↑

Cell
biology.

1
January 9,

kednesday.)
Monday.
*
E ·

Canuary',
* msk I

# January
*
is,
Friday. '
January
*
10, wednesday
3
were
M January
*
so, friday.
on line

I can
*
vary 23, Monday ship
*
Canvaryab, wednesday.
January 27, Friday
*

exam prep.

Monday
3
*
Januaryso,
↳ exami week 4
February
*
wednesday.
1,

reblarys, Friday
*

I skipped.
*
mondays, monday
*

*
wednesdays, wednesday
Friday to Friday
3 week 5
B10LZ005C Tores.

[Jan10 -

1/30 A.
Miderm 1 10727]
[Feb 1 -
2/22.
Miderm 2 Feb 20]
. .

[reb24-3/10
Mideon 3 March 10] &

·
[MaN21- 4/10
Millterm? Apro]
[Jan q-
4 25
Final Exam Apr 21]
Mon Jan 9: Introduction to cell and molecular biology - Read sections 1.1-1.3
and Experimental Pathways: “The origin of eukaryotic cells” in Karp.
Skip: The human perspective: the prospect of cell replacement theory (p18-22)
v
1. Review: Draw a diagram of a prokaryotic cell, a plant cell, and an animal cell.
Label and describe the most important functions of the following structures (if
present): cell membrane, cell wall, nucleus, genetic material, ribosomes, rough
ER, smooth ER, Golgi, mitochondria, chloroplast, lysosome, peroxisome, vacuole,
microtubules, actin filaments, intermediate filaments.
2. List and explain the three tenets of Cell Theory.
-

3. Describe at least five basic properties of cells. How do these properties differ
-
from the
basic properties of life?
4. Explain who Lynn Margulis is and her most important contribution to the field
of
cellular biology.
5. Describe the findings that support the symbiotic origin of mitochondria and
chloroplasts in modern eukaryotes.
Wed Jan 11: Basic Chemistry - Read sections 2.1, 2.3-2.5 in Karp
1. Define electronegativity and explain how it changes across the periodic table.
2. Determine which types of covalent bonds are polar or non-polar based on a
table of
electronegativity
H 2.2 C 2.5 N3
O 3.5
P 2.2
S 2.4
- Here are some examples for you to practice
A. HCl B. CO2 C. CH4 D. H2O E. H2S F. NH3
Element
Electronegativity
3. Describe the properties that characterize different types of noncovalent
bonds
4. Draw from memory the functional groups shown on Table 2.2 and identify
which are
capable of forming hydrogen bonds.
5. Define acid and base. Explain how acids and bases modify pH by affecting H+
and OH-
concentrations. Make sure you can give an example of one acid and one base and
how they affect pH in an aqueous solution.Fri January 13: Carbohydrates,
Lipids and Proteins: Structure and Chemistry- Read section 2.7
Read until p65 (stop before “primary and secondary structure of proteins”)
1. Draw a molecule of glycogen, starch and cellulose, each containing at least 6
glucose monomers. Draw and name the bonds that are responsible for the structure
of each polypeptide (details do not need to be at atomic level- something similar to
figure 2.19 will work). Identify at least one example in which each of these
polymers can be found.
2. Draw from memory the general structures of a fatty acid, a fat and a
phospholipid. Identify and circle the functional groups (from table 2.2) in each of
these structures.
3. Define saturated and unsaturated fatty acids in terms of structure and melting
temperature. Also answer: What are trans fats and what is their main source?
4. Define pK (aka pKa) and illustrate the structure of a carboxyl group and an
amino group above and below their respective pKs
Mon: Jan 9:

sell
theoryon
*

by schwann i schleidn

↳
all cells.
organisms are composed of one or more
1st and and tenent
->
cell in the structural unit of life.

-Schwann & Material.

Schleidn
agreed that cells could arise from noncellular

->
This, however, didn't explain how cells arose
↳
the third tenet of the cell theory:
Vichrow
God
↳ gave beneat
cells
of preexsisting
cells.
can arise
only by division

->
Since the you tenet added:
discovery ofnatural
DNA a was

is
cells contain called 4th
genetic DNA tenet

informations
Parent cell
Daughter cell

BasicPropernice ofcelinl
al
organised
->

complex and

Genetic Programe
I gene
L chromosomes
Necess

-construst cellular structures, mutation, cell rep.

->
Aquire & Utilize E

-
Respond to stimule

-
self regulate
-cells evolve

↳LUCA: last universal common ancestor.

* Two basic classes of cells,

Eukaryotic Prokaryotic
I ↳
structurally
more
complex structurally simpler bastia)
clant
<protists, fungi, & animals)

Eukayoti:

plant f animal &

PLANT ANINA I

- -
nucleus
v -
RER
- -
SER

cell wall - X
- -
plasma me-
brane
r
Plasmacles ma X

- -
resides.

- -
Micro tabless
- x
Chloroplast
- -
glogi complex
- X
vacule. - -
peroxisomes -
* L
lys some
""
→ cell wall .

<
plasma
hllhlbrahl
_
.

1.
↳

}
%
>

nucleolus .

Chloroplast only

: *.E
RER < plant
>
ribosomes -
Vaueloe
<

Mitochondria .

peroxisome
'

vesicles ÷

Plank have actin filament

Micro -

< <
but
tub bills .
taek intermediate

filahllht
.

golgi apparatus
<
<
SER °
g p U
✓
p u

plants + animals .

{ y-so.net
^

. -
-
i ' '
'
.

*B
. .

.
' >
^
.
nucleolus .

:
.

: nuclear aualbrane

-
> nuclear
pore
: :
>
i chromatin

: i '
'
-
nuclear envelop .

.
'

:
-

← "

,
, ,
Prokayotic -
L
- outter membrane
> plasma membrane.

o
I

I -
cytoplas
&
> - ribosomes.
-

>
DNA
-
I

> ~
proleosome.
3
d
-> cytskyth filament
3 to activi
similar
d
&
c
tubtiin
U
JAN 9,
Monday.

