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Life

Basis of

Michelle Starz-Gaiano (guyAN-no)

Biol 303 Lecture 2
(Alberts Chapter 2)

BIOL 303 Administrative

Issues

Please refer to the Biol303 Blackboard site

for official, current information
including course policies, TA contacts,
discussion schedules, and the exam schedule
Please review the rules of Academic
Integrity
tutoring - LRC or Biology Tutorial center
supplemental instruction (SI)
Monday sections will not meet in person on
Labor day but will have the same work as
all other sections

BIOL 303 Learning Goals

About cell biology: 1) to know the structure and
function of cellular components and organelles; 2) to
understand how molecular mechanisms enable cellular
functions; 3) to relate genetic inputs to cellular function
and genetic changes to potential pathologies; 4) to
understand the experimental evidence informing current
models in cell biology.

In preparation for future work (in upper level

courses and beyond): 5) to develop/sharpen skills in
question-asking; 6) to improve mathematical
competency and intuition in biology, as required for
addressing modern biological problems; 7) to augment
problem-solving and critical thinking skills through
problem sets, reading and writing assignments, and

Clicker test questions.

learning goals
By the end of this topic you should:
know what kinds of chemical properties are important
in cells (how does the chemistry you know already
apply to cell biology?)
compare and contrast the types of chemical bonds
that are critical for cellular function
explain why water is essential to biochemistry in the
cell
know: the four major classes of biological molecules,
important properties of each, where they are found in
the cell, and recognize visual representations of each
describe the key factors that determine
protein/macromolecular structures, and explain why
the structure of proteins is important

what can cells do?

acquire chemical energy ATP and use it to
maintain homostasis and order -ie, constantly
replace/update molecules as needed (via enzymes)
reproduce
carry out specialized functions
make and release molecules (ie hormones, peptides)
move or contract (prokaryotes; muscle cells)

respond to the environment

kill themselves if necessary
regulate themselves (autonomy- choose what to do)

LL THE CAPABILITIES A CELL HAS ARE ENCODED IN ITS GENE

nd carried out by many kinds of macromolecules

Cell bio intro

movie
http://www.studiodaily.com/main/searchlist/6850.html

Cells may be magical,

but cellular functions are chemistry

how is chemistry in living things

different from that in the rest of
the world?

the cell biologists version of the

periodic table of elements

remember any chemistry?

Source=Created with Inkscape |Date=28

January 2006 |Author=
DynaBlast |Permission=Creative Commons
Attributio

name the types of chemical bonds

atoms like to share or borrow

biologists favorite functional groups

(atoms linked by ______ bonds)

these are often linked like

this:

o
r

water has important, unique chemical

properties

water is a
polar
solvent

water has important, unique chemical

properties

water is a
polar
solvent and
good at
making H
bonds

high surface tension, high specific heat, high heat of vaporiza

water dissolves salts

Na+ and Cl- ions in salt crystals are held

together by electrostatic interactions

HYDROPHILIC molecules
dissolve in water

some biological molecules love water - (the ones

that interact well with it, sugars, ions, amino
acids, polar molecules )-

HYDROPHOBIC molecules are

insoluble in water

non-polar biological molecules like hydrocarbons

hate water- fats (the uncharged, insoluble ones,
like fats)

in an aqueous solution,
hydrophilic molecules associate by hydrogen
bonds
hydrophobic interactions hold hydrophobic
structures together

wa
t

er
i

sE

XC
LU
D

ED

he
re

water breaks
ionic bonds

many biological molecules are

AMPHIPATHIC

what does it mean to be

AMPHIPATHIC?

 so, what bonds do we know?

