Download The Chemistry of the cell

The Chemistry of the cell
M. Saifur Rohman, MD. PhD. FIHA. FICA
Chemical Component of The Cell
• Cell Chemistry Is based on Carbon Compounds .
• A living cell is composed of C, H, N, and O make up
nearly 99% of its weight.
• The most abundant substance of the living cell is water.
(70% of a cell's weight), and most intracellular reactions
occur in an aqueous environment.
• All organisms have been designed around the special
properties of water, such as its polar character, its
ability to form hydrogen bonds, and its high surface
tension.
Percentage Component of The Cell
The Carbon
• If we disregard water, nearly all of the molecules in a cell
are carbon compounds
• The carbon atom, because of its small size and four
outer-shell electrons, can form four strong covalent
bonds with other atoms.
• Most important, it can join to other carbon atoms to
form chains and rings and thereby generate large and
complex molecules with no obvious upper limit to their
size.
• The other abundant atoms in the cell (H, N, and O) are
also small and able to make very strong covalent bonds
Covalent bond
Covalent bonds - form when atoms share electron
pairs.
– strongest type of bond
– tend to form when atoms have 3, 4 or 5
valence electrons
– can be nonpolar or polar
Cells Use Four Basic Types of Small Molecules
• Certain simple combinations of atoms - such as the
methyl (-CH3), hydroxyl (-OH), carboxyl (-COOH), and
amino (-NH2) groups - recur repeatedly in biological
molecules.
• The small organic molecules of the cell have molecular
weights in the range 100 to 1000 and contain up to 30 or
so carbon atoms.
• They are usually found free in solution, where some of
them form a pool of intermediates from which large
polymers, called macromolecules, are made.
• They are also essential intermediates in the chemical
reactions that transform energy derived from food into
usable forms
Sugars, Fatty Acid, Amino Acid and Nucleotide
• All biological molecules are synthesized from and broken
down to the same simple compounds.
• Biochemical Energetics for cellular reaction and function
• Broadly speaking, cells contain just four major families of
small organic molecules: the simple sugars, the fatty acids,
the amino acids, and the nucleotides.
• Although some cellular compounds do not fit into these
categories, the four families, and especially the
macromolecules made from them, account for a
surprisingly large fraction of the mass of every cell
Suggested reading topics
• Lodish et al. Chemical foundations in 4th
edition Molecular Cell Biology. WH Freeman
and Company 2000. Pp 14-49.
• Cooper GM. The chemistry of the cell in The
cell: A molecular Approach. ASM PRESS. 1997.
pp. 39-85.
Amino Acid
M. Saifur Rohman, MD. PhD. FIHA
Amino Acid
•
•
•
•
Structure
Classification
Peptide Bond
Force
Amino Acid
• Amino acids are molecules containing an amine
group, a carboxylic acid group and a side chain that
varies between different amino acids.
• These molecules contain the key elements of
carbon, hydrogen, oxygen, and nitrogen.
• Particularly important in biochemistry, where this
term usually refers to alpha-amino acids with the
general formula H2NCHRCOOH, where R is an
organic substituent.
Amino Acids
amino
group
alpha
carbon
O
H3N+
O
H
R
side chain
group
Lecture 6.3
• The general formula for
an amino acid
• R is commonly one of 20
different side chains
• At pH 7 both the amino
and carboxyl groups are
ionized
carboxyl
group
13
Families of Amino Acids
• The common amino acids are grouped according to
whether their side chains are:
–
–
–
–
acidic D, E
basic K, R, H
uncharged polar N, Q, S, T, Y
nonpolar G, A, V, L, I, P, F, M, W, C
• Hydrophilic amino acids (uncharged polar) are usually on
the outside of a protein whereas nonpolar residues cluster
on the inside of protein
• Basic or acidic amino acids are very polar and are
generally found on the outside of protein molecules
Protein AA : Polymerization
• As both the amine and carboxylic acid groups of
amino acids can react to form amide bonds, one
amino acid molecule can react with another and
become joined through an amide linkage.