ATP as seller
operation
plasma
neembrane mitochondria: create
cytoplasm. Necess production.
DNA
protein
site of old cell
ERi breaks down
lysosome . make protein
ribosome
pea
golgi aparatus:
s
*
key points:
the main description.
->

organels and short

3 chdoroplast
Do
->

mitochondria contain ribosome

-
Jan 1
 because it dissolves in water
polar:
polar
polar
non polar
polar
polar

↳ the ring's symmetry

makes it
non polar

this sat electronegative

because I has
aleadly
forned your bonds.
 bio
*
polar Enm polar in terms of cell
* covalent
bonding ->
O,N, the binds with
hydrogen bonding.
* H.

* ionic
bonding -
bond btw o, Nete nionic

covalent bond in
stronger than innic bond because there water whole
every
*
hydrocarbons are non polar because of symmetry
 Jan 13 ,
Friday .

4 macromolecules :
types of
org '
Tenic
t
die
↓ ↓

lipids protein aeids

carbohydrates
.

1K¥
:
carbohydrates
→ branched liver cell
gylwgen : , .

"
¥
✗ ( I 6) bmd
glycosidic
→ → .

t
4)
> ✗ (I →
glycosidic bond
.

Starch :

¥¥X→1
→ unbranded swarm
grains
-

amytoplash

cellulose

t.EHWEIA.IE#wEx
plant cell wall .

↳ pct → 4)
glycosidic bond
.
 p glycerol

}
fat's
tai
hydrocarbon
M
É mm
o
Triglyceride
- -
-
.

Yn -
o
-
É - mum

w w w.
cttz -0
%
-

↳ eskrbmd →
carboxyl group .

double I triple bonds unsaturated present

:
double / triple bonus
saturated
fats no
:

↳
in cis
no ↳ naturally
trans tats
configuration .

unhealthy butter
-

w -w
.

Yz
o
.
-

o
-

11°
-

É → ~- s c→~~-
92-0
-0
cuz
- -
-

two g- → ~- → É-0 → ~- →
Yz
-
- -

° - w-
-0
g-
-

cuz
↳ butter , animal
fats .

0 → cis

# double bonds ✗ Kinks

↳
Phospholipids .

margarine
.

g→ phosphate
.

0
M3
carbonyl
#
I
.

Ch }
.
-

Mt -

@ 2) , -

O -
P -

O
-

Ctlz
-0
Ch } lot 1
↓ cuz -0 -
É -
→~-
→

1
choline c-→→~
.

no
-

µ, "
backbone
O
→
glycerol .

WHERE IS HYDROXYL GROUPS ?

 999 bonds .

C. 6,000 (6h12 06

}
→

" → 121000 1998 each time a

glycosidic
1000,2
-
.

informed
=

05 6000 999 bond a molecule

5,00
-

water in
of
•
lost .
2.
POLAR POLAR UNCHARGED NONPOLAR.
CHARGED

* as partic acid * serine alanine

*

*
Tryptophan
*
Gultamic acid. Theorine
* * Valine
*
phenyloraine.
lysine.
* *
Gltanline leucine
*

Mbond
VDW
Arginine Asparagine
*
* Iso Lucine

/
*
imic.

Histisidne.
*
x Tyrosine. aethisime.
*

x
SECONDARY
3.
TERTIARY QUATERNAM

amino
* acid ** helix conformation
* main have

sequence of a pleated. of entire poly two or more distinct

Replic
a
protein modules or domains
Fiberous or
*

globular protein covalent

* disulphist
binch, non covalent
H
*
binding. *
non covalent
band/bl hydrophobic
binds patches, non covalent

bonds
 a helixes:
M IP
E N
/

I c =0's 0 HB
i with
u
Hof N-H.

o
C
H
n
-

sheet:11 or anti I1
p

11
termint matches with
a terminus
17
or N N

0 H

↓ 1 N
- a
-> N terminus.

cherminus. n ... ...

16. A
binding
0 H
↑ 1
11 -1- a terminus
N
-
↓ n 'S. i

anti terminus.

terminous|jn
matches with a

il H
1 ↑
H
↓ - a termines.
-7 -1 /
cterminus's N
↳
1
o'
:
1
n
in

entermine X / - N ↑ -> ctermines

!
N
d M 1

Types hot covalent

of
binding protein conformations:
present in
↳
↳ vpW

HB.
↳ imic bands.
 smaller pla means more acidic.
acids donate proton.

⑦ on o

n-
o

11 1 11 11 H 10 -
1 104 X 1 --0

NHL

pla. -

7 7.5. 18 20 25

increasing acidity

decreasing pla

Iso
.
=
tomake an amino group
u
more acidic
"basic
protonate carboxy).
deprotonate NH2
1
(pka 3)
=

*
carboxyl group becomes
charged above its plea (pnspka)
amino
*
group becomes charged itsplea (pua 0)
=
Jan 18, wed.

cit,
-

100

NUST NH2

i 0
blu38 charge

100- 100-

NHS f

-
1. 0
 Jan 20, Friday.

are called heat shock

Hsp: heart shock protein. they
protein because thier synthes is m

cells increased to cell.

protein unfolding:brought by different agentsthat interfer

*
about with
various interactions that stabliss a proteinstertiary structure.
done
typically unfolding is with
reducing agents
Protein
* the
protein folds determined linear
folding:
the
- way
a is
by
&quence5 quits.
amino
of
native letter it in
is its Esrae.

to prims will nerve cells.

