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Cell Biology > Lecture 2 Slides > Flashcards

Lecture 2 Slides Flashcards

0
Q

Bacterial cell innovations

A

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

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1
Q

Homologous traits

A

Shared traits inherited from a common ancestor

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2
Q

Archaea innovations

A

Actin cytoskeleton
N linked glycans
Core histone
Proteasome

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3
Q

Eukarya innovations

A 
Endo membranes (nucleus, ET, Golgi)
Mitochondria endosymbiotic (gamma-proteobacteria)
Cilia
Sphingolipids
Sterols (eg cholesterol)
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4
Q

Methods of evolution of eukaryotic genomes

A

Intragenic mutation
Gene duplication
DNA segment shuffling
Horizontal transfer

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5
Q

What caused eukaryotic genomic expansion

A

Noncoding DNA

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6
Q

Orthologs

A

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

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7
Q

Paralogs

A

Duplication and divergence of a gene. Exist in same species.

Have different, specialized functions

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8
Q

HSP70

A

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

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9
Q

Folding and interactions beyond protein primary structure are made by

A

Noncovalent bonds

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10
Q

Types of noncovalent bonds

A

Electrostatic interactions
Hydrogen bonds
Hydrophobic forces
Van der waals attractions

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11
Q

What do secondary structure folding patterns depend on

A

On hydorgen bonding bet. N-H and C=O groups in the backbone;are independent of side chains

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12
Q

Protein domain

A

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

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13
Q

Intrinsically unstructured polypeptides

A

Lack tertiary structure

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14
Q

Where do covalent disulfide bonds form

A

Between cysteine side chains within one polypeptide chain or between two polypeptides but cannot form in reducing environment of cytosol.

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15
Q

Major types of proteins

A

Enzymes

Structural elements

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16
Q

Polymerases, ligases, synthases

A

Build up biological polymers and biochemicals

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17
Q

Hydrolysis and lyases

A

Break down biological polymers and biochemicals

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18
Q

Phosphatases

A

Remove phosphate groups

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19
Q

Isomerases

A

Move chemical groups around on a molecule

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20
Q

Transferases

A

Move chemical groups from one molecule to a other

21
Q

Kinases

A

Add phosphate groups

22
Q

Oxido-reductases

A

Oxidize or reduce

23
Q

ATPase

A

Use or create ATP

24
Q

GTPases

A

Use or create GTP

25
Q

Transporters/channels

A

Move chemicals and small polymers across membranes

26
Q

Translocons and pores

A

Move large bio. Polymers across membranes

27
Q

Molecular chaperones

A

Aid in folding /stabilizing bio. Polymers

28
Q

Molecular motors

A

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

29
Q

Scaffold proteins

A

Serve as binding sites or assembly sites for other enzymes

30
Q

Cyto skeletal proteins

A

Internal skeleton, allow application of forces

31
Q

Extracellular matrix proteins

A

Cell shaping, tissue formation, allow application of force

32
Q

How are protein kinases used

A

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
Q

Histidine kinases

A

Signaling proteins found in prokaryotes, fungi and plants

34
Q

Protein Phosphatases

A

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

35
Q

Can a protein be a target for multiple kinases

A

Yes. Each targets a different amino acid residue

36
Q

Kinase domains

A

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

37
Q

Association rate

A

K-on [X][Y]

38
Q

Dissociation rate

A

K-off [XY]

39
Q

At equilibrium

A

K-off = k-on

40
Q

Equilibrium constant

A

K = k-on/k-off

41
Q

What does K (liters/moles) indicate

A

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
Q

ESP

A

Eukaryotic signature proteins

43
Q

LECA

A

Last eukaryotic common ancestor

44
Q

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

A

Gene duplication
Horizontal gene transfer
Gene genesis

45
Q

Eocyte theory

A

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

46
Q

Three lessons from detailed reconstruction of eukaryotic genome content

A
  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
Q

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

A
  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
Q

PhAT

A

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
Q

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

A

From phagocytosis ingestion of prokaryotes

50
Q

Acc to PhAT, why was nucleus formed

A

As a defense mechanism against phagocytosis induced HGT

Cell Biology (35 decks)

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