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Assistant Professor of Biochemistry at Loyola Marymount University trying to make biochemistry fun and accessible for all. I aim for lots of detail without lots of jargon (or at least with jargon explained). I do not monetize any of my content. All of it is freely provided out of an effort to "pay it forward." Much more on my blog. I sincerely hope it helps you!

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Tags

biochemistry
structural biology
molecular biology
x-ray crystallography

Stats

Joined September 8, 2012
3,353,133 total views
United States

Featured video

About me: Who is the bumbling biochemist?

14,630 views

1y ago

Videos

BCA, Bradford, and other ways of measuring protein concentration - a practical comparison
8:43
BCA, Bradford, and other ways of measuring protein concentration - a practical comparison

572 views

17h ago

Structural biology coloring schemes - element coloring, chainbows, charge, etc.
33:19
Structural biology coloring schemes - element coloring, chainbows, charge, etc.

617 views

1d ago

My favorite books by or about biochemistry-related Nobel Prize winners
22:58
My favorite books by or about biochemistry-related Nobel Prize winners

762 views

3d ago

Who's who inside & outside of academic labs helping research happen (PI, students, postdocs, etc.)
15:13
Who's who inside & outside of academic labs helping research happen (PI, students, postdocs, etc.)

512 views

3d ago

Hopefully back in the game - next week, it's on!
4:21
Hopefully back in the game - next week, it's on!

585 views

4d ago

Chirality in biological molecules - Nobel prizes & enzymes
6:44
Chirality in biological molecules - Nobel prizes & enzymes

1,400 views

5d ago

Why and how we purify proteins with FPLC (aka - what's an AKTA and why should I care?)
6:43
Why and how we purify proteins with FPLC (aka - what's an AKTA and why should I care?)

1,300 views

6d ago

Solid state oligonucleotide synthesis – phosphoramidite method
31:01
Solid state oligonucleotide synthesis – phosphoramidite method

860 views

9d ago

Cryoprotecting crystals – how I like to do it...
6:33
Cryoprotecting crystals – how I like to do it...

1,100 views

12d ago

Silent vs. synonymous mutations - they’re not the same thing!
14:11
Silent vs. synonymous mutations - they’re not the same thing!

873 views

2w ago

Key information to know about amino acids & tips for remembering
19:52
Key information to know about amino acids & tips for remembering

2,000 views

2w ago

Protein variant amino acid nomenclature – shorthand for representing substitutions, deletions, etc.
10:49
Protein variant amino acid nomenclature – shorthand for representing substitutions, deletions, etc.

936 views

2w ago

Playlists

Using various databases
31 videos
Using various databases
Using the PDB (Protein Data Bank)
22 videos
Using the PDB (Protein Data Bank)
My research
5 videos
My research
Gene & genome editing
17 videos
Gene & genome editing
Organization strategies & tips
21 videos
Organization strategies & tips
Biopharmaceutical sciences
37 videos
Biopharmaceutical sciences
Hidden curriculum of academic science
34 videos
Hidden curriculum of academic science
PyMOL
17 videos
PyMOL
CHEM373 Spring 2026
7 videos
CHEM373 Spring 2026
Book recommendations
17 videos
Book recommendations
20 Days of Amino Acids 2025
24 videos
20 Days of Amino Acids 2025
Biochemistry practice problems
6 videos
Biochemistry practice problems

lab techniques and equipment

the bumbling biochemist
Biochemistry techniques - overview of some biochem, molecular biology, & structural biology methods
1:18:37
Biochemistry techniques - overview of some biochem, molecular biology, & structural biology methods

6,200 views

3y ago

the bumbling biochemist
Lab equipment: What's what in wet work!
1:01:00
Lab equipment: What's what in wet work!

1,800 views

3y ago

the bumbling biochemist
Inducible protein overexpression in bacteria with the T7 expression system
49:54
Inducible protein overexpression in bacteria with the T7 expression system

4,700 views

3y ago

the bumbling biochemist
Bacterial growth media (LB, TB, SOB, SOC, etc.)
26:31
Bacterial growth media (LB, TB, SOB, SOC, etc.)

