Chapter 8 Flashcards
How are cells differentiated? Give the two most common methods.
Differences in which genes are transcribed/translated
Combinations of transcriptional regulators
Epigenetic maintenance
What are the three ways epigenetics are passed on?
Positive feedback loops (remember signal even after replication)
Inheritance of condensed chromatin structure
DNA methylation by maintenance methyltransferse to match template (silencing, on cytosine)
What are the three purposes of controlling gene expression?
cell differentiation
adapting to the environment
efficiency
How do transcription regulators bind to DNA? How do they know where to bind? What are their partners?
Bind (H-bond, hydrophobic) to specific DNA sequences
Recognize AT/GC by availability of H bond donors/acceptors
Needed as well as transcription factors to get high expression
How do repressors work for prokaryotes (transcription)? Where do they bind?
Repressors bind on operator, can block sigma factor
What does the TRP operon control? What repressors/activators are involved?
Codes for enzymes needed for tryptophan biosynthesis
Off when trp (tryptophan) is high
Trp binds to and activates repressor (allosteric), which blocks sigma factor
What does the Lac operon control? When is it off and when is it on?
Codes for galactoside permease and B-galactosidase (needed to make lactose glucose)
On when lactose is high and glucose is low (has both activator and repressor)
Describe the activator/repressor in the Lac operon
Repressed when lactose is absent
Lactose converts repressor to inactive form (allosteric)
Active when cAMP (signaling molecule, made from ATP) is high
(cAMP produced when glucose is low)
Binds/Activates (allosteric) activator protein (CAP, activates RNA polymerase)
What is the area where activators bind called? How do they interact with the gene? How do they activate?
Enhancers are binding sites for activator proteins
Work from a distance by bends and loops in the DNA and recruiting mediators
Stabilize RNA polymerase complex and increase rate of transcription
Can prokaryotes, eukaryotes, or both control gene expression by histones?
Only eukaryotes, prokaryotic DNA is naked
Match histone acetal transferase (HAT) and histone deacetylase (HDAC) to gene activation and gene repression
Histone Acetal Transferase (HAT) → gene activation
Histone DeACetylase (HDAC) → gene repression
What are the three ways activators can function?
stabilize transcription preinitiation complex through proteins (ex:Mediator)
Chromatin remodeling complexes
HAT
Describe MyoD
MyoD forms a complex with other regulators and binds to DNA to turn on muscle specific sequences, can convert fibroblasts to muscle cells
What are the three ways repressors can function?
block or destabilize transcription preinitiation complex
Chromatin remodeling complexes
HDAC
Describe gene regulation by steriods
Steroid hormones/receptors can regulate DNA, need regulatory sequence + activator protein (one of the ways regulation can be grouped)
Describe grouped regulation in prokaryotes and eukaryotes
Prokaryotes have many proteins under the same promoter (operon)
Eukaryotes have one promoter per gene, but may have shared regulatory sequence (combinatorial control, control by committee)
Describe the involvement of UTRs in control of gene translation in both prokaryotes and eukaryotes
Both prokaryotic and eukaryotic mRNAs contain UnTranslated Regions
Pro → RBS
Eu → 5* cap, Poly A tail (controls mRNA stability)
Describe translational control in prokaryotes
Translation repressor protein hides RBS from small ribosomal subunit, binds to hair-pin loop formed by base-pairing
Describe translational control in eukaryotes
Repressor proteins hide start codon from small ribosomal subunit, binds to hair-pin loop
Describe negative regulation of eLF2 (and what it does)
Repressor proteins hide start codon, binds to hair-pin loop
Helps tRNA bind to ribosome
Give a short description of miRNA and how it is made
Noncoding, 20-22 bp, made by processing precursor miRNA with dicer
What does miRNA do and how does it work?
Complementary base pair (3/5 UTR) with mRNA to target for degradation
Form RISC (RNA induced silencing complex) before searching for matches
Involved in fate decisions
Describe siRNA and its role in the cell
small interfering RNA
Foreign double-stranded RNA cleaved by dicer to form siRNAs
Those siRNAs used to search for complementary RNA
What are the similarities and differences between miRNA and siRNA?
Same active complex, same dicer protein
miRNA is cell-produced single stranded RNA
siRNA is invader double-stranded RNA
Describe protein phosphorylation (include enzymes, reversibility, and effects)
Kinase adds P, phosphatase removes P (P comes from ATP)
Rapid and reversible, can activate or inactivate (depends on protein)
Affects binding to ligands, catalytic activity, cellular localization, ubiquitination and destruction
Describe the degradation of proteins (enzyme, identification, purpose)
Degradation by proteasome is controlled by ubiquitination
Breaks peptide bonds and uses ATP to unfold protein
Targets misfolded proteins and is used for quick regulation
Enzymes (E1, E2, E3) and ATP is used to attach ubiquitin proteins to target
Short peptides are recycled into amino acids
Describe the specificity and possible levels of interaction of miRNA
Milder effects if not a complete base pairing
Each one targets multiple mRNAs (only need to pair short sequences)
