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Promoter
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regulatory region of DNA, where RNA polymerase other proteins involved in transcripton initiation bind
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Enhancer sequences
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regulatory DNA sequences that bind transcriptions factors and enhance transcription of the gene they are associated with
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General transcription factors
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set of proteins, that bind to the promotor of a gene and are involved in initiating transcription
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Transcriptional activator proteins
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proteins that bind to enhancer sequences to begin transcription
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Enhancer sequences
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sequences in the DNA that are bound by transcription activator proteins that activate transcription
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Nonpolar covalent bond: Electron pairs are shared equally
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Polar covalent bond: Electron pairs shared unequally (electronegativity)
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Hydrogen bond: Weak electrical attraction between a covalently bonded H atom and an electronegative atom
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Ionic bond: Electric attraction between opposite charges due to differences in electronegativity
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Electronegativity is the tendency between atoms and their ability to attract electrons
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- Hydrophobic interactions occur with nonpolar molecules in the presences of polar molecules
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Cohesion is the attraction of molecules for other molecules of the same kind
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Ex: a molecule of water sharing a hydrogen bond with other water molecules
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Hydrophilic Amino Acids
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Basic
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Acidic
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Polar
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Lysine
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Aspartic Acid
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Asparagine
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Arginine
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Glutamic Acid
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Glutamine
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Histidine
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Serine + Threonine
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Hydrophobic Amino Acids
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Alanine Valine Leucine Isoleucine Methionine Phenylalanine Tryptophan
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lots of carbon-hydrogens + not many functional groups
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Special Amino Acids
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Glycine Proline (group is part of a ring) Cysteine
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Primary Structure
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Sequence of amino acids in a protein
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Secondary Structure
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Hydrogen bonds causes folding of the polypeptide chain
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Tertiary Structure
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R groups determines the function and formation
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Quartenary Structure
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Made up of 2 or more subunits that determine the activity of the protein
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Removal of introns (non-coding) and leaving exons (protein-coding intact) - done by Spliceosome
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Spliceosome – binds to both the 5’ and 3’ ends (splice sites)
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Introns loop on itself then gets broken down into nucleotides
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Exons join each other and have no interruptions from introns
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Primary transcripts have introns and exons and depending on what's cut off and what exons are joined, protein is made
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Phosphodiester Bond
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Chemical bond (by condensation) between phosphate and hydroxyl groups from sugar groups
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Example
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The backbone of DNA or RNA molecules
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Pyrophosphate
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Group of phosphates released by hydrolysis which creates energy to join bases to the RNA transcript
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Example
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Adding a uracil to the 3' end of a transcript
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Central Dogma : DNA codes for RNA and RNA codes for protein, the flow of information from DNA to Protein
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Transcription: mRNA carries instructions for making polypepetides from DNA, DNA serves a template for polypoptide synthesis (transcribed from DNA to mRNA)
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New RNA strand grows in 5' to 3' direction - DNA strand is oriented in the 3'-5'
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3 stages: Initiation, Elongation, Termination
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RNA polymerase and associated proteins bind to the DNA duplex at promoter sequences
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- When RNA polymerase binds to the promoter region – doesn’t start right away (starts downstream (abt 25 nucleotides from the box)) before starting
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How the promotor is recognized: Promoter region needs to be identified (TATA box- green box) and bound by GTF;
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TAP (activators) bind enhancers to recruit mediator proteins which then recruits RNA polymerase to the promoter region (can cause DNA loop - mediator complex)
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Polymerization Reaction - 3' -OH group attacks the 2 phosphate which get released and turn into pyrophosphates (irreversible)
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Once RNA polymerase bumps into the termination sequences, it falls off and the transcript is released
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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
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RNA tha combines with riobsome to direct protein synthesis : mRNA
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