2,000 views

3y ago

the bumbling biochemist
Practical lab tip - prepare lots of SDS-PAGE samples in a PCR strip
7:03
Practical lab tip - prepare lots of SDS-PAGE samples in a PCR strip

1,100 views

3y ago

the bumbling biochemist
Choosing a gel percentage for gel electrophoresis (polyacrylamide & agarose)
19:25
Choosing a gel percentage for gel electrophoresis (polyacrylamide & agarose)

3,700 views

3y ago

the bumbling biochemist
Pull-down assays (co-IPs (co-immunoprecipitations), etc) - what, how, & what to look for
45:31
Pull-down assays (co-IPs (co-immunoprecipitations), etc) - what, how, & what to look for

5,300 views

3y ago

the bumbling biochemist
Why we use secondary antibodies (indirect detection method) - in western blots, etc.
16:55
Why we use secondary antibodies (indirect detection method) - in western blots, etc.

3,900 views

3y ago

the bumbling biochemist
Practical lab tips for working with protease inhibitor tablets
4:15
Practical lab tips for working with protease inhibitor tablets

2,100 views

3y ago

the bumbling biochemist
Nucleic acid UV absorption & purity ratios (260/280 and 260/230)
16:01
Nucleic acid UV absorption & purity ratios (260/280 and 260/230)

8,900 views

3y ago

the bumbling biochemist
cDNA (complementary DNA), its uses, & some nuances to take into account when molecular cloning
29:21
cDNA (complementary DNA), its uses, & some nuances to take into account when molecular cloning

2,800 views

3y ago

the bumbling biochemist
Tips for setting up, loading, & running PAGE gels
9:57
Tips for setting up, loading, & running PAGE gels

1,500 views

3y ago

Practical lab tips & tricks

the bumbling biochemist
The finger flick - an awesome lab trick! Finger vortexing & other mixing methods
2:52
The finger flick - an awesome lab trick! Finger vortexing & other mixing methods

12,000 views

4y ago

the bumbling biochemist
Making a 80% glycerol stock solution - a simple lab hack that makes glycerol way easier to work with
4:19
Making a 80% glycerol stock solution - a simple lab hack that makes glycerol way easier to work with

13,000 views

4y ago

the bumbling biochemist
Pipetting viscous liquids - reverse pipetting, etc.
6:53
Pipetting viscous liquids - reverse pipetting, etc.

14,000 views

4y ago

the bumbling biochemist
Lab labeling - some tips to labeling tubes, etc. effectively
14:39
Lab labeling - some tips to labeling tubes, etc. effectively

8,600 views

4y ago

the bumbling biochemist
Keeping a detailed plasmid inventory
21:32
Keeping a detailed plasmid inventory

1,500 views

4y ago

the bumbling biochemist
Protein prep inventory-ing: keeping a detailed inventory of cell pellets and purified proteins
14:55
Protein prep inventory-ing: keeping a detailed inventory of cell pellets and purified proteins

865 views

4y ago

the bumbling biochemist
Flash freeze fishing - and other tricks for snap freezing eppendorf tubes in liquid nitrogen
3:39
Flash freeze fishing - and other tricks for snap freezing eppendorf tubes in liquid nitrogen

8,500 views

4y ago

the bumbling biochemist
Tips for loading PAGE gels - the strategy that works for me
12:14
Tips for loading PAGE gels - the strategy that works for me

9,800 views

4y ago

the bumbling biochemist
Mastering master mixes - calculations & concepts
24:34
Mastering master mixes - calculations & concepts

5,900 views

4y ago

the bumbling biochemist
C1V1 = C2V2 (aka M1V1=M2V2) is so useful for calculating solution volumes & concentrations!
13:34
C1V1 = C2V2 (aka M1V1=M2V2) is so useful for calculating solution volumes & concentrations!

