Lecture 9

Some notes about entropy

Molecular Biology continued

How does genetics help us to find interesting objects and find relationships between them?

There will be NO LECTURE on Tue, March 3

TSHG

The Gibbs free energy:

STHG

0 BAG

The process A→B will go spontaneously if

WkS ln

W = multiplicity of microscopic degrees of freedom (# of microstates)

B

A

B

AT

CpdT

T

dQS

Classical definition(from analysis of steam machines)

Statistical definition

0T

dQ

A

B

The ENTROPY

k – Boltzmann constant

V

P

T

dQdS

dQ – heat imparted to the system by the surroundings

t

i

ii ppk

S

1

ln

1 2 3 4 5 1 2 3 4 5 1 2 3 4 5

S = maxS = min

n

lattice position

Show this!

WkS ln

p – probabilities of states

What if microstates are occupied unequally? How to write the entropy?

pdVdTCdQ V

Classical property of entropy:

dVV

R

T

dTC

T

dQdS V

dVV

RTdTCdQ V

RTpV

for a mole of ideal gas:

integrating

VRTCS V lnln

1

2

1

221 lnln

V

VR

T

TCS

V

or

( = integration constant)

2

1

1

2 lnlnC

CR

V

VRS

At constant T and n

V

nC

so, entropy logarithmically depends on concentration

1

2

1

2 lnlnV

VR

T

TCS V

If perfect Watson-Crick pairing was strictly enforced, then every organism should have no less than 61 different tRNAs. Many creatures get away with a considerably smaller variety because of the ‘promiscuity’ or ‘wobble’ at the third position in many codons.

Phe codons UUU and UUC (5’-3’) can both be recognized by the tRNA that has GAA (5’-3’) anticodon

T. thermofilus 70S ribosome (M. Yusupov et al., 2001)

Low-resolution (EM) model of E. coli 70S ribosome

The assembly of a functional ribosome starts with initiation factors elF6 and elF3

Methionyl-tRNAiMet recognizes the AUG start codon before mRNA is loaded

There are two types of Met tRNA: Initiation tRNA can bind only to the P siteMet tRNA used in synthesis can bind to A site and than translocate

E site P site A site

Peptyidyl transferase reaction

Translocation

Binding of incoming amino acyl tRNA

Termination is assisted by RFs(release factors)

UAA – stop codon

Circular structure of mRNA increases the translation efficiency

The replication fork: leading strand and lagging strand

LargeT = helicase

Pol = priming DNA polymerase

Pol = DNA polymerase

PCNA - displaces Pol

Why GENETICS? (Chapter 5)

X X

In Haploid organisms complementig genes can be expressed on extra-chromosomal elements (plasmids), i.e. “in trans”

Diploid organisms

Generation of temperature-sensitive mutations

Tes

ting

mut

ants

for

com

plem

enta

tion

and

sort

ing

them

into

com

plem

enta

tion

grou

ps