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Molecules: electronegativity, bonds, polarity
Transcription
Translation
Proteins + Amino Acids
Transcription - Key terms
Promoter |
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 |
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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
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
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 |
Basic |
Acidic |
Polar |
Lysine |
Aspartic Acid |
Asparagine |
Arginine |
Glutamic Acid |
Glutamine |
Histidine |
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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 |
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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 |
Example |
The backbone of DNA or RNA molecules |
Pyrophosphate |
Group of phosphates released by hydrolysis which creates energy to join bases to the RNA transcript |
Example |
Adding a uracil to the 3' end of a transcript |
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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 |
Initiation
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) |
Elongation
Polymerization Reaction - 3' -OH group attacks the 2 phosphate which get released and turn into pyrophosphates (irreversible) |
Termination
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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