5,500 views

4y ago

the bumbling biochemist
Don't let your electrophoresis gels smile - gel electrophoresis voltage, heat, buffers etc.
22:21
Don't let your electrophoresis gels smile - gel electrophoresis voltage, heat, buffers etc.

2,800 views

4y ago

the bumbling biochemist
What to do when a plasmid comes for you: agar stab to plate to glycerol stock, miniprep & sequencing
10:36
What to do when a plasmid comes for you: agar stab to plate to glycerol stock, miniprep & sequencing

7,400 views

4y ago

Recombinant protein expression & purification

Quick tip for balance-making: add/remove 1 mL/g (1 µL/mg)
Quick tip for balance-making: add/remove 1 mL/g (1 µL/mg)

1,900 views

Tips for unclogging empty chromatography columns
Tips for unclogging empty chromatography columns

2,100 views

grad school stuff

the bumbling biochemist
Tips for writing strong personal statements for science grad school applications
17:33
Tips for writing strong personal statements for science grad school applications

1,000 views

3y ago

the bumbling biochemist
Core biochemistry toolbox - software, databases, etc. to get familiar with
10:41
Core biochemistry toolbox - software, databases, etc. to get familiar with

1,100 views

3y ago

the bumbling biochemist
Grad school research topics and lab rotations
13:56
Grad school research topics and lab rotations

763 views

3y ago

the bumbling biochemist
Abstracts and advice for writing awesome ones
22:55
Abstracts and advice for writing awesome ones

325 views

3y ago

the bumbling biochemist
Troubleshooting and optimizing lab experiments
14:43
Troubleshooting and optimizing lab experiments

1,500 views

4y ago

the bumbling biochemist
Experimenting thoughtfully - good practices for getting the most out of each experiment
26:05
Experimenting thoughtfully - good practices for getting the most out of each experiment

807 views

4y ago

the bumbling biochemist
Reproducing and adapting experimental protocols - get ready to Google! (and think critically)
27:22
Reproducing and adapting experimental protocols - get ready to Google! (and think critically)

544 views

4y ago

the bumbling biochemist
Getting familiar with Python (and not intimidated by it) as a bench scientist
34:56
Getting familiar with Python (and not intimidated by it) as a bench scientist

759 views

4y ago

the bumbling biochemist
Choosing majors and programs in college and grad school
10:33
Choosing majors and programs in college and grad school

222 views

4y ago

the bumbling biochemist
Making the most of school - some tips for learning effectively
11:21
Making the most of school - some tips for learning effectively

517 views

4y ago

the bumbling biochemist
IUBMB Trainee Initiative Graduate School Roadmap Resources
3:39
IUBMB Trainee Initiative Graduate School Roadmap Resources

105 views

4y ago

the bumbling biochemist
Resources: a guide to some of my favorite biochemistry, biology, chemistry, & coding resources
30:46
Resources: a guide to some of my favorite biochemistry, biology, chemistry, & coding resources

868 views

4y ago

lab math-y stuff

the bumbling biochemist
Working with molecular weights (molar masses, formula weights) - calculations, Daltons, etc.
5:24
Working with molecular weights (molar masses, formula weights) - calculations, Daltons, etc.

3,600 views

4y ago

the bumbling biochemist
Concentration - ways to report it (molarity, molality, mole fraction, percentages, etc.)
15:14
Concentration - ways to report it (molarity, molality, mole fraction, percentages, etc.)

2,200 views

4y ago

the bumbling biochemist
Making 70% ethanol solutions (the right way)
7:15
Making 70% ethanol solutions (the right way)

28,000 views

4y ago

the bumbling biochemist
Working with relative concentrations (in terms of stock solutions)
10:51
Working with relative concentrations (in terms of stock solutions)

1,100 views

4y ago

the bumbling biochemist
Resuspending, diluting, & working with DNA & RNA oligos (primers you order, etc.)
14:15
Resuspending, diluting, & working with DNA & RNA oligos (primers you order, etc.)