* CTD:rare fatal disorder that attacks the brain cause motor loss &
dementia.
->
can be inherited or
sporadic. Itcan also red from a donated organ
be
it has also been noted that it was
aquired by eating contaminated beef
↳ -
from a

mad
cow

cow
that had

disease
the overall course of CTDwas a
prim protein that encoded

the PRNP within the

cells chromosome
gene own

->
normal brain lissua CFD brain protein:
that
Prpsc:insoluble fibrils
are resistant
gene encodes protein:
pr pC
to enzymatic
digestio
↳ monomeric molecule, protein
by digestiving enzymes
soll
salts
soluble in
readily degraded
 the same acid but the
However
* both have amino
sequence vary in
way
they are folded.
helical
PrpC
sequenti and interconnecting coils

Props
largely p sheets
-

so
mode ofinfection:pop binds to Pros which caress it to
fold abnormally

Alzheimers:memory loss, confusion, loss ofreasoning.

↳ inherited or sporadic
↳
↳ B-amyloid proteins are the cause

affectinfectirent
ng parts
non
↳ to
of the brain compared cap.

#AAPERONS

help sent proteins folding by preventing them from interacting

* in

the cell
no
selectively with other to scales in

also
*
help misfolded proteins to fold properly.
bind to short speckles of ofhydrophobic amino
* arich.

Chaperm of Hsp70 family bind

* to
elongating polypep
ticle chain as they exist from the cibo some this
preventsthe
nasent protein to bind with other proteins cysts
in

once completely formed, it is sent into the chaperonin to

told into

3D structure.
->
Hsp70

&
->
*..8 - M -> 3D structure

1)
naseat protein
Hsp70 - Msp6O.
Chaperonin or

Hsp68
GroE19
* Rubio are a part oftsp to family
the thesubunit
role
* to
is
dedicate assembly of
 v ⑥
/ / /
~

cyestine -

lysine- glutamati:ionic
:HB.
serine -

Tugrosine
alanine:Van Der
Waal.
valine -

systeine- cystine:disulficle

-
* sequence DNA
*
biopsy. =
 :rx coupling.

* do work:
Energy:capacity to
change I move something.
Thermodynamics:the
*
study of the changes in Ethat accompany universe
events in
↳ doesn't take time into account

If law of be created
* Thermo:Ecan neither nor destroyed. can be
I
transdug
↳ universe
Total Ein remains constant.
*

·suslem 3 universe.

surrounding.
->

G
*yslem
internal E DE =
=
-

w
s
o mechanicalrd.
work E
heat E
↓ ↓ ↓
+Ve o -
ve

AE<8
AESO no net change
absorb heat in
system. lose heart.
exothermic
endothermic
-
doesn't tell us itevent likely
is

to occur or not
 * and law thereeventsin
of the universe have a direction.Downhill
↑ Estate to lower Estate.

*
spontaneous rxn:
thermodynamically far likely to occur with our part ofexter
in

not E

*
entropy.AS:measure of disorder
TDS.
entropy
second law
A indicates that disorder must ↑
↳
living things are able to
decrease their son
entropy by increasing the
entropy

sotheir
environment.
↳ smaller molecules amino acidsto
eutropy in
is organisms when
relatively larges
ones (proteins), and vice versa
glycogen >CO2 + H20.

↳ Don
ismaintained in its low state
by constantly
expanding EDNA
it would defiestriate
repair and stuffwithoutthis

* AG
An atT
= or AH-TAS
=

Enthalpy. measure spontanity

of
a rxx our exis
-Ye
AG ve:spintaneous exergonic: exothermic
=-

AG tve nmspltaneousendergone .. and

them
:

equilibrium
* constant:
k, kz
Req.
=

A B +
c
= + X.

kI (AJ[B] k2 (C][D]
=

Req k,/kz [C][D]

= =

V
[A][B]

predicting if
helps in
rxx will
go forward reverse.
Equilibrium is
steady state metabolism.

the
* farther a ran is from equilibrium > irrevessible
↳ to do is lost
capacity work

due to
entropy.
4 in

cellular
* metabolisin
basically
is non equilibrium metabolism. This
keeps the rxn one
going in
way.
The cell is E material
an
open system
-
constantly
in
fining i

3
the is
this at
flow of
dynamic a
i
steady state the cell.
in

non equilibrium. and product

concentration of reactant
are
relatively constantbut not necessarily
at equilibrium-

Thermodynamics:
↳
19:Free change

keq:

↑ Estate ->
I E state 1970.
 CFrutuse Ophosphate] =
0.5 =
5
-

keq
= =

Ighose-6-phosphatis

C ①the
How does

F-SP

is
a cell

is

an
maintain

continuously converted
open system
the is

with a
ratio?

into F , BP.

nutrient
② the call

amoted into it
 -
-
T
-

·men -1
 of metabolism,responsible
Mediators
*
enzymes:catalyst. for
virtually
every reactionin a cell.
the
protein part ofan enzyme that is inorganic cheetal)
factor.
* Co non

the non protein part of an enzyme that is

*
coenzymes: organic.
-
vitamins their derivatives often function as coenzymes.
Turnover #:the
I
#o-rxn
catalysing by a single enzyme
*

substrate
molecule
tim.
(see when
operating at a
saturating concentrat

activation E.covalent bonds must be broken reaction to

for
* a

to occur. For this

the need
reactant a certain amount KE
of
This is
KE called activation E

activation I,
barrier,transition state, activation site.
 27th.
Friday, January

* kM IS]
=

When V Umax/2
=

in
* lineweaver burks model:
km /X
intercept
-
=

umax
yy intercept.
=

m
=
km/vmax.
substrati
* am provides a measure
of the
affinity of the
enzymes for
->
km < 1

affinity.
Penicillin
* blocks cell wall
formation
sheptonycin tetracyclines
*
bind to bacterial ribosomes.
that catalyse
sulfa drugs:affect enzymes ox
specifically enzymes.
* in
reversible
* inhibitors losely bound to
enzyme.
competitive inhibitors:compete for enzyme's active sile
kmV ↳ resemble actual substrate but
from different
produ
Cq -

but t km.
effect
5 on max
no
N
& non-competitive inhibitor 4 substrate].
by
-

can be overcome
inhibitio :substrate inhibitor don't compete for the same site.

↑umaxuninhibited enzyme level ofinhibition

<
[inhibitorssubstrate can not over

oinicommniminmi
en.

moni
-niceinueneme
 +...
&

km 1.1
=

1.98.

