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29 Cards in this Set
- Front
- Back
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Transcription Factor
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A protein that binds DNA at specific sites where it can regulate transcription
Essential |
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Constitutive Expression
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Always on
Gene is always being transcribed and protein is always being made Examples: |
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Induced Expression
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When some genes are induced or repressed
Both switched on and off Sunburn *Trnascript abundance increasing when temperature increases |
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Transcript Abundance
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Measures transcription indirectly by measuring how much mRNA is present
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Northern Blot Analysis
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Measures transcript abundance
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Western Blot Analysis
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Measures protein abundance
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Peptides
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Two amino acids with the third linked by a covalent bond
A peptide bond links the two amino acids to the third amino acid by a dehydration reaction |
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AA Characteristics
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Amino Group
Carboxyl Group R Group |
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Amino Group
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Conists of a nitrogen bonded to two hydrogen atoms on one side
Bonded to a carbon chain on the other side Acts as an organic base |
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Carboxyl Group
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The functional group
Formed by the combination of carbonyl and hydroxyl groups |
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R Group
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The side chain of an AA
Distinguishes AA There are 20 different R groups Many AA are polar due to the R group |
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Peptide Bond
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Formed by a dehydration reactions between the amino group of one amino acid the the carboxyl group of the second amino acid
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Difference between peptides and proteins
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Peptides are synthesis by ribosomes and are unfolded
Proteins are functional when they are folded correctly |
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Van der Waals Forces
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Weak interactions between molecules due to momentary changes in electron density
Exist in all compounds - the only attractive forces in nonpolar compounds Stronger with larger SA |
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Dipole - Dipole
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Attractive forces between permanent dipoles of two polar molecules
Dipoles in adjacent molecules align to put the partial positive and partial negative charges in close proximity |
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Hydrogen Bonding
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Occurs when a hydrogen atom covalently bonded to a very EN atom is attracted to a lone electron pair on another electronegative atom
Strongest & will also include D-D |
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Primary Protein Structure
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The linear sequence of AA that constitutes the peptide
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Secondary Protein Structure
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Hydrogen bonding between atoms in the backbone
Backbone consists of the carboxyl group and the amino group Two major forms: Alpha helix & beta sheet |
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Alpha Helix
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Every fifth amino acid interacts
Hydrogen bond is linear Spontaneous Stabilized by the hydrogen bonding between amide nitrogen and the carbonyl carbon of the peptide bonds Orientation of H bonding produces a helical coiling of the peptide backbone such that the R group lie on the exterior of the helix & perpendicular to its axis |
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Beta Sheet
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Composed of 2 or more different regions of at least 5 - 10 AA
Stabliized by hydrogen bonding between amides nitrogen and carbonyls carbon H bonding are present in adjacent stretches of the polypeptide backbone |
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Tertiary Protein Structure
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Essential to protein function
Folding of the peptide Bonding arrangement between R groups R groups interact Hydrogen and ionic bonding VD waals/hydrophobic bonding No covalent bonds for they would make the protein too rigid - the protein must by flexible in order to be functional! |
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Afinsen's Dogma
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Isolated E coli cells & purified the protein
The protein can be studied in vitro (outside of the cell) Got the protein to unfold using a denaturant such as urea Shields hydrophobic bonds so hydrophobic bases can interact more freely Urea breaks tertiary structure so the protein unfolds ADD BUFFER The protein will then refold and gain 90% of its original activity Protein folding is spontenous - the instructions for folding is the primary structure itself Protein folds fast - amino end starts to form before the protein is out of the ribosome |
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Levinthal Paradox
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Assume each AA backbone can be in three conformational states
BB consists of 2 AA and a peptide bond Many conformations If the protein starts to fold by sampling each formation it would take WAY too long Therefore, the protein is using info to dictate how it folds...It folds in pre-arranged paths |
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What Drives Protein Folding?
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Energy - When the protein is unfolded the energy is much higher
Alpha helix structure formed first Hydrophobic effect takes place AA want to interact with each other, not water Hydrophobic AA burry themselves deep in the protein This is because it will be in a higher energy state if the hydrophobic surfaces are exposed |
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Factors Required for Proper Protein Folding
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AA sequence
Solvent & concentration Temperature pH |
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Consequences of Protein Denaturation
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Hydrophobic residues are exposed to the cytosol when a protein is denatured
Protein will mis-fold |
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Chaperones
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Interacts and stabilizes non-native forms of protein during times of crowding
Not part of the final assembly of proteins Assist in folding and assembly Change conformation Transport Break down aggregations that occur when proteins are denatured ATP dependent |
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Quarternary Protein Structure
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Two or mole native polypeptides come together to make a functional protein
Example: Hemoglobin |
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Prosthetic Groups
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Many proteins need non protein components in order to function
In hemoglobin, oxygen is bound to molecules called heme |