van der Waals

forces

(a strange schematic of)

van der Waals forces occur due to transient dipoles

interacting
van der Waals forces are individually weak but very
important in biological interactions because there
are often a lot of them between interacting
molecules
cue clickers

salad dressing
question

4 types of organic building

blocks

 4 classes of biological molecules

1

different biological molecules are

required in different parts of the cell

biological molecules
1

C-------------------

used for energy storage, cell structure, and in

modifying
other macromolecules
simple sugars glucose,
fructose
(find the carbonyl group)

di- and oligosaccharides simple sugars joined linearly

by glycosidic bonds (C1 to hydroxyl)
- sucrose and
lactose
polysaccharides glycogen, starch,
cellulose (all glucose-based), and
glycosaminoglycans (2 sugars)

biological molecules
2

L-----

dissolve in organic solvents but

not water

fats= triacylglycerol = glycerol

linked to 3 fatty acids (by ester

bonds) oil if liquid at RT
fatty acids can be different
lengths and saturated or unsaturated
phospholipid=diacylglycerol =
glycerol linked
to 2 fatty acids and one phosphategroup+polar group

Lipids are essential

in membranes,
energy storage
AND other
functions like
signaling

biological molecules
2

L-----

dissolve in organic solvents but

not water

fats= triacylglycerol = glycerol

linked to 3 fatty acids (by ester

bonds) oil if liquid at RT
fatty acids can be different
lengths and saturated or unsaturated
phospholipid=diacylglycerol =
glycerol linked
to 2 fatty acids and one phosphategroup+polar group
isoprene-based molecules

also in this class:

steroids cholesterol
and hormones

biological molecules
N-------- ------

rRNA folded

DNA helix drawn differently

Encode genetic information, and energy storage;

some catalytic functions
DNA (nucleus) and RNA (cytoplasm) are made up of
nucleotides
Plus, nucleotides ATP and GTP (purines) are

GATACAATTGCGCG

nucleotide

biological molecules
N-------------

biological molecules
4

P----------

found throughout the

cell carry out most of
the cellular activities (can
be metabolic, structural,
growth regulators,
sensors, antibodies, etc
etc)
Made up of amino acids
tens of thousands of
possibilities
translated from genes

proteins carry out many functions

function depends on form (structure)
Most abundant molecules (8 x 109 proteins/liver
cell!!)
10,000 different proteins/liver cell
Ratios can differ: 5 x 108 actin molecules vs. 5 x
105 immunoglobulin molecules (lymphocytes)
Composition, structure, sizes can
differ:

about protein structure

N-terminus

C-terminus

different amino
acids
have different
properties
-5 are polar and
charged can form
ionic bonds, are
hydrophilic
-5 are polar and
uncharged,
hydrophilic, form Hbonds
-7 are non-polar,
hydrophobic
-3 are unusual

e sequence of the amino acids is the PRIMARY structu

N-terminus

C-terminus

the sequence of the amino

acids is the PRIMARY
structure

TERTIARY protein structure - myoglobin

protein function depends on

form

ribbon model

associations between
AAs drive the folding of
SECONDARY structures
(-helix, -pleated sheet)

ball and stick model

amino acids

you should understand these classifications!!!

amino acids that are commonly

modified (post-translational
modifications)

cysteine in disulfide
bridges

serine, threonine, or tyrosine

by phosphorylation

Proteins can also be modified by covalent linkages to sugars, lipids, or

other proteins there are many types of post-translational
modifications that regulate protein function

secondary protein
structures

alpha helix

conformati
ons

beta-pleated sheet

l regions of proteins are organized into these structures

ere are regions that are disordered or flexible
ondary structure is largely a result of interactions between aas in the polypeptid

tertiary protein structure myoglobin

tertiary structures are usually

determined by
X-ray crystallography (great for
ordered regions, soluble proteins,

quaternary structure hemoglobin

4 separate
proteins held
together by
non covalent
bonds
protein dimers,
tetramers
(including some
transporters!),
etc are examples

bonds that maintain protein

structures
non-covalent bonds

nds
o
b
t
n
e
coval

side chains

folding can occur spontaneously or

via chaperones

what factors/conditions might

cause a folded protein to unfold
(denature)?
often it is energetically
favorable to be folded

why is a denatured protein a bad

thing for a cell?

non-covalent bonds mediate interactions

between biological molecules

DNA
binding
domain

protein -protein
interaction

DNA-protein interactions

for next time

read/review chapter 3
go to your discussion section!
assignment for your second
discussion section(or online)