0.99204.

I
km = -

intercept
x
umax I
=

>
Iintercept
umax
-
->
higher affinity.

vm

drumhigher actinic

one
Exam 1:week 1 revision:
*
no mitotic spindle to
separate
cell afterreplication
prokaryotic genomic
·

copies

0
-> outter menbrane, a wall

⑤
o
>plasma aexubran
> DNA

o
ribosomes.

wn
o s

apparation
of
provide
ATP cell walls.
present in

3 cytskeleton filament sincilian

to actin tubalin.

Prokaryote Eckaryotes.
material bound abrane
genetic
* into *
nuclear
presents
in nuclear extract

mitotic
* spindle absent milotic
*
spindle present

meatbant bound
* membrane bound
organelles A
organels present
absent Is have
cytoplasmic
complex
organels.
not
* diploid diploid.
*

*
simple cytokeltm. *
complexsytoneletal systine
+
Motor
protions.
 27/
Cell Biology 2085C – Practice Exam

/
1)Which of the following is NOT common to both eukaryotes and prokaryotes
A. Ribosomes
B. Mitotic spindle
C. Nucleus
D. DNA
E. B and C

/
2) The last eukaryotic common ancestor should contain all the following except:
A. Endoplasmic Reticulum
B. Chloroplast
C. Mitochondria
D. Nucleus
E. Lysosomes

/
3). According to the theory of endosymbiosis promoted by ________, our earliest prokaryotic ancestor was an
________ , who ingested an _____ , the precursor of modern day mitochondria. Ingestion of a second
endosymbiont, a _________, later evolved into chloroplasts.
A. Lynn Margulis; Anaerobic heterotroph; Aerobic prokaryote; cyanobacteria
B. Luis Pasteur ; Aerobic heterotrohoph; Aerobic prokaryote; cyanobacteria
C. Lynn Margulis; Aerobic autotroph; Anaerobic prokaryote; cyanobacteria
D. Robert Hooke; Aerobic heterotroph; Anaerobic prokaryote, amoeba
E. Lynn Margulis; Anaerobic autotroph; Anaerobic prokaryote; algae

4). Which of the following is NOT a property of covalent and non-covalent bonds
A. Covalent bonds are formed between atoms that make up a molecule
B. Covalent bonds depend on shared electrons between atoms
C. Non-covalent bonds require a large amount of energy to break
D. Non-covalent bonds depend on attractive forces between atoms
E. B, C and D.

/
5). Based on the following table of electronegativity, which of the following represents the order of polarity, most
to least? 1 A. C=O, O – H , C—N, C—H, C—C
+
B. O=O, O—H, , C – C, C—H, C=O
1 C. C=O, C—H, O=O, C – N, O—H
XD. C—S, O—H, C—N, C=O, C – C
② E. O – H , C=O, C—N, C—H, C—C
1.3 ⑨

-
6). In a covalent bond formed between Nitrogen and a less electronegative atom, the N atom would have a _______
while the less electronegative atom would have a _______ charge.
A. Partial positive; Partial negative
B. Partial negative; Partial positive
C. Positive; Negative
D. Negative; Positive
E. None of the above are correct

⑨
7) Particular groupings of atoms that often behave as a unit and give organic molecules their physical properties,
chemical reactivity and solubility in aqueous solutions are known as:
A. Amphipathic groups D. Kinetic groups
B. Ionic groups E. Conformational groups
C. Functional groups
D. Kinetic groups
~
8). Which of the following characteristics below (from 1 to 7) are typical of the polysaccharide cellulose?
1. Polymer of glucose 5. Long, unbranched chains
2. Contains α (1—>4) glycosidic linkages 6. Branched, coiled chains
3. Contains β (1—>4) glycosidic linkages 7. Good source of fiber
4. Water soluble
A. 1, 2, 4, 6, 7 D. 1, 3, 5, 7
B. 1, 3, 4, 5, 7 E. 1, 3, 5
C. 1, 2, 4, 7

/
9). Compounds rich in ________ tend to be liquid at room temperature. These compounds can be altered so they are
solid at room temperature by ____________ .
A. Unsaturated fats; Decreasing the amount of double bonds
B. Saturated fats; Decreasing the amount of double bonds
C. Unsaturated fats; Decreasing the amount of single bonds
D. Saturated fats; Decreasing the amount of single bonds
E. Unsaturated fats; Increasing the amount of double bonds

-
10). The following structures represent ______, which are maintained _____ at room temperature, due to the
______ of double bonds.
A. Saturated fats; Solid; Absence
B. Unsaturated fats; Solid;
Presence
C. Saturated fats; Liquid;
Presence
D. Unsaturated fats; Liquid;
Absence
E. Saturated fats; Solid; Presence
11).
2A patient with hyperlipidemia has been counseled to reduce the saturated fats in his diet, so he has replaced
butter with a butter substitute that he knows is made from a polyunsaturated oil. The manufacturer of this butter
substitute has partially hydrogenated this product. Which one of the following is the best description of why this
product was partially hydrogenated?
A. The trans-fatty acids produced by commercial hydrogenation are very healthy in humans.
B. Hydrogenation reduces the double bonds, creating a more saturated product, which is more marketable.
C. Hydrogenation makes the product less expensive to produce.
D. Hydrogenation reduces the cholesterol content of the oil.
E. Hydrogenation increases the cholesterol content of the oil.

v
12). As a scientist you find an unknown sample and run some tests to identify this unknown sample. Molecular
analysis found glycerol, fatty acids, phosphate and choline. Given this, which conclusion is most probable?
A. It can be a sample of carbohydrate only.
B. It can be a sample of phospholipid and fat.
C. It is only phospholipid.
D. It is only fat.

