Lecture 2 Slides Flashcards
Bacterial cell innovations
Ribosomes, translation
Phospholipids
Nucleic acids, DNA replication, transcription
Core metabolism (eg, glycolysis)
Homologous traits
Shared traits inherited from a common ancestor
Archaea innovations
Actin cytoskeleton
N linked glycans
Core histone
Proteasome
Eukarya innovations
Endo membranes (nucleus, ET, Golgi) Mitochondria endosymbiotic (gamma-proteobacteria) Cilia Sphingolipids Sterols (eg cholesterol)
Methods of evolution of eukaryotic genomes
Intragenic mutation
Gene duplication
DNA segment shuffling
Horizontal transfer
What caused eukaryotic genomic expansion
Noncoding DNA
Orthologs
One gene breaks into two homologous ones, one each for two new species . Inherited vertically, not from duplication. Presumed to have same function,
Paralogs
Duplication and divergence of a gene. Exist in same species.
Have different, specialized functions
HSP70
Genes encoding Hsp70s in organisms from all three major branches were derived from a common ancestral gene
Folding and interactions beyond protein primary structure are made by
Noncovalent bonds
Types of noncovalent bonds
Electrostatic interactions
Hydrogen bonds
Hydrophobic forces
Van der waals attractions
What do secondary structure folding patterns depend on
On hydorgen bonding bet. N-H and C=O groups in the backbone;are independent of side chains
Protein domain
A sequence that folds into a thermodynamically stable structure under physiological conditions and has a particular function
Intrinsically unstructured polypeptides
Lack tertiary structure
Where do covalent disulfide bonds form
Between cysteine side chains within one polypeptide chain or between two polypeptides but cannot form in reducing environment of cytosol.
Major types of proteins
Enzymes
Structural elements
Polymerases, ligases, synthases
Build up biological polymers and biochemicals
Hydrolysis and lyases
Break down biological polymers and biochemicals
Phosphatases
Remove phosphate groups
Isomerases
Move chemical groups around on a molecule
Transferases
Move chemical groups from one molecule to a other
Kinases
Add phosphate groups
Oxido-reductases
Oxidize or reduce
ATPase
Use or create ATP
GTPases
Use or create GTP
Transporters/channels
Move chemicals and small polymers across membranes
Translocons and pores
Move large bio. Polymers across membranes
Molecular chaperones
Aid in folding /stabilizing bio. Polymers
Molecular motors
Powered by hydrolysis of ATP to convert chemical energy into mechanical work
Scaffold proteins
Serve as binding sites or assembly sites for other enzymes
Cyto skeletal proteins
Internal skeleton, allow application of forces
Extracellular matrix proteins
Cell shaping, tissue formation, allow application of force
How are protein kinases used
For controlling activity and stability of target proteins, for regulating protein-ptotein interactions, importsnt in signaling, each protein kinase phosphorylates the hydroxyl group of a specific serine, threonine or tyrosine
Histidine kinases
Signaling proteins found in prokaryotes, fungi and plants
Protein Phosphatases
Perform reverse of kinase. Typically less specific than protein kinases with regard to substrates, but are just as important for signaling
Can a protein be a target for multiple kinases
Yes. Each targets a different amino acid residue
Kinase domains
Conserved amino acid sequences in the active site of enzyme that are recognized by computer algorithms
Association rate
K-on [X][Y]
Dissociation rate
K-off [XY]
At equilibrium
K-off = k-on
Equilibrium constant
K = k-on/k-off
What does K (liters/moles) indicate
The strength of the binding between X and Y. The larger the number, the stronger the bond. The dissociation constant k-d is the reciprocal of k-a. The smaller k-d, the stronger the binding.
ESP
Eukaryotic signature proteins
LECA
Last eukaryotic common ancestor
What three evolutionary forces played a role in the emergence of eukaryotes
Gene duplication
Horizontal gene transfer
Gene genesis
Eocyte theory
Suggests that eukaryotes have emerged from within the archaeal domain of life, TACK superphylum
Three lessons from detailed reconstruction of eukaryotic genome content
- Ancestral euk gene repertoire seems to have doubled in size before the onset of major euk radiations
- Gene duplication seems to have played a primordial role I. The emergence of euk features
- Significant part of paralogous gene content of ancestral euk gene content seems to be a result of lateral gene transfer, which, at least in part, was acquired via the endosymbiosis that gave rise to mito
Emergence of ESPs is the result of what molecular innovation events? 3
- Reuse of prokaryotic proteins and domains for the same biochemical function, but in a different context
- Emergence of new biochem. Functions and protein super families, but within existing protein folds
- Domains with bona ride new folds, invented during thr early stages of eukaryotic evolution
PhAT
First explicit model that implements archaeal phagocytosis as the basis of the process of eukaryotes edits, as it provides am explanation for the origin of the nucleus and mito, as well as for mosaic bacterial gene content In Eukaryotes
Acc to PhAT, where do bacterial genes in euks come from
From phagocytosis ingestion of prokaryotes
Acc to PhAT, why was nucleus formed
As a defense mechanism against phagocytosis induced HGT
