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Bio 1010U - Module 1 Cheat Sheet by

Molecules: electronegativity, bonds, polarity Transcription Translation Proteins + Amino Acids

Transc­ription - Key terms

regulatory region of DNA, where RNA polymerase other proteins involved in transc­ripton initiation bind
Enhancer sequences
regulatory DNA sequences that bind transc­rip­tions factors and enhance transc­ription of the gene they are associated with
General transc­ription factors
set of proteins, that bind to the promotor of a gene and are involved in initiating transc­ription
Transc­rip­tional activator proteins
proteins that bind to enhancer sequences to begin transc­ription
Enhancer sequences
sequences in the DNA that are bound by transc­ription activator proteins that activate transc­ription

Molecular intera­ctions

Nonpolar covalent bond: Electron pairs are shared equally
Polar covalent bond: Electron pairs shared unequally (elect­ron­ega­tivity)
Hydrogen bond: Weak electrical attraction between a covalently bonded H atom and an electr­one­gative atom
Ionic bond: Electric attraction between opposite charges due to differ­ences in electr­one­gat­ivity


Electr­one­gat­ivity is the tendency between atoms and their ability to attract electrons
- Hydrop­hobic intera­ctions occur with nonpolar molecules in the presences of polar molecules


Cohesion is the attraction of molecules for other molecules of the same kind
Ex: a molecule of water sharing a hydrogen bond with other water molecules

Amino Acid categories

Hydrop­hilic Amino Acids
Aspartic Acid
Glutamic Acid
Serine + Threonine
Hydrop­hobic Amino Acids
Alanine Valine Leucine Isoleucine Methionine Phenyl­alanine Tryptophan
lots of carbon­-hy­drogens + not many functional groups
Special Amino Acids
Glycine Proline (group is part of a ring) Cysteine

Protein structures

Primary Structure
Sequence of amino acids in a protein
Secondary Structure
Hydrogen bonds causes folding of the polype­ptide chain
Tertiary Structure
R groups determines the function and formation
Quartenary Structure
Made up of 2 or more subunits that determine the activity of the protein

RNA Splicing - Introns and Exons

Removal of introns (non-c­oding) and leaving exons (prote­in-­coding intact) - done by Splice­osome
Splice­osome – binds to both the 5’ and 3’ ends (splice sites)
Introns loop on itself then gets broken down into nucleo­tides
Exons join each other and have no interr­uptions from introns
Primary transc­ripts have introns and exons and depending on what's cut off and what exons are joined, protein is made

Key Terms

Phosph­odi­ester Bond
Chemical bond (by conden­sation) between phosphate and hydroxyl groups from sugar groups
The backbone of DNA or RNA molecules
Group of phosphates released by hydrolysis which creates energy to join bases to the RNA transcript
Adding a uracil to the 3' end of a transcript

Transc­ription (brief overview)

Central Dogma : DNA codes for RNA and RNA codes for protein, the flow of inform­ation from DNA to Protein
Transc­rip­tion: mRNA carries instru­ctions for making polype­petides from DNA, DNA serves a template for polypo­ptide synthesis (trans­cribed from DNA to mRNA)
New RNA strand grows in 5' to 3' direction - DNA strand is oriented in the 3'-5'
3 stages: Initia­tion, Elonga­tion, Termin­ation


RNA polymerase and associated proteins bind to the DNA duplex at promoter sequences
- When RNA polymerase binds to the promoter region – doesn’t start right away (starts downstream (abt 25 nucleo­tides from the box)) before starting
How the promotor is recogn­ized: Promoter region needs to be identified (TATA box- green box) and bound by GTF;
TAP (activ­ators) bind enhancers to recruit mediator proteins which then recruits RNA polymerase to the promoter region (can cause DNA loop - mediator complex)


Polyme­riz­ation Reaction - 3' -OH group attacks the 2 phosphate which get released and turn into pyroph­osp­hates (irrev­ers­ible)


Once RNA polymerase bumps into the termin­ation sequences, it falls off and the transcript is released
RNA transcript is called the primary transcript (not processed yet) – has to go thru a series of processing steps before it can be called mRNA
RNA tha combines with riobsome to direct protein synthesis : mRNA


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