-
13) You treat a partially purified preparation of protein with mercaptoethanol, a reagent that can break bonds
formed between sulfur atoms. Which level of protein structure is likely to be affected?
A. Secondary
B. Tertiary
C. Quaternary
D. C and D are correct
E. A, B and C are correct
 ~
14). Amino acids 1 to 4 are all part of the same solution at a particular pH. If kept at the same pH, hydrogen bonds,
could be formed between the R groups of:
A. Between 1 and 2
B. Between 2 and 3
C. Between 1 and 3
D. Between 2 and 4
E. All of them are capable of
forming hydrogen bonds

15). Amino acids 1 to 4 are all part of the same solution at a particular pH. If kept at the same pH, ionic bonds could
/
be formed between the R groups of:
A. Between 1 and 2
B. Between 2 and 3
C. Between 2 and 4
D. Between 3 and 4
E. None of these pairs is capable
of forming ionic bonds unless pH is changed.

16). How many amino acids are in this peptide?

⑤
A. Seven
B. Eight
C. Nine
D. Ten
E. Eleven

-
17). What is the role of misfolded proteins in Creutzfeld-Jakob Disease?
A. Misfolded proteins act as infectious agents by inserting themselves in the host genome
B. Misfolded proteins act as infectious agents by propagating their misfolded protein state
C. Misfolded proteins accumulate around the ribosomes, making them unable to synthesize more proteins
D. Misfolded proteins block activity of molecular chaperones HSP70 and HSP60
E. B, C and D are correct.

X
18). Free energy is ________. A reaction will be spontaneous when ________.
A. The total energy of the system; The free energy of the reactants is lower than that of the products.
B. The total energy of the system; The free energy of the products is lower than that of the reactants.
C. The energy available to do work; The free energy of the reactants is lower than that of the products.
D. The energy available to do work; The free energy of the products is lower than that of the reactants.
E. The energy available to do work; The energy of activation is lowered by an decrease in the free energy.

/
19). Conversion of A → B is an endergonic reaction. Which of the following reactions could be coupled with
A→B so that both A→B and C→ D can occur?
A. C → D (ΔG = -5.4 kcal/mole)
B. C → D (ΔG = +9.3 kcal/mole)
C. C → D (ΔG = -10.2 kcal/mole)
D. Both A and C
E. None of the above
⑤
20). The continual flow of oxygen and other materials into and out of cells allows cellular metabolism to exist in a
steady state because
A. The concentrations of reactants and products fluctuate frequently.
B. The concentrations of reactants and products change as the cell grows.
C. The concentrations of reactants and products remain relatively constant.
D. The concentrations of reactants and products in a living cell are always at equilibrium
E. None of these statements are true

/
21). Enzymes speed up reactions by lowering the _______ . This can be accomplished by forming an enzyme-
substrate complex, where the R chains of the amino acids in the enzyme’s _____ and the substrate are bound
together by _________
A. Activation energy; Transition state; Permanent covalent bonds
B. Free energy; Transition state; Permanent covalent bonds
C. Activation energy; Active site; Permanent covalent bonds
D. Free energy; Active site; Noncovalent bonds
E. Activation energy; Active site; Noncovalent bonds

/
22). Dissolving a sugar cube in water and breaking down complex glycogen molecules into smaller molecules are
examples of decrease of entropy in a system
A. True
B. False

23). The amino acids glutamine and glutamic acid are shown below. They differ only in the structure of their side
chains (circled). At pH 7, glutamic acid can participate in molecular interactions that are not possible for glutamine.
What types of interactions are these?

~
A. Ionic bonds
B. Hydrogen bonds
C. Van der Waals interactions
D. Covalent bonds

/
24). What type of bond is this and what structure do long chains of this make up?

A.Alpha1,4 starch
B. Beta1,4 cellulose
C. Alpha1,6 starch
D. Beta1,6 cellulose
-
25). A fatty acid consists of three hydrocarbon chains linked to a glycerol backbone.
A.True
B. False

v
26). Is the following statement correct? “Amino acids used in making a polypeptide have an amino group and a
carboxyl group, and these groups can be present on any carbon atoms”.
A. Yes, when looking at the structure of amino acids we can see that these groups are attached to a carbon
therefore they can be spread out on other carbons too.
B. Yes, amino acids vary in size and can have multiple carbons in the backbone.
C. No, amino acids require a very specific structure and must have all groups attached to the alpha carbon.
D. No, amino acids require both groups to be attached to two different alpha carbons that are bonded together.

27). What happens when more substrate is added to a reaction at Vmax?

/ A. More substrate is converted to product at a faster rate
B. Vmax remains unchanged
C. Vmax increases
D. A and C
E. None of the above

/
28). What happens when more enzyme is added to a reaction at Vmax?
A. Vmax stays the same
B. Vmax decreases
C. Vmax increases
BIOL2085C SI
Lucas Klaus
Dr. Torres
1-18-23
Worksheet 2

1. Looking at the amino acid leucine, what will the net charge be at a pH of 1?
f.

2. Throwback to lecture. Fill out the table of functional groups at various pH levels.

Functional group pH 7 pH<pKa pH>pKa pKa (average)

⑤
COOH 0 3
NH2 · 8
+1

3. Draw the process of two amino acids bonding together. What is this bond called?

Replidebrd.orgor
R o

↑ NMz
18.Xw-n -X/
I
↓
n R'
H28

4. For the following amino acids, find the net charge based on the given pH and pKa values.
Valine, pH 7, Carboxyl pKa 3, Amino pKa 8
 8.
wetP
to

was
Phenylalanine, pH 11, Carboxyl pKa 3, Amino pKa 8

-
8 .

Glutamic Acid, pH 5, Carboxyl pKa 3, Amino pKa 8, R-group pKa 4.3

Lysine, pH 1, Carboxyl pKa 3, Amino pKa 8, R-group pKa 10.5

NUsI

5. Count the number of amino acids in the following figures.

8
 /

⑩ m

Hydrophobic amino acids are expected to be found where in a protein?

6.