• This polymerization of amino acids is what creates
proteins. This condensation reaction yields the newly
formed peptide bond and a molecule of water.
An illustration of Polymerization
Peptide Bonds
• Amino acids are joined together by an amide
linkage called a peptide bond.
• The two bonds on either side of the rigid planar
peptide unit exhibit a high degree rotation
peptide
bonds
O H
H3N+
H
rotation occurs here
R1
N
H
R2 H
N
O H
O H
R3
N
H
R4
O
O
Peptide bond
• Protein is a chain of amino acids linked by
peptide bonds
• Peptide bond
– Type of covalent bond
– Links amino group of one amino acid with
carboxyl group of next
– Forms through condensation reaction
Protein Sequence Features
• Proteins exhibit far more sequence and
chemical complexity than DNA or RNA
• Properties and structure are defined by the
sequence and side chains of their constituent
amino acids
• The “engines” of life
• >95% of all drugs target proteins
• Favorite topic of post-genomic era
Protein Sequence Databases
• Where does protein sequence information reside?
– Entrez Cross Database Search
• http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi
– Swissprot & TrEMBL
• http://ca.expasy.org/sprot/
– PIR
• http://pir.georgetown.edu/
• As of December 2003, all of this information is integrated
into unified protein database called Uniprot.
– Uniprot
• http://www.pir.uniprot.org/
Protein Structure & Function
• Protein structure - primarily determined by sequence
• Protein function - primarily determined by structure
• Globular proteins: compact hydrophobic core &
hydrophilic surface
• Membrane proteins: special hydrophobic surfaces
• Folded proteins are only marginally stable
• Some proteins do not assume a stable "fold" until they bind to
something = Intrinsically disordered
 Predicting protein structure and function can be very hard -- &
fun!
D Dobbs ISU - BCB 444/544X:
Protein Structure & Function
22
4 Basic Levels of Protein Structure
D Dobbs ISU - BCB 444/544X:
Protein Structure & Function
Basics of Protein Structure
• Primary
• Secondary
• Tertiary
primary structure
ACDEFGHIKLMNPQRSTVWY
Primary structure
• Sequence of amino acids
• Unique for each protein
• Two linked amino acids = dipeptide
• Three or more = polypeptide
• Backbone of polypeptide has N atoms:
-N-C-C-N-C-C-N-C-C-N-
Primary Structure & Protein Shape
• Primary structure influences shape in two
main ways:
– Allows hydrogen bonds to form between
different amino acids along length of chain
– Puts R groups in positions that allow them to
interact
Secondary Structure
– Local spatial arrangement of amino acids
– Description of short-range non-covalent
interactions
– Hydrogen bonds form between different parts of
polypeptide chain
– These bonds give rise to coiled or extended pattern
– Periodic structural patterns: -helix, b-sheet
D Dobbs ISU - BCB 444/544X:
Protein Structure & Function
Common Secondary
Structure Elements
• The Alpha Helix
The a-helix is a common secondary
structure element
acidic
nonpolar
• A helical wheel is a
representation of the 3D
structure of the a-helix.
