ES243

BIOLOGY FOR

ENGINEERS
 Lecture 1

04/08/23
Equation
#Drake's

LIFE IS RARE!

Universal Features
#
of Biology
(biotic)
I.
only living
beings can rise
give
to
beings
living
living systems evolve Abiogenesis only happened once,
2. *

however it
cannot be
entirely
ruled out.

#
Properties of the
living

living
respiration
adaption

response to stimulus

homeostasis

reproduction
7 ↑

evolution

controlled &
organized
growth &
decay
complex!
 # Growth

sun > food > respiration > . .

CEM energy) (chemical energy ( (break down

energy (

Whydoes humangrowa humanandeatenedin

Q. a into the
a

~answer is the DNA!

-> instructions
for everything:
~Form
Material reproduction, Inheritance ~ Growth
Genetic
~ Life Span

#
Living Systems
the laws
of physics and
chemistryis
followed by living systems

#Glucose

non-living systems,
in
CH,zOs+O2 < heat +
fire
butin systems,
living
is
this
effortless.

You don't
feel a
fire burning inside
you
do
you? no

Tutorial 1

07/08/23
D. Whatare the
properties of living?
Response
1) to stimulus-toachieve homeostasis achieve a state
(state
of normalcy is specific) of normalcy
age
↓ why?
to then to
exist.
grow, reproduce & cease
C. Do
living of thermodynamics?
beings obey laws
the

change form butnot be created/destroyed.

=>>
Yes, energy
can

chemical mechanical/electrical ATP)

->
(glucose ->

[RMP=resting membrane potential)

SV= TOMV Nat
a
Nat
ATP spentto pump
is
againstconcentration gradient

1
[Nat] 4

-
Out (ATP-> ADD)
In Nat
when
you touch, pover
[K+]b and
*

open

gushes
in
giving us sensation
the
of touch

CELL MEMBRANE

ea -en

quee nee

Maintenance
*
of form requires a
arrangement of
specific the chemical
that
we
ingest food-reduction entropy-energy
↑

as e
is
spentto
maintain order

analogy
-
its easier to constructa sentence
from words rather than letters

plants are more endothermic -

use more
energy
as
they make
energy
from the basic elements.
very
outmore
respiration, excretion, decomposition.
-

exothermic
we are -

give
-
# What are the
differences between
living &
non-living
systems.
to stimuli

-> visible features shorttermresponse

infinite
-
? -growth
span - invisible but measurable form
features reproduction
-
life
homeostasis
-finitelife span
-> invisible features: 'logic'-classification differentspecies
into (NA)

&Do living systems obey

the laws of thermodynamics?
living system
are
'open systems -

exchange of mass/energy
exchange of energy inwards
is
(endo) for plants

exchange of energy is
outwards (exo) for animals

endothermic & exothermic

is
synthesis decomposition is

↳ small molecules to
fewer larger I opposite of synthesis
many
ones

accumulate biomass and biochemical

as we
grow, we
energy
as a resultof that;this
energy is
given out when we

decay; we use
energy to reduce
entropy to maintain order.

energy changes form.

Lecture
2
dead?
⑰)
Similarities between
living and

08/08/23
made of the same element
up
-

->
the laws
of chemistry
-

obey physical laws, the

especially
laws
of thermo-

dynamics
#Open Systems

Living systemsmatter open systems.

are

Exchange of (in the form of food) and

energy
the form
(in of radiation).
 # Plants
plants

:" -

iningthe
small molecules molecules
large
non-livingsystems I can,
et 3
-

en

Carb
#
chydrates
simple carbs ->
polymers; glycogen
breaks down to

glucose & provides energy

what happened
CO2 - > Carbs ...
... Carbs-> CO2
H20 here? H20

Search
hi
102 ->
H20
glucose se

it
is.

breakdown
X · use
glucose as

only enough - ~ .) absorb

glucose and then use it.