7. What ultimately determines the conformation and function of a protein?

8. Draw both structures involved in secondary structure of proteins. What bonds are present
in these phenomena? How do these bonds interact within these structures

9. What are the classifications of amino acid R groups?

10. What level of protein structure is depicted below? How do you know?
11. You discover a new peptide but are unsure of what level it is. What might you look for
to determine if it is in a tertiary level? Think about structure and bonds.
 Fobuary 1, Wednesday.

plasma membrane
* is the outer most layer of the cell that separat
the inside the cell from the external environment
of

the
*
plasma membrane has I
functions:
mitochondrial
membrane: ->
continuous
allows Kerb compartmentilization:membranes are unbroken sheets.

cyla and
mitochondrial
I ->
plasma
that allow specialized activities to
proce
on membrane with at external interference
ribosomes
↳ outside and inside
genetic separates
concenta
separati
↳ nuclear membrane:
be
separates
genetic material from cytoplasm
↳ eytoplasmic membrands the reactions.

->
scaffold for biochemical activities:there are biochemical axis that can

happen on the membrane.

->
barrier:promote passive and
selectively permeable active transport.
unwanted
also prevent particles from entering.

->
solute transport:so, active passive transporthelps create concentration
gradient
receptor
->
to externalstimuli
4
ligand
Response signal transductions ·

·
·

receptors repond to
ligands (molecules the enviroment) ⑥
in

and react to it. This iscalled signal transduction

->
cell is cell communication:
I postains allow for exchange ofmaterial information
she.
⑤

MEMBRANEUPIDS

are
·3.cosy hudrophilicheadone
*
amphipathic:

*
contain a backbone.
phosphate group.glycerol
--
↓
->

PROOPhOgGCende,N phosphoglycericles.

TRIGLY CERIDE basic structure phosphoquyrice:

of

0 hydrophillic Fatty acid

a
-

(0-11xx ↑

t
1 fatty
-
-

o
choline phosphate
-

2 -
0 -
11XXXX serine acid

=1 p -
-1 11x
inositol
w ↓
midro
↳ ot physiological more detailed.
phobic

↳ pri: -
we charge orneutral.

Triglyceride.
variable
->
glycerol:this dont change
highly
o

group. -8-1 11x

acid
a

0
->
fatty
*XXXXXX chains (R)
0

N bo this vary.
can
-

-
O
1
I constant phosphate
group.

diglycrick
phosphocholine group.
 SPHINGOURIDS:
->
derivative
*
sphingosine:amino alcohol-long
of

hydrocarbon chain. 04 0H
04 0H

-ceramide.
1--x z, 1-x -,
-
-nz
why R
asand
-
sphingosine.
fatty
->

phosphocholine -
so Paramide tally acid =
o 04
sphingotine
1
-

-, ② ceramide
phosphochio-
-x

why
+

R ine sphinomyline
=

③
-> ceramide -
carbohydrati
- glycolipid.
sphing my line simple
sugar-glycolip
↑

->

A hydrophic ↳ scluster sugars of

=

ceramicle
subsitulism, ↓ ganglioside.
1x -11

I hydrophobic.
glycolipids are found nervous
in
↓
than
systems.
↳ ceramide
usually such longer

glactase phospholipids
+
=

cerebrosidle.
glacts
->

also play a role infectious

in

diseases.
 choles hol
* cholestrol is a sterol.

hydrophillic hydroxyl group towards the membrane

surface
↳ hydrophobicrings of cholestrol molecules are fat and rigid.
↳ this stillers the bilipid layer

CARBOHYDRATES
MEMBRANE

than 90%
more
of membrane carbohydrates covalently landed
* a

proteins to form
to
glycoproteins. The remaining are linked to lipids t
from glycolipids
-
Formed process called glycosylation
through a

*
short, branched, hydrophobic. 15
8800meter sugars.
-

· extracellular
If
these
carbohydrate projections play a major
3·;33.33303 role in cell-environment interactions.

888. sorting
(like
ofmembrane proteins to different cellular
partement an IP
rag)
intracellular

ROLE
* OF CARBONYDRATES IN RBC IDENTIFICATION:
Blood group antigens determined by short
sugar covalently attached to
membrane
apid and proteins the RBC membrane.
he
of

[
A
acetyl glactosamineto end ofthe chann
Type:enzyme adds of

B
Type enzyme adds glactose to the end ofthe chain
AB
Type:enzyme addle both to the end.
↳ ·
Type:lack enzyme capable of adding sugars to
enzymes are alternate
Both the same
end
the

gene- yet recognize

versions
of
different substrates.
indicator for several major diseases.
> is a
AB
gene strong
membrane proteins:
extracellular space
· Tmembrane protein has
specific orientation

1(y)
5.3.33,333

and
88%.
ye
intracellular space
each half ofthe protein has different
rolsand characteristics based which side is faces.
is called
this
SIDENESS

There a kinds
are of
membrane proteins.

peripheral proteins
& V
extracellular space

·.00000000000000000
8 33333333333333333
D
intracellular space.
Frans * covalent band
integras
membrane protein ↳ lipid anchored o
protein.
INTEGRAL MENBRANE

amphipathic
*

Is inside embrane hydrophobic

↳ outside embranehydrophillic

*
functions:
#) channels
bind to
specific substances
transporters:movement ofions/solutes,e-

*
aming acid residues form up interactions
faltacyl chairs ofbilipid

layer Thisseats
the lipid wall

PERIPHERAL MEMBRANE
PROTEINS:

* associated with membrane by weak on covalent bands

I can be solublised extraction with
by conce salt so that weak
a

en electrostatic bands
holding peripheral proteins to a membrane

function:
*
mostly found o sybolic side.
↳
'provide mechanical support for the membrane and function as an

anchor for integral membrane proteins

function:
*
mostly found on
peripheral side.
↳
enzymes, factors that transmit signals specialized coats

HIPID NENBRANE PROTEINS

bound to the
*
plasma membrane by small oligo sacchrid
chain linked to phosphatidylinsitol. This
linkage acalled
a GPI anchored protein glycosyl phosphatidylinostal linkage

normal cellular Prps a GPI linked

*
prion protein is molecule
I various
receptors, enzymescell adhesion proteins are GPI
linned.
 rare
type ofanemia l noctural hemoglobinria] results
from GPI
synthesi deficiency, which creates
RBC lysis

toon the cytoplasmic side plasma membrane is anchored to

the embrane by or more to chain.

