Exam 2 + 3 Material Flashcards
Genetic Code
- Some codons do not encode any amino acid
- The initiation codon establishes the reading frame for ribosomes
- Every possible codon has some function in translation
- Methionine is only encoded by one codon
What is false about genetic code
- All amino acids are encoded by more than one codon
- WRONG because most are but all are not
Aminoacyl-tRNA Synthetase functions
- Attachment of amino acid to AMP
- Attachment of amino acid to tRNA
- Proofreading correct amino acid-tRNA linkage
Ubiquitylation
- Targets a protein for degradation
Random coils
Flexible regions that link secondary structures together
What steps of protein synthesis that requires ATP hydrolysis
Attachment of amino acid to tRNA
What steps of protein synthesis that require GTP hydrolysis
- Translocation of a ribosome from one codon to another
- Proofreading anticodon-codon pairing
- Binding a release factor to a stop codon
- Ef-Tu
- eIF2
Kd value
- Lower Kd = strong binding
- High Kd = weak binding
Function of phosphorylation as a post-translational modification
- Adds a negative charge to a protein
- Generates a binding site for proteins containing an SH2 domain
How can antibiotics selectively affect prokaryotic cells and why are there side effects on eukaryotic cells
- Affect prokaryotes due to differences in ribosomes
- There are side effects because organelles such as the mitochondria and chloroplasts have similar ribosomes to prokaryotes
Where does proofreading occur in protein synthesis
When aminoacyl-tRNA synthetase checks for codon-anticodon pairings to prevent mistakes during protein synthesis
Domains
- Independent folding regions within a protein that contains different functions
- The tertiary structure of proteins contains different domains
Post-transcriptional modifications
- Addition of 7-methylguanosine cap to the 5’ end of RNA
- mRNA splicing
- Formation of 3’ end poly-A tail
Advantage of the addition of a 7-methylguanosine cap to the 5’ end of RNA
This signals that this is an mRNA to be and the 5’ end is intact
Advantage of mRNA splicing
- Splicesome removes introns from the codon sequence
- This allows for a diversified production of proteins through alternative splicing
Advantage of 3’ end poly-A tail
- The original 3’ end of RNA is cleaved off
- About 200 A’s are added to the 3’ end via poly-A polymerase
- This signals that the RNA is now mature and can be exported to the cytoplasm for translation
Introns
- Non-coding sequences
- Interrupts actual coding sequence
- However: They allow many different variations of proteins through alternative splicing
Features of 5’ cap on pre-mRNA
- Has 5’ to 7’ methylguanosine
- It is 5’ to 5’
- Has a triphosphate linkage
Outer mitochondrial membrane
Contains porins that exchange material between the cytoplasm and mitochondria
Inner mitochondrial membrane
- Cardiolipin
- Cristae: site of ETC and provides SA
Mitochondrial Intermembrane space
- Cytochrome C
- Factors that program cell death
Mitochondrial matrix
- Site of oxidative metabolism
- Contains mDNA and ribosomes
Enzyme Catalysis
- Decrease the activation energy for a chemical reaction
- Increase the rate of forward and reverse reactions
What can enzymes NOT do
- Do not alter delta G
- No effect on net equilibrium
- No effect on reactant and product concentrations
- Cannot make a reaction occur spontaneously
Irreversible inhibitors
- Covalently bind to amino acid residues
- Cannot be overcome by increasing substrate concentration
- Inactive and remove active enzymes
- Lower Vmax
Reversible Inhibitors
- Competitive
- Non-competitive
Non-competitive inhibitor
- Reduces Vmax
- No effect on Km
- Bind away from the active site
Competitive inhibitor
- Increase Km
- No effect on Vmax
- Compete with the substrate to bind to the active site
DNA binding motifs WITH a dimerization region
- Leucine zipper
- Helix-loop-helix
- Second class of zinc fingers
DNA binding motifs WITHOUT a dimerization region
- Helix-turn-helix
- Homeodomain
- First class of zinc fingers
Homeodomain characteristics
- Contains 3 alpha helices
- Similar to helix-turn-helix
- In contact with major and minor groove of DNA
Advantages of cell surface receptors using second messengers
- Signal does not have to travel through the membrane
- Difficult signaling pathways can occur from the same signal
Examples of second messengers
- cAMP
- Ca2+
What does a homeobox domain contain
Helix-turn-helix region
How can complexes be organized to increase the speed and efficiency of signaling
- Complexes can be organized into scaffolds
- Scaffold proteins bind to a cell surface receptor
- Intracellular signaling molecules bind to the scaffold protein
- When a signaling molecule is bound to a cell surface receptor, the signaling complex is activated
- The scaffold sends the signal downstream and further amplifies it
- Receptor activation can be used
- Once a receptor is turned on, intracellular signaling proteins can assemble near the receptor which can result in downstream signaling occur
Advantage of second messengers
Amplifies the signal
Types of RNA
- tRNA: responsible for bringing amino acids to ribosomes for translation
- snRNA: makes up the splicesome and is responsible for splicing RNA
Promoters
- Found upstream of DNA
- Bind to RNA polymerase and initiation complexes
- Start transcription through binding of TF
Enhancers
- Found anywhere on DNA
- Do not bind to RNA polymerase or initiation complexes
- Enhance transcription through binding of TF
Allosteric regulation
- Allosteric regulators bind away from the catalytic site of an enzyme to a regulatory site
- This causes a conformational change at the catalytic site which can act as an activator or inhibitor for substrates binding to proteins
- Can be competitive or non-competitive
How can enzymes stabilize the transition state of a chemical reaction
When 2 substrates bind to the enzyme, it can orient them in a way that encourages a favorable reaction to occur between them
Primary structure
Chain of amino acids
Secondary structure
- Folding and twisting of the peptide backbone
- Held together by weak hydrogen bonding between carbonyl and amine groups
- Contain alpha helices and beta sheets
- Alpha helices: held together by weak hydrogen bonding between carbonyl and amine groups every 4 amino acids
- Beta sheets: held together by weak hydrogen bonding between amine and carbonyl groups on adjacent polypeptide chains (run parallel and antiparallel)
Tertiary structure
- 3D arrangement of secondary structure
- Results from noncovalent interactions between R groups or R groups and their environments
Quaternary Structure
- Arrangement of multiple tertiary structures
- Held together by weak bonds and disulfide bonds