5,700 views

4y ago

the bumbling biochemist
Some solid solutions to making solutions (or at least some bubbly tips)
12:31
Some solid solutions to making solutions (or at least some bubbly tips)

961 views

4y ago

the bumbling biochemist
C1V1 = C2V2 (aka M1V1=M2V2) is so useful for calculating solution volumes & concentrations!
13:34
C1V1 = C2V2 (aka M1V1=M2V2) is so useful for calculating solution volumes & concentrations!

5,500 views

4y ago

the bumbling biochemist
Mastering master mixes - calculations & concepts
24:34
Mastering master mixes - calculations & concepts

5,900 views

4y ago

the bumbling biochemist
Why Kd doesn't depend on concentrations, but what you measure might; binding vs titration range, etc
16:26
Why Kd doesn't depend on concentrations, but what you measure might; binding vs titration range, etc

3,300 views

4y ago

the bumbling biochemist
Michaelis-Menten kinetics - giving enzymes a performance review; derivation & Km, kcat measurement
54:23
Michaelis-Menten kinetics - giving enzymes a performance review; derivation & Km, kcat measurement

1,700 views

4y ago

the bumbling biochemist
Molarity & other ways to talk about solution concentrations (molality, osmolarity, mole fraction..)
26:10
Molarity & other ways to talk about solution concentrations (molality, osmolarity, mole fraction..)

314 views

4y ago

the bumbling biochemist
Osmolarity, tonicity, & predicting solvent flow - with some biochemistry implications & examples
36:21
Osmolarity, tonicity, & predicting solvent flow - with some biochemistry implications & examples

1,000 views

4y ago

nucleic acids

the bumbling biochemist
DNA & RNA precipitation with alcohols & salts - theory, practice, & options (EtOH vs IsOH, etc.)
20:56
DNA & RNA precipitation with alcohols & salts - theory, practice, & options (EtOH vs IsOH, etc.)

9,500 views

4y ago

the bumbling biochemist
Why and how our bodies use ATP as energy storage
28:44
Why and how our bodies use ATP as energy storage

1,100 views

4y ago

the bumbling biochemist
Gel extraction with the "crush and soak" method
22:05
Gel extraction with the "crush and soak" method

4,600 views

4y ago

the bumbling biochemist
Fluorescent nucleic acid stains & fluorescence basics
35:44
Fluorescent nucleic acid stains & fluorescence basics

1,900 views

4y ago

the bumbling biochemist
Low melting point agarose
20:46
Low melting point agarose

1,100 views

4y ago

the bumbling biochemist
Mutation mumbo-jumbo: terminology, types, & potential effects
16:59
Mutation mumbo-jumbo: terminology, types, & potential effects

484 views

4y ago

the bumbling biochemist
Nucleic acid sequence terminology (e.g., reverse complement), interconversion & sequence translation
14:21
Nucleic acid sequence terminology (e.g., reverse complement), interconversion & sequence translation

690 views

4y ago

the bumbling biochemist
Sequence annotations (genomic & proteomic)
9:46
Sequence annotations (genomic & proteomic)

1,000 views

4y ago

the bumbling biochemist
Nucleic acid memory tips and intuition
13:44
Nucleic acid memory tips and intuition

1,300 views

4y ago

the bumbling biochemist
Coprecipitants like GlycoBlue (and normal glycogen or LPA) in nucleic acid precipitation
10:32
Coprecipitants like GlycoBlue (and normal glycogen or LPA) in nucleic acid precipitation

1,400 views

4y ago

the bumbling biochemist
TRIzol extractions of RNA, DNA, and protein
34:53
TRIzol extractions of RNA, DNA, and protein

13,000 views

3y ago

the bumbling biochemist
Hot start PCR & avoiding "nonspecific products"
13:54
Hot start PCR & avoiding "nonspecific products"

1,200 views

3y ago

Structural biology

the bumbling biochemist
What do structural biologists do?
31:36
What do structural biologists do?

