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Homologous traits

Shared traits inherited from a common ancestor

1

Bacterial cell innovations

Ribosomes, translation
Phospholipids
Nucleic acids, DNA replication, transcription
Core metabolism (eg, glycolysis)

2

Archaea innovations

Actin cytoskeleton
N linked glycans
Core histone
Proteasome

3

Eukarya innovations

Endo membranes (nucleus, ET, Golgi)
Mitochondria endosymbiotic (gamma-proteobacteria)
Cilia
Sphingolipids
Sterols (eg cholesterol)

4

Methods of evolution of eukaryotic genomes

Intragenic mutation
Gene duplication
DNA segment shuffling
Horizontal transfer

5

What caused eukaryotic genomic expansion

Noncoding DNA

6

Orthologs

One gene breaks into two homologous ones, one each for two new species . Inherited vertically, not from duplication. Presumed to have same function,

7

Paralogs

Duplication and divergence of a gene. Exist in same species.
Have different, specialized functions

8

HSP70

Genes encoding Hsp70s in organisms from all three major branches were derived from a common ancestral gene

9

Folding and interactions beyond protein primary structure are made by

Noncovalent bonds

10

Types of noncovalent bonds

Electrostatic interactions
Hydrogen bonds
Hydrophobic forces
Van der waals attractions

11

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

12

Protein domain

A sequence that folds into a thermodynamically stable structure under physiological conditions and has a particular function

13

Intrinsically unstructured polypeptides

Lack tertiary structure

14

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.

15

Major types of proteins

Enzymes
Structural elements

16

Polymerases, ligases, synthases

Build up biological polymers and biochemicals

17

Hydrolysis and lyases

Break down biological polymers and biochemicals

18

Phosphatases

Remove phosphate groups

19

Isomerases

Move chemical groups around on a molecule

20

Transferases

Move chemical groups from one molecule to a other

21

Kinases

Add phosphate groups

22

Oxido-reductases

Oxidize or reduce

23

ATPase

Use or create ATP

24

GTPases

Use or create GTP

25

Transporters/channels

Move chemicals and small polymers across membranes

26

Translocons and pores

Move large bio. Polymers across membranes

27

Molecular chaperones

Aid in folding /stabilizing bio. Polymers

28

Molecular motors

Powered by hydrolysis of ATP to convert chemical energy into mechanical work

29

Scaffold proteins

Serve as binding sites or assembly sites for other enzymes

30

Cyto skeletal proteins

Internal skeleton, allow application of forces

31

Extracellular matrix proteins

Cell shaping, tissue formation, allow application of force

32

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

33

Histidine kinases

Signaling proteins found in prokaryotes, fungi and plants

34

Protein Phosphatases

Perform reverse of kinase. Typically less specific than protein kinases with regard to substrates, but are just as important for signaling

35

Can a protein be a target for multiple kinases

Yes. Each targets a different amino acid residue

36

Kinase domains

Conserved amino acid sequences in the active site of enzyme that are recognized by computer algorithms

37

Association rate

K-on [X][Y]

38

Dissociation rate

K-off [XY]

39

At equilibrium

K-off = k-on

40

Equilibrium constant

K = k-on/k-off

41

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.

42

ESP

Eukaryotic signature proteins

43

LECA

Last eukaryotic common ancestor

44

What three evolutionary forces played a role in the emergence of eukaryotes

Gene duplication
Horizontal gene transfer
Gene genesis

45

Eocyte theory

Suggests that eukaryotes have emerged from within the archaeal domain of life, TACK superphylum

46

Three lessons from detailed reconstruction of eukaryotic genome content

1. Ancestral euk gene repertoire seems to have doubled in size before the onset of major euk radiations
2. Gene duplication seems to have played a primordial role I. The emergence of euk features
3. 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

47

Emergence of ESPs is the result of what molecular innovation events? 3

1. Reuse of prokaryotic proteins and domains for the same biochemical function, but in a different context
2. Emergence of new biochem. Functions and protein super families, but within existing protein folds
3. Domains with bona ride new folds, invented during thr early stages of eukaryotic evolution

48

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

49

Acc to PhAT, where do bacterial genes in euks come from

From phagocytosis ingestion of prokaryotes

50

Acc to PhAT, why was nucleus formed

As a defense mechanism against phagocytosis induced HGT