big idea
← your definition IS your methodA protein's shape is held together by many weak interactions. One idea is that enzymes from heat-loving organisms have more ion pairs, where oppositely charged side chains sit close together, helping to hold the fold at high temperature. You choose one enzyme family, collect structures from organisms with different optimum growth temperatures, and count the pairs using a fixed definition. Your definition of a salt bridge is your method, so state it and keep it identical for every structure. Then ask whether the count really goes up with temperature, or whether some other feature explains the difference.
Make it yours: pick one twist
Copying a classic won't show your choices. Pick one of these (or invent your own) and your IA becomes yours.
Swipe for more twists →
Count salt bridges with two distance cut-offs and see whether the pattern depends on your choice.
→ Turns the biggest hidden choice into data. Your graph has two series.Use the percentage of charged amino acids in the sequence, not the structure.
→ Easier data, because you need only sequences, but you lose the link to actual contacts.Compare a heat-loving enzyme with a close relative from a cooler organism, in detail.
→ Gives a clean comparison and a deeper look at which residues differ, but only two data points for statistics.Count hydrogen bonds or hydrophobic contacts alongside salt bridges.
→ Asks which feature changes most. Harder and needs careful definitions.Count salt bridges on the surface and in the interior separately.
→ Tests where the extra pairs sit. You need a rule for surface and core.Your Biology IA research question: run the check
Write your own question first. Then make sure it ticks every box:
- Names the enzyme family, the independent variable (optimum growth temperature of the organism, with range in °C) and the dependent variable (a clear count or percentage).
- Says exactly how a salt bridge is defined (which atoms, what distance) and how counts are made.
- Says how structures are chosen (resolution, length, same family) and how many organisms you will use.
- Says where growth temperatures come from.
- Says which statistic you will use, and is honest that a handful of structures limits what you can claim.
The workflow
A database investigation has no apparatus, so the 'set-up' is the structure you inspect and your data pipeline. Draw your own version, with your real entries, for the Method section.
How your Biology IA could be laid out
The usual order for a topic like this, what each part needs to show, and roughly how much of your 3,000 words it takes. The words are all yours.
Your question; why stability at high temperature matters; what you expect and why.
Protein structure levels and the bonds that hold them; what is known about stabilising interactions in heat-tolerant enzymes (cite); your prediction.
Independent and dependent variables, plus controls for a database: family, resolution, length, definition.
Which database and viewer; how you chose entries; your exact definition and counting steps; enough detail to repeat.
Short: screen use only; credit database entries.
Table of organisms, entry IDs, growth temperatures, resolutions and counts, with the date accessed.
How counts became a per-100-residue measure, treatment of chains and repeats; one worked example per calculation.
Count against growth temperature, with the uncertainty from your definition; correlation or regression; what the plot shows.
Answer in terms of direction and strength, with a statistic; compare with published studies; keep your claim to your sample.
Weaknesses of the definition and the sample; which matters most; limits of structures as a snapshot; linked improvements.
Every database entry, tool and paper.
What your Biology IA graph could look like
n = ? say it on the graphMade-up data, to show you the form of a strong graph, not the answer. Yours will look different. example only
- Error bars show something real: how much the count changes if you change your definition.
- A flat line is drawn as well, so the reader can see what 'no relationship' would look like.
- Say how many organisms are plotted. Six points make a weak case for any trend.
- Use per 100 residues, not raw counts, because larger proteins have more of everything.
- Another graph to consider: plot the difference in salt bridges for each heat-loving and cool pair of relatives.
Your game plan
two structures by hand FIRSTTick steps off as you go. We'll remember on this device.
0 of 10 done
- Read and predictFind what is known about stabilising features in heat-tolerant proteins. Write down your prediction and what would count as no relationship.
- Learn the viewerOpen one structure and find a salt bridge by eye. Check how the viewer measures distance, and what residues carry charge.
- Trial run (1 lesson)Count in two structures by hand. Do you and the viewer agree? How long does it take? Is your definition clear enough for someone else to repeat?
- Choose the family and entriesChoose a family with structures from many organisms. Write down rules for resolution, length and which chain you use.
- Write the definitionDecide which atoms count, the distance cut-off and how you handle multiple chains or ties. Write down why.
- Collect the dataRecord entry ID, organism, growth temperature (with source), length and counts straight into the table.
- ProcessConvert counts to a per-100-residue measure. Decide how you will show sensitivity to the definition.
- Graph and interpretPlot count against temperature, with the sensitivity shown. State the direction, strength and sample size, and what you can't say.
- EvaluateRank the weaknesses by their effect on your answer. Make every improvement specific.
- Check before your teacher's draftRun the checklist below, then get your RQ or draft checked. Your teacher reads one draft only, so make it count.
Biology you'll need
Traps to avoid in this Biology IA
- Comparing proteins that are not true homologues, so the structures differ for other reasons.
- Drawing a trend from two pairs: use at least five organisms and say how you chose them.
- No clear definition of a salt bridge, so counts drift between structures.
- Raw counts instead of a per-length measure.
- Mixing structures of different quality, such as a low-resolution one next to a very sharp one.
- Saying salt bridges cause stability, when you only showed a link.
More Biology IA ideas like this
- Beetroot and freeze–thaw●○○
- How far does a molecule diffuse in a gel?●○○
- Stomata: sun leaves vs shade leaves●●○
This guide shows how a topic like this is usually approached. It is not an IA. Your question, choices, data, analysis and words must be your own: change something, tell your teacher where the idea came from, and follow your school's rules on outside help.