6,600 views

3y ago

the bumbling biochemist
X-ray crystallography and cryo-em (cryo-electron microscopy): an overview & comparison
21:44
X-ray crystallography and cryo-em (cryo-electron microscopy): an overview & comparison

9,100 views

3y ago

the bumbling biochemist
It's just a model! Understanding x-ray crystallography & cryo-EM maps, models, and resolution
30:58
It's just a model! Understanding x-ray crystallography & cryo-EM maps, models, and resolution

2,000 views

3y ago

the bumbling biochemist
Resolution of molecular structures - an overview
15:16
Resolution of molecular structures - an overview

1,000 views

3y ago

the bumbling biochemist
Viewing maps & evaluating resolution (global & local), B factor, contour, etc. - look in Pymol
18:58
Viewing maps & evaluating resolution (global & local), B factor, contour, etc. - look in Pymol

4,300 views

3y ago

the bumbling biochemist
X-ray crystallography maps (viewing & understanding 2Fo-Fc, Fo-Fc, etc.) & overview of phase problem
28:53
X-ray crystallography maps (viewing & understanding 2Fo-Fc, Fo-Fc, etc.) & overview of phase problem

7,000 views

3y ago

the bumbling biochemist
Levels of protein structure (primary, secondary, tertiary, quaternary) & terms (motif, domain, etc.)
41:37
Levels of protein structure (primary, secondary, tertiary, quaternary) & terms (motif, domain, etc.)

979 views

3y ago

the bumbling biochemist
Protein flexibility, conformational changes, and intrinsically disordered regions (IDR's)
33:30
Protein flexibility, conformational changes, and intrinsically disordered regions (IDR's)

3,900 views

4y ago

the bumbling biochemist
A short intro to crystal structure interpretation & evaluation using the PDB
11:03
A short intro to crystal structure interpretation & evaluation using the PDB

1,400 views

5y ago

the bumbling biochemist
Using the PDB to investigate x-ray crystallography structures: resolution, R-factor, outliers & more
39:31
Using the PDB to investigate x-ray crystallography structures: resolution, R-factor, outliers & more

1,900 views

5y ago

the bumbling biochemist
Understanding x-ray crystallography structures
19:27
Understanding x-ray crystallography structures

9,600 views

5y ago

the bumbling biochemist
Protein structure representations, ribbon diagrams, and Jane Richardson
11:23
Protein structure representations, ribbon diagrams, and Jane Richardson

2,300 views

5y ago

terminology

the bumbling biochemist
Endogenous vs. Exogenous - terminology, techniques, and biochemistry experimental considerations
11:14
Endogenous vs. Exogenous - terminology, techniques, and biochemistry experimental considerations

7,500 views

3y ago

the bumbling biochemist
Homology terminology (homolog, ortholog, paralog) - plus sequence similarity and identity
15:45
Homology terminology (homolog, ortholog, paralog) - plus sequence similarity and identity

4,000 views

3y ago

the bumbling biochemist
What "residues" are, how they compare and relate to amino acids, and why the distinction may matter
7:05
What "residues" are, how they compare and relate to amino acids, and why the distinction may matter

4,200 views

3y ago

the bumbling biochemist
Ligands, substrates, agonists, antagonists, inverse agonists & more binding partner terminology!
11:10
Ligands, substrates, agonists, antagonists, inverse agonists & more binding partner terminology!

1,100 views

3y ago

the bumbling biochemist
Housekeeping genes/proteins, internal references/loading controls & related terms: constitutive etc.
13:39
Housekeeping genes/proteins, internal references/loading controls & related terms: constitutive etc.