X . breakdown
glucose to CO2 & H20 and extractenergy
their chemical bonds.
from

breaking down complex carbs to

simpler ones

(glycogen, cellulose, starch) (glucose)

and
energy
extracted
is
from these via
respiration.

about
Facts
Carbohydrates:
*

dissolve water evolved seas)

- can in
(life in the

Bilayer Lipids
* to store
glucose in water

plasma membrane of cells

xM ⑳ 10x M
=
②
glucose ② . glucose
O =energy

dehydrophillside bidin
of
cholesterol
 # Proteins
-
acids
amino around 20
different
types
-

proteinsare
polymers of amino
these acids

9. How do
differentorganisms process protein?
=>

o eat cat-same
dog
lion cat A-B-c-D
say,
a a a
protein

options
-

doesn't
work- x a) implant
direct
just perfect ~b) -

A-B-C-D-> A -

B, A, c, c-D, etc.
too much-X() A-B-c-D-> C, H,0,N

glucose
-

polymeric Ewrie-Miller
lipids - assembled
amino acids -

proteins experiments
(Mouseshake)
the
enzymes
are

magic ingredient!
&

Lecture 3
STORY
THE OF CELL
THE
11
August

bymagic
as CO2 soluble
glucose
->

NO -> cenergy)
02
-isea
amino acids

variety)
->
hydrophilic/hydrophobic
S

⑧
GG G G lpics
00:

(duality)
G GG G G <
GGG
GG

G G G
Le 0
O
bilayer lipid boundary bo / H20
hydrophillic I
Q O

hydrophilic Of lipids
tunnel to let
&

-
>O-
0
in
glucose
0
0 pocketa
this complex tunnel is
db
E Esilgein
-
made combination
from a

acids &
of amino proteins
 lup ophullec diffuse
Glucose
substances
· &
⑧

S can
I

&
I↓ D
↓
through vilipid layer;
↑
the
- e ·

glucose
Glucose

diffused veal
to maintain conce gradient can
G -

↓
Grgy/Atp
6 -

P
S ↳
I
o

.... se
excess
glucose-> lipids ·
a

-> -[G]
I
-

[Glucose] 4
-
camcor - concentration ...
-

-
-
higer
I

↓
I
2

low protein (glucose smuggler)

glucose is
actively transported from cone to
high conc.
by some

by spending energy (1-2 ATP)

some

a
varietyof such tunnel proteins are presentto
1
glucose + O
2
-> 32 ATP

I
glucose %2
I 2 ATD
smuggle
S
different
t
molecules:
O ->

Accumulation
of and molecules allows structure
to
glucose other the

grow.
As the
slow-there
size
is
grows,
size
the
limit
diffusion
to which it
of glucose becomes
impractically
grow.
a can

thumans are not

one all
only!
-

Cell divides: the

glucose, amino acids, etc.
split but code
of
=>>
are

conduct is carried over

unaffected

cellular star
identityintact
-

-selectively
instructions (DNA)->
set

&
-
to make, structure
function proteins

outlow
plants-endothermic-take in high entropy, give entropy
animals-exothermic-take in low
entropy, give
out
high entropy
 Lecture 04
18/08/23

0.) from from then how

they
All alls
single zygote, do
-

-a
have different functions
⑳

L -
stemness tissue specific
Human Human
DNA - DNA

how
DNA
sequence doesn't
change. But functions,
it does.

DNA
is a
exact
chemical capable of duplicating itself the
in

same
molarity
cells
DNA the
idently
. . . .

gives an -

protein
enzymes
-
Structural
-

Functional

All while also

the
giving rise to
diversity.
of data.
Ig DNA
can store 215
Petabytes
Unless the DNA is
duplicated I
cell cannot divide.
Once the DNA
duplicated, all divide.
must
-

is

duplicatingcell
DNA in division
in
ATD
=>

With a small
change, ATP becomes part of DNA

④ 0

4
A
-

3 2

remove
or > OH
"yga
-

doxy CdATP
 Durinus (R)
Pyramidines (Y)

3P
3 ATT
basic

5 -
7

↳
nitrogenous
GEC
↳'H A t, G,c
A&T:weak
affinity
e 5' phosphote G &
strong affinity
C:

morter
sugar 3'
hydroxyl

PPP
-
A

3
S -

↓ facilitates polymerization
phosphodiestor bond enzyme
PP
P
** *
.