-ERGENT
& UPIDS

detergentare
* used to isolate proteins from lipid membrance because
because detergent lipid membranes has similiar structure
and can help membrane proteins stable

sDS:
imicdetergentdenatus
to

↳ and aller shany shades

Problems
* faced membrane proteins are:

① low ↓
in

② unstable detergent
in sol
③ prone to
aggration
④
heavily glycosylated
important lecture points:
RBCs cell to
study membranes?because they lack hasand other
* why are a
good
organells that also posses membrane.

*
all membrane lipids are amphiphatic

lipide
* with
sugar glycolipid sphingolipich
*
carbohydrate modifications always face the extra cellular membrane.
phosphoapids choline
-

Panopea

it will be oppositeto ours.

33marophilic ->
hydrophobic.

integral embrane protein.

 peripheral
tunchm: mostlyfoundable sidetrane
*

and funchas an

anchor for integral membrane proteins

function:
*
mostly found on
peripheral side.
↳
enzymes, factors that transmit signals specialized coats
Friday, February 3.

res
Itis
*

#
hard to
image a integral membrane protein
produce a of

However, oncea structure is found

/ understood of one membrane
ofa brace protein family indetermine researches can usually apply a
to learn about structure
stragstsly called
homology modeling
members the
the

and
activity of other
of family.
Transmembrane
* domains: which are
sequentof the proteins usually
embedded

within a membrane.
They have simple structures, they one ist of a
shing of
about 20 predominant NONPOLAR amino acids. that are a helixes

·
charge protein uncharged polar

sosos os os oossososoossosto is
charged uncharged
domain,non

polar
polarnadro is

protein.

Hydropathy
* plotused to
identify transmembrane segmentsusing this
In which
plot. each site along a polypeptic chain assignedis value a

that provides ofhydrophobicity acid at that

a measure
of the amino

site as well as that of its neighbours.

* isdetermined using
Hydrophobicity various criteria such as
spid solubility
E used to
transfer them from non polar ->
aq nedium.

understanding hydrophobicity charl:

-> # of peaks determine

# tans numbrane

I
domain.

+ A4
->
E required to move form.
to a solution.
nonpolar
L fav.
an rx ... more
hydro-
phobic tic chain

->
polar region
AG
-

more the ->

cytoplasm side.
more
- we -
extracellular side

Transition
*
temptthe top at which lipid is covered from
a
liquid crystalling phase to a
frozen crystalline phase.
February 6,
Mmday

movement
* across cell numbrand.
↳ to did radiated
all communication cell extracellular he in
by
cell membrane.
↳ membrane
the bilipidlayer ofthe ideally
is suited prevent
to the loss
of
charged and polar solutes from a cell

through plasma membrane.

&ment 1

↓
passive active.

↳ diffusion
4
simple diffusion through lipid layer facilitated by protein
·
·
a

simple diffusion through an aq transporter

transport via driven
protein-lined channel. active E
pump
·

↳ moves substances
against
mcgradient
↓
with
always move
smcgradient
: [low].
Chigh]
-
 channel. membrane
ag. integral ⑥

......................potin.......high extra cellulars

&

390000000000000000000 Re
33333333333333333333e
~
...
· W

low (intra cellular

& ->

- &

simple diffusio
↳ substances
simple diffusion through
↓ facilitated diffusion
that don't where solute bind
an aq. channel formed within
need any help going
in

integral membrane protein: Not specific

to
receptors on the

through the plasma membrane protein carrier

membrane:
:64,286
->

Diffusion is a spontaneous process. High [low]

* -

and
eventually elimina

Ling C diff.blw two regions (equilibrium)

:--
↳
depends on random
thermal motion exergonic process driven by
-

i
entropy. diffusion equilibrium

&exergoni
* in

occurs when extracellular

<inmacsllur e
release E.

:- ATP ~
moves
/ ADD +PI
against one
gradient & requires E.

sj..::............... - high Linractor one

-

33333333333333333333e ·

o-low
.

lextracellulars
⑭
-

↓
out ofcell.
goel
God m
④
 OFIONS THROUGH MEMBRANES
NSION
is

cells contain ion channels. that are

I

* in the membrane
openings
permeable to
specific im

>are a
through which is can be transported
>
aquaporin.

integral membrane protein.

->

io
* channels are:

I highly selective.
passive diffusion.Indown hits.
↳ most channelsbe
I closed gated
in
in can either
open

THREEMAJOR CATEGORIES OF
GATER CHANNELS.

voltaged gated:conformation depends inthe difference in

->

ioic the sides the membrane

charge on
of
to
ligand gated conformational depends
state on the
ligand molecule
that binds to
gate. some may be open befor binding or closed

↳
before binding.
mechano-gated channels:conformational state depends o

mechanical forces that are

applied to the membrane

Na+1k+ ATPase
pump. Typepumrulation
-

on e

the same structure

* that is responsible for ATP
hydrolysisin
also responsible for Nakransport:
outside cell

42k y ↑(Na 1
+
+

inside all
*
unlike other integral membrane proteins, the Natlk-pump doent

bring the [NaB [k+] to equilibrium

->
the the
charge balanced
in out with the
charges carried
by
various allims.

outside cell.

4 (Na+], ↑ [a] ].

↑ (k y
+

-
ve
+

inside
i3-ve
↑ [DNAT
cell. 4 (proteins

For 3 Nathere are 2 k

3
for each ATP hydrolyzed.
↳ 3Na+ out
electrogenic contributes to
separation ofcharge
↳ 2k
+

m across membrane.

