Molecular Biology

Front 1

Parvalbumin

parVALbyoomin

Back 1

Calcium-binding protein.

Selectively expressed by GABAergic interneurons.

A lot of different types of them.

Front 2

Calcium-binding proteins

Back 2

Proteins in the cytosol that affect the behavior of the calcium ions.

Selectively expressed by different neuron types:

- Parvalbumin

- Calretinin

- Calbindin-D28K

Front 3

Wnt proteins

Back 3

Metazoans.

Signalling transduction molecules.

Regulate cell migration, fate determination, etc.

19 Wnt proteins.

Bind to Frizzled receptors.

Front 4

Signalling transduction

Back 4

Extracellular proteins hit receptors and affect cell's shape / metabolism / gene expression / ability to divide / etc.

Front 5

Adaptor proteins

Adapter proteins

Back 5

Involved in signalling transduction.

Encode protein-binding motifs that help proteins interact and form larger signalling complexes.

Front 6

Kinase

Back 6

Enzyme.

Catalyzes phosphorylation.

Front 7

Phosphorylation

Back 7

Form of post-transcriptional regulation of enzymes.

A molecule gains a phosphate group.

Phosphorylation --> conformational change --> change in behavior.

Prokaryotes and eukaryotes both use reversible phosphorylation.

Proteins can have many sites for it.

Front 8

Enzyme

Back 8

Usually a protein.

Catalyze chemical reactions.

Folded chain of amino acids.

Front 9

Ribosome

Back 9

All living cells.

Site of translation. Binds to mRNA chain.

Small subunit reads mRNA.
Large subunit links amino acids, in order.

Front 10

Interferon

Back 10

Signalling protein.

Released in response to pathogen.

Often to signal other cells to increase defenses.

Viruses, bacteria, parasites, cancerous cells.

Front 11

Transcription factor

Back 11

Protein (or short noncoding RNA).

Binds to DNA.

Promotes or blocks RNA polymerase.

Controls rate of transcription of gene.

Binding site is adjacent to gene.

Genes can be flanked by >1 binding site, for specific TFs.

Defining feature: a protein-binding domain.

Front 12

Histone

Back 12

Eukaryotes. Within cell nucleus.

Proteins.

Spools around which DNA winds.

Package/order DNA into nucleosomes.

Main protein components of chromatin.

Front 13

Nucleosome

Back 13

Eukaryotes.

Segment of DNA wound around 8 histones.

Basic unit of DNA packaging.

"Folded through a series of successively higher order structures to eventually form a chromosome."

Front 14

Chromatin

Back 14

Eukaryotes.

Complex of macromolecules.

DNA, RNA, and protein.

Packages chromosome.

Front 15

Cis-regulatory element

CRE

Back 15

Region of non-coding DNA.

Regulates transcription of nearby gene.

Usually by TF binding to it.

"Cis" because it's on the same DNA molecule as the gene it's regulating.

Front 16

ChIP-Seq

Chromatin-Immunoprecipitation followed by sequencing

Back 16

Identifies binding sites of proteins along DNA.

Front 17

Enhancer

Back 17

Pro/eukaryotes.

Type of cis-regulatory element. 50-1500 bp.

Proteins bind to increase chance of transcription.

Can be up to 1 Mbp from gene.

Can be upstream or downstream from start site.

Front 18

Promoter

Back 18

Pro/eukaryotes.

Type of cis-regulatory element. ~100–1000 bp.

Initiates transcription.

Near start site.

Upstream.

Front 19

Cofactor

Back 19

Non-protein chemical compound.

Or metallic ion.

Enzymes need them to catalyze chemical reactions.

Front 20

Sequence motif

Back 20

Short, recurring pattern in DNA.

One thought to have biological significance.

Often indicate binding sites.

Sometimes involved in RNA-level processes:

ribosome binding,

mRNA processing (like splicing or editing),

transcription termination.

Front 21

Amino acid

Back 21

Building blocks of proteins.

20 amino acids found within proteins.

Humans produce 10. Rest through food.

Alanine, asparagine, aspartic acid, cysteine,

glutamic acid, glutamine, glycine, proline, serine, tyrosine, arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine.

Front 22

Polyadenylation

Back 22

Poly(A) tail added to 3' end of mRNA as transcription ends.

But not all transcripts, and some genes' transcripts might be cleaved to add the tail at several possible points.

Tail shortens over time, til mRNA is degraded by enzymes.

Prokaryotes: shorter tails, fewer transcripts have.

Front 23

Ribosomal RNA

rRNA

Back 23

All known forms of life.

Over half of the ribosome.

Usually over 90% of a cell's RNA.

Large and small subunits.

During translation, mRNA is between them.

Front 24

Isoforms

Back 24

mRNAs from the same locus, but with different start site, or coding sequence, or untranslated region.

So same gene, different form.

Front 25

Cell-autonomous phenotype

Back 25

Phenotype only exhibited by genetically mutant cells.

If those cells cause other cells to exhibit the phenotype, it's non-cell-autonomous.

Front 26

Channelrhodopsin

Back 26

Proteins (a subfamily of rhodopsins).

Function as ion channels.

They're light-gated, so if you put them in a cell you can control the cell's activity with light.

Front 27

Retrobeads

Back 27

Deliver bioactive agents to a specific area.

Then retrograde transport tells you which cells received the agents.

Front 28

Floxed

Back 28

Flanked by LoxP sites.

(A DNA sequence.)

Once it's floxed, you can use Cre recombinase to knock it out, invert it, or translocate it.

Front 29

Monomeric receptors

Heteromeric receptors

Back 29

(Iffy on this.)

Monomeric is the usual: One gene, one receptor.

Heteromeric receptors are when receptors from different genes combine.

Front 30

Adenosine

Back 30

Neurotransmitter.

Contains adenine, which is its precursor.

Front 31

Dicer

Back 31

Enzyme. Humans, at least.

Cleaves pre-miRNA, maturing it to miRNA.

Cleaves dsRNA into siRNA.

Front 32

RNA Polymerase II

RNAP II

Pol II

Back 32

Eukaryotes.

Enzyme in cell nucleus.

Catalyzes transcription to mRNA.

There are also an RNAP I and III, but II is the most-studied.

Front 33

Ligand

Back 33

(In biochemistry.)

Molecule that forms a complex with a biomolecule.

Most often binds to a site on a protein and changes its conformation, producing a signal.

Can bind to DNA.

Front 34

Peptide

Back 34

Like a protein, chain of amino acids

But smaller, 2-50 amino acids.

Less well-defined in structure.

Neurons use some as signalling molecules:

neuropeptides.

Front 35

Metabolite

Back 35

Intermediate product of metabolic reaction.

Usually refers to small molecules.

Amino acids, nucleotides, alcohols, antioxidants, organic acids, vitamins, and polyols (like glycerol) are metabolites.

Front 36

Cytokine

Back 36

Small proteins. Loose category.

Cell signalling.

Produced by a lot of differenct cells.

Front 37

Camk2

Back 37

An enzyme.

Specifically a kinase.

Part of calcium-triggered signalling cascade.

Promotes dendritic spine & synapse formation.

So, enables LTP.

Can be used to control Cre expression?

Front 38

Heterochromatin / Euchromatin

Back 38

Some parts of your chromatin are each of these.

Hetero is more densely packed.