• Projection of aa side chains
onto a plane perpendicular to
axis of helix
• Hydrophobic arcs stabilize
helical interactions
• Amphipathic helices are
common
Common Secondary
Structure Elements
• The Beta Sheet
Secondary Structure &
Protein Folding
• Understanding the forces of hydrophobicity:
nonpolar
side chains
Hydrogen bonds can
form with polar side chains
on outside of the protein
polar
side chains
hydrophobic core contains
nonpolar side chains
unfolded or partially
folded polypeptide
folded conformation
Tertiary & Quaternary Structure
• Tertiary
– Overall 3-D "fold" of a single polypeptide chain
– Spatial arrangement of 2’ structural elements;
packing of these into compact "domains"
– Description of long-range non-covalent
interactions (plus disulfide bonds)
• Quaternary
– In proteins with > 1 polypeptide chain, spatial
arrangement of subunits
D Dobbs ISU - BCB 444/544X:
Protein Structure & Function
32
Tertiary Structure
Lactate
Dehydrogenase:
Mixed a / b
Immunoglobulin
Fold: b
Hemoglobin B
Chain: a
Tertiary Structure
heme group
Folding as a result
of interactions
between R groups
coiled and twisted polypeptide
chain of one globin molecule
Quaternary Structure
Some proteins are
made up of more
than one
polypeptide chain
Hemoglobin
Force important for protein structure
•
•
•
•
Ionic bonds
Covalent bonds
Van der waals forces
Hydrogen bonds
Folding of a polypeptide chain
Non-covalent amino acid interactions
• Hydrogen bonds
C=O …. HN
• C=O :
Glu, Asp, Gln, Asn
• NH :
Lys, Arg, Gln, Asn, His
• OH :
Ser, Thr, Glu, Asp, Tyr
Folding of a polypeptide chain
Non-covalent amino acid interactions
• Ionic bonds
COO- …. +H3N
• COO- : Glu, Asp
pKa < 5
• NH3 + : Lys, Arg
pKa > 10
Folding of a polypeptide chain
Non-covalent amino acid interactions
• Van der Waals forces
• electrostatic in nature, short ranges
• dipole-dipole, ion-dipole etc.
Folding of a polypeptide chain
Levels of protein folding
• Primary structure
(unfolded state)
• Secondary structure
(a-helix, b-sheet)
• Tertiary structure
(domains, subunit)
• Quaternary structure (several pp chains)
• Intra- and intermolecular disulfide bonds
Suggested reading topics
• Lodish et al. Protein structure and function in
4th edition Molecular Cell Biology. WH
Freeman and Company 2000. Pp 50-99.
Protein Synthesis,
Processing and Regulation
M. Saifur Rohman, MD. PhD. FIHA
Protein Synthesis Intracellular
• In cells, this reaction does not occur directly;
instead the amino acid is first activated by
attachment to a transfer RNA molecule through an
ester bond.
• This aminoacyl-tRNA is then a substrate for the
ribosome which catalyzes the attack of the amino
group of the elongating protein chain on the ester
bond.
• All proteins made by ribosomes are synthesized
starting at their N-terminus and moving towards
their C-terminus
Protein synthesis
• DNA
• mRNA (transcription)
• Protein (translation)
From DNA to Protein
Mutation consequence on Protein seq
Post-Translational Modification
• New polypeptides usually fold themselves spontaneously into
their active conformation. However, some proteins are
helped and guided in the folding process by chaperone
proteins
• Many proteins have sugars, phosphate groups, fatty acids, and
other molecules covalently attached to certain amino acids.
Most of this is done in the endoplasmic reticulum.
• Many proteins are targeted to specific organelles within the
cell. Targeting is accomplished through “signal sequences”
on the polypeptide. In the case of proteins that go into the
endoplasmic reticulum, the signal seqeunce is a group of
amino acids at the N terminal of the polypeptide, which are
removed from the final protein after translation.
Posttranslational modifications
Chemical alterations after protein
synthesis
• May alter activity, life span or cellular location
• Chemical modification
• Acetylation, phosphorylation, glycosylation
• Processing
• Proteolytic (in)activation, selfsplicing
Protein processing and regulation
Protein modification : becoming a functional
protein
• Folding
• Proteolysis
• Glycosylation
• Signal sequence
Protein synthesis on the ER
Protein folding by chaperonin
AAAAAAAAAA
AAAAAAAAAA
BiP
(HSP70)
HSP40
Signal peptidase
Signal peptide
Membrane proteins
• Complications: proteins embedded in membranes
• protein contains a stop-transfer sequence which is too hydrophobic
to emerge into aqueous environment of ER lumen
• stop-transfer sequence therefore gets stuck in membrane
• ribosome lets go of translocon, finishes job in cytoplasm
• translocon dissociates, leaves protein embedded in membrane
• example = LDL receptor
Suggested reading topics
• Cooper GM. Protein synthesis, processing and
regulation in The cell: A molecular Approach.
ASM PRESS. 1997. pp. 273-311.
Thank You