H +
k+ -
ATPase type pamp

found
* in
epithelial lining of the stomach

which secretes
a [P acid solution into the stomach

resting
* state Good,hormonal actives are

(no food) cell (food

·
cytoplasmic NM-
* move to apical cell
scufase,fuse with

brane ofparietal plasma membrane and selete

mid
cells of stomach
PVilosec:block n+lk+-ATPase

Zantac, Peplid, Tagament:block receptors on surface ofthe paristal cells

onygen, water, gases.

gluse
water
+
(k+
.

Na
Februarys, wednesday.

cotransport:a process
* that couples the movement of two

solutes across a membrane.

same direction:symport
to

I
opposite direction:antiport

Free E
* stored in the form concentration
in a
in cell of m
gradieah
Na+,k +, n=
formed by
 Is in
of potential
the E stored in
the form E

sodium to
This
Glucose against ions. transport with sodium
->
moves

ims a mantration
creates gradient. allows
This
glucose to move

24
into cells. glucose inside cell, I glu
Na+/ glucose to transporter
-
k aR cose] outside cell
+
L

at s
channels are, glucose glucose
oukic insicl
1G>0
aways opensee ③ #

Nah, H ,2Na+

O
insic
For resting nerve cell 14K 8
12
+

2Na

these channels are closed. 1C6M1206

moving Na+
gluton

orr.
2 +

inside cell

!
AG <0
②

3
& ..

· -

~ L

3k
+
~
....
· -
-
~ · .....
-
C ~ -
-
-
& .
....

... . . ·
① I moves Not out
↓

.
ofcell.. keeps [Na+]
low cell
in
so now. (Na+Jm
↑
(NaI
transport cell,
more
primary active
our ofcell

· Nat
·
glucose.

MEMBRANE POTENTIALS

electric
*
voltage or
potential difference:
·
-
+Ve
-
u
· +R
creates potential
-> PD =-70mU
difference.
-ve
magnitude
* directions the voltage across the plasma
of

membrane are determined by the diff in[irns] on either side

of the membrane and these relative permeabilities.

*
Resting potential:when a cell in
as an unexcited state.

POTENTIAL GIOMS.
55
m X sodium =

equilibrium potential. CN a +
TOm RoHasium equilibrium potential. (k +).
-

RESTIN
vast
majority ofion channels in membrance
* the plasma of a

G nerve are closed.

Depolarization:when
* the nerve cell is excited and

allows for sodium gates to open and for sodium

ions to flow in making the cell more true.

pr-50mX
*
Threshold:a "threshold" for depolarization at

and
which voltage gated sodium channels open
allows Notto
freely diffuse into thecell until
is +yomy
the charge ⑤
equilibrium potential for sodium
 I
depolarization. repolarization
to Nat
*
cell permeable cells
*
impermeable to Nat
ims ...
Nogales open
pottasium gate
*
open.
makes cell more
*
sodium closed.
gate
*

Ve
+

so lium
*
gott
closed.

Threshold:voltage gated
sodium channels open

polarization.
70mX
phyper resting state:
-

↑
-

2
sodium &
stimulus
poHasium gult
cloxl
*
k =
leah
at values
excess channels are
the cell of,
↓
cell cannot be
resimulated

PROPAGATION OFACTION POTENTIAL

The
*
greater the diameter ofthe axm less resistance to

action potential at
local current
I file can
flow and here
rapidly
activate the next
an
 day's
T
Aos
⑨
This
-
days
#
Friday, Is, February.

TABOCSMCM ofbiochemical rats that occur within a cell and

such oxes are

grouped into metabolic pathways
↑and a like to build
>anabolism:synthesisofmore complex compounds
↓ I
always Erequiring.
reduction -> use chemical from
metabolism
↓ exergonic carabolic
NADPH pathways.

-> catabolism:disassembly of complex compounds form

to

simpler products
-

I make raw material availible for anabolic

oxidante h
metabolism.

provide required
chemical E for the cell
It store E in
the form ATP
of
and NADH.

OXIDATION -

REDUCTION REACTIONS

OIL oxidation is loss

RIG reduction
gain.
in
 1
-

8+ the
* more
hydrogens can be removed
* C H
from
-

a molecule the more ATPs can

↓ X
reduced oxidised be
generated
state state.
- oxidation of
*
glucose moucule

·=
8.1 >36 A TP.

oxidation HOW IS ATP FORMED?

of
glucose.

1
mostof
A
the chemical energy ofglucose
is stored in the form
of 4Ee-.
#
glycolysicy
toplasm these are removed as substrat

as molecules are oxidized during

prguvate-> both
#AC. glycolysi & cycles.
TCA
Is this
is
ultimately used
to form ATP

GLYCO (YSIS
oxygen dependentox:aerobic
glucose CAD + 2Pi CNADT >2
pyruvate + CATP>2NADH +Ch +
+
+

2420.
+

rxn occurs in
cystal eukaryotesof
a prokaryoti
input. I
glucose molecule. OUTPUT.2
Pryurate
:2 ADP 2 Pi
+
:2.ATP
:2NADT :2 NADH.

FERMENTATION :(H
+
2H20.

-ygen
independent oxnarobic

NADH TH NADT
a

Fermentation yeast pryquate

in Ethyl alcohol
NADH-H + NNIADT
astate
Fermentation muscle ceses:
in
projuvate lactate the orogenase
why fermentation?

↳
one the
of

in short
key least and
in
glycolysisis NADA

REGENERATED
it i
supply incells must be
from NADA.
h no NAD+
NO FURTHUR GUOMSIS.
glyuraldehyde-3-phosphate
①

thegoaloffermentalintoregenerateMADA. guys see

so that

compound
prycevate
derived from prosate &3 /
NADH >lactate
alcohol +
e
NAD+

REDUCING POWER
*
NADPH reduces metabolites that are required to make
fals
amount
*
of NADPH a cell REDUCING POWER
1
cells usable content.
* NADPH has
⑳
the ability to VEelectrons DUCEasetabolites.
->
"high Icompound because of42-transfer potential'

merneogenin
Monday, IB
february