3,100 views

3y ago

the bumbling biochemist
Receptor agonists vs. antagonists vs. inverse agonists, and constitutive receptor activity
18:19
Receptor agonists vs. antagonists vs. inverse agonists, and constitutive receptor activity

1,900 views

3y ago

the bumbling biochemist
Biochemistry & biology word parts: key prefixes, suffixes, roots, etc. with examples
29:55
Biochemistry & biology word parts: key prefixes, suffixes, roots, etc. with examples

1,500 views

3y ago

the bumbling biochemist
Alanine biochemistry - amino acid chirality, alanine scanning, glucose-alanine cycle, & more
35:04
Alanine biochemistry - amino acid chirality, alanine scanning, glucose-alanine cycle, & more

1,100 views

3y ago

the bumbling biochemist
Ketogenic vs glucogenic amino acids and the biochemistry of leucine
34:02
Ketogenic vs glucogenic amino acids and the biochemistry of leucine

1,000 views

3y ago

the bumbling biochemist
Quick overview of thinking about atoms. electronegativity, polarity, in biochemistry
3:58
Quick overview of thinking about atoms. electronegativity, polarity, in biochemistry

228 views

3y ago

the bumbling biochemist
Threonine, polar amino acids & power of oxygen: electronegativity, nucleophilicity & phosphorylation
40:53
Threonine, polar amino acids & power of oxygen: electronegativity, nucleophilicity & phosphorylation

822 views

3y ago

the bumbling biochemist
Aromatic amino acids, resonance/electron delocalization, and phenylalanine biochemistry
32:03
Aromatic amino acids, resonance/electron delocalization, and phenylalanine biochemistry

945 views

3y ago

biochemistry concepts

the bumbling biochemist
Glycobiology - an overview of sugar biochemistry
40:23
Glycobiology - an overview of sugar biochemistry

2,200 views

4y ago

the bumbling biochemist
Homology terminology (homolog, ortholog, paralog) - plus sequence similarity and identity
15:45
Homology terminology (homolog, ortholog, paralog) - plus sequence similarity and identity

4,000 views

3y ago

the bumbling biochemist
Endogenous vs. Exogenous - terminology, techniques, and biochemistry experimental considerations
11:14
Endogenous vs. Exogenous - terminology, techniques, and biochemistry experimental considerations

7,500 views

3y ago

the bumbling biochemist
Targeted protein degradation (via PROTACs, molecular glues, etc.) and stabilization (via DUBTACs)
36:12
Targeted protein degradation (via PROTACs, molecular glues, etc.) and stabilization (via DUBTACs)

4,700 views

3y ago

the bumbling biochemist
Phenol red and pH buffering of cell culture media
14:03
Phenol red and pH buffering of cell culture media

3,000 views

3y ago

the bumbling biochemist
Science of plant color (and color in general)
16:54
Science of plant color (and color in general)

564 views

3y ago

the bumbling biochemist
Bioorthogonal chemistry & the 2022 Nobel Prize in Chemistry
32:51
Bioorthogonal chemistry & the 2022 Nobel Prize in Chemistry

917 views

4y ago

the bumbling biochemist
Protein concentrations & molecular weights - on paper & in lab! (mg/mL's only part of the story!)
21:24
Protein concentrations & molecular weights - on paper & in lab! (mg/mL's only part of the story!)

1,600 views

4y ago

the bumbling biochemist
Working with molecular weights (molar masses, formula weights) - calculations, Daltons, etc.
5:24
Working with molecular weights (molar masses, formula weights) - calculations, Daltons, etc.

3,600 views

4y ago

the bumbling biochemist
Concentration - ways to report it (molarity, molality, mole fraction, percentages, etc.)
15:14
Concentration - ways to report it (molarity, molality, mole fraction, percentages, etc.)

2,200 views

4y ago

the bumbling biochemist
Electrolytes vs non-electrolytes: dissolution vs dissociation & the van’t Hoff factor
7:19
Electrolytes vs non-electrolytes: dissolution vs dissociation & the van’t Hoff factor

515 views

4y ago

the bumbling biochemist
Chelators in the lab: EDTA & EGTA biochemistry
15:47
Chelators in the lab: EDTA & EGTA biochemistry

5,800 views

4y ago