-
S- N
I I I
OH
di YH H ...

↳ T,C
t
DNA,
buffer >(3) A, G, T, a

monomer

-
template * 5
-
AATTGG CCAT 11 Il
GC
III III
-
3
T-T --A-G-G-T 5
GG
PA - -

-o
- /
↑I'll
M
- ut
m I fixit!

...
fill it!
these black
↑

↑
I'll
no &
↑
all
dots
&
I
are monomers
-
↑
&
& -

↑
 3

1 damage, 1 I
~ I
...
-
5'

bonds
- 1 hydrogen
b I

3 V

is contained
damage

3
S-12 double stranded structure
hous
duplicate
Ho one is the template, other is the
daughter
DNA! && G:C
A:T base
complementarity
no
energy
-> no
replication of DNA

C.) How does this create

diversity?
0.) (cancer)
cannot
DNA work
autonomously
it
should inputs cellular
-> take from the

surroundings
replicateor dot.the
-

to
-
to
 Lecture 05
#DNASequence
22/08/23
5
ps-o-ps-"-p-S-...
3
...
~
S - -

I I

A I ↳ C

N N
I I
P S - -
0 P -

P -
P -
S -
0

nucleoside nucleotide

direction 51 3'!
DNA
* is
always from to

5'overhangs and 3'

overlap
template
5/
-
=
-> enzyme
performs
complimentarity
base

E3'
-

3
en

template
3' 5
no extension have
5 >3

# Semi Conservative DNA Replication

⑧ >8

5'. -
⑳

· 3 <
-> strands
DNA are
30
-

85 &
anti-parallel
⑧

>

· C ⑧
 ninge
primer ↳

r
lagging
&

r vo

·..
strand

ris
L

stand
I
3

Grading
synthesis
.

·
I
1
strand
arch
continuous
1

lagging
strand
~ .
sealing

polymerization
1
m
activity.
2
m ↓
m
11/
mm-

5 3

3
I
5

-↳ W
--- 3
31 7 5
&
-

↳ - - -

59 3
3) S

31
51
3'51

Enz Enz Enz

2 dS > 4 ds > 8 ds > . . . . ~

dNTPs dNTPs dNTPs

 Sears
the

i n SS

I
550C>
+

dNTPs
In
SS
primer

Enz
I

v
I

72°
+
si
primer

x35

PCR
↑
"I
do
enzymes (in humans) not work at
high temperatures
E DNA
Synthesis& Enzymes Lectron 06

ORIP/PHIP
25/08/23
CH20

Exonuclease
DNA
->
OH
DNA
ligase HOH-RNA

Fucks Fixes
#Enzyme Up- Enzyme

51 3
i
A C G G T A
11 III III 11 11

3 T A C G T C A T 5)

polymerise
-
C comes back and
5'- 3

rechecks;then removes

them: 5'-3' exonuclease

types of5'-3'DNA enzyme

work:
strands
DNA
polymerise synthesize new DNA
-

3'-5' exonucleus incorporated bases

remove
wrongly
-

5'-3' exonucleus obstructions

way
remove in the
any
-

L
can
only extend an

already presentshortpolymor

denature, anneal
I ds extends 2 dS

de
ideally Ix increase
e
4ds
a
>

per cycle
ch e
8dS
a
>

:
Is more like (1.8)"-(1.9)" ds
#Measurementof DNA

CNA
N
100 -
critical PCR

efficiency of
w/o red took 2
one
cycle
eng
to
lag
more

critical rate
·

S
I
=>>
lines
-

less DNA.

clical
-
DNA
50 ,
concentration
even less initial DNA!

20-

S id
I
15 20
I > cycles