Chapter Macromolecules 4 & 5
Macromolecules are polymers,
built from monomers
The versa;lity of carbon makes possible the great
diversity of organic molecules
Carbon chains form the skeletons of most organic
molecules. Many organic molecules, such as fats,
have hydrocarbon components
Macromolecules are large molecules composed of
thousands of covalently connected atoms
All living things are made up of four classes of large
biological molecules: carbohydrates, lipids, proteins,
and nucleic acids
Protein Structure and Func;on
A func;onal protein consists of one or more polypep;des
precisely twisted, folded, and coiled into a unique shape
The sequence of amino acids determines a proteins
threedimensional structure
A proteins structure determines its func;on
Groove
Groove
(a) A ribbon model
(b) A space-filling model
Protein Structure and Func;on
Tertiary
structure
Secondary
structure
Quaternary
structure
helix
Hydrogen bond
pleated sheet
strand
Hydrogen
bond
A functional protein consists of one or
more polypeptides precisely twisted,
folded, and coiled into a unique shape
Transthyretin
protein
Transthyretin
polypeptide
A proteins structure
determines its function
What Determines Protein Structure?
In addi;on to primary structure, physical and
chemical condi;ons can aect structure
Altera;ons in pH, salt concentra;on, temperature, or
other environmental factors can cause a protein to
unravel
This loss of a proteins na;ve structure is called
denatura/on
A denatured protein is biologically inac;ve
Diseases such as Alzheimers, Parkinsons, and mad
cow disease are associated with misfolded proteins
What Determines Protein Structure?
naturat i
Normal protein
naturat i
Denatured protein
Protein folding in the Cell
Polypeptide
Correctly
folded
protein
Cap
Hollow
cylinder
Chaperonin
(fully assembled)
Steps of Chaperonin
Action:
1 An unfolded polypeptide enters the
cylinder from
one end.
2 The cap attaches, causing 3 The cap comes
off, and the
the cylinder to change
properly folded
shape in such a way that
protein is
it creates a hydrophilic
released.
environment for the
folding of the polypeptide.
Chaperonins are protein molecules that assist the proper folding of other proteins
Scientists use X-ray crystallography to determine a proteins structure. Another
method is nuclear magnetic resonance (NMR) spectroscopy, which does not
require protein crystallization
Nucleic acids store, transmit, and help
express hereditary informa;on
The amino acid sequence of a polypep;de is programmed by a unit
of inheritance called a gene
Genes are made of DNA, a nucleic acid made of monomers called
nucleo;des
There are two types of nucleic acids
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
DNA provides direc;ons for its own replica;on
DNA directs synthesis of messenger RNA (mRNA) and, through
mRNA, controls protein synthesis
Protein synthesis occurs on ribosomes
Figure 5.25-1
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
Figure 5.25-2
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into
cytoplasm
Figure 5.25-3
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into
cytoplasm
Ribosome
3 Synthesis
of protein
Polypeptide
Amino
acids
The Components of Nucleic Acids
5+ end
Sugar-phosphate backbone
Nitrogenous bases
Pyrimidines
5+C
3+C
Nucleoside
Nitrogenous
base
Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA)
Purines
5+C
1+C
5+C
3+C
Phosphate
group
3+C
Sugar
(pentose)
Guanine (G)
Adenine (A)
(b) Nucleotide
3+ end
Sugars
(a) Polynucleotide, or nucleic acid
Each nucleotide consists of a nitrogenous
base, a pentose sugar, and one or more
phosphate groups
Deoxyribose (in DNA)
(c) Nucleoside components
Ribose (in RNA)
The Components of Nucleic Acids
Nucleoside = nitrogenous base + sugar
There are two families of nitrogenous bases
Pyrimidines (cytosine, thymine, and uracil) have a
single sixmembered ring
Purines (adenine and guanine) have a six
membered ring fused to a vemembered ring
DNA, the sugar is deoxyribose;
RNA, the sugar is ribose
Nucleo;de = nucleoside + phosphate group
The Structures of DNA and RNA
RNA molecules usually exist as single polypep;de
chains
DNA molecules have two polynucleo;des spiraling
around an imaginary axis, forming a double helix
In the DNA double helix, the two backbones run in
opposite 5+ 3+ direc;ons from each other, an
arrangement referred to as an/parallel
One DNA molecule includes many genes
Nucleo;de Polymers
5+
3+
Sugar-phosphate
backbones
Hydrogen bonds
Base pair joined
by hydrogen
bonding
3+
5+
(a) DNA
Base pair joined
by hydrogen bonding
(b) Transfer RNA
Nucleo;de Polymers
Nucleo;de polymers are linked together to build a
polynucleo;de
Adjacent nucleo;des are joined by covalent bonds
that form between the OH group on the 3+ carbon
of one nucleo;de and the phosphate on the 5+
carbon on the next
These links create a backbone of sugarphosphate
units with nitrogenous bases as appendages
The sequence of bases along a DNA or mRNA
polymer is unique for each gene
The Structures of DNA and RNA
The nitrogenous bases in DNA pair up and form
hydrogen bonds: adenine (A) always with thymine (T),
and guanine (G) always with cytosine (C)
Called complementary base pairing
Complementary pairing can also occur between two
RNA molecules or between parts of the same
molecule
In RNA, thymine is replaced by uracil (U) so A and U
pair
DNA and Proteins Measure Evolu;on
The linear sequences of nucleo;des in DNA molecules
are passed from parents to ospring
Two closely related species are more similar in DNA
than are more distantly related species
Molecular biology can be used to assess evolu;onary
kinship
Higher levels of organiza;on result in the emergence of
new proper;es
Organiza;on is the key to the chemistry of life
Figure 5. UN12
The Cell: An overview
Chapter 6 & 7
Human height
1m
0.1 m
Length of some
nerve and
muscle cells
Chicken egg
1 cm
Frog egg
1 mm
Human egg
Most plant and
animal cells
10 m
1 m
100 nm
10 nm
Nucleus
Most bacteria
Mitochondrion
Smallest bacteria
Viruses
Ribosomes
Proteins
Lipids
1 nm
0.1 nm
Small molecules
Atoms
Superresolution
microscopy
Electron microscopy
100 m
Light microscopy
All organisms are made of
cells
The cell is the simplest
collec;on of macer
that can be alive
Cell structure is correlated
to cellular func;on
All cells are related by their
descent from earlier cells
10 m
Unaided eye
The Fundamental
Units of Life
Light Microscopy (LM)
Electron Microscopy (EM)
Brightfield
(unstained specimen)
Confocal
Longitudinal section
of cilium
Cross section
of cilium
50 m
Cilia
50 m
Brightfield
(stained specimen)
2 m
2 m
Deconvolution
10 m
Phase-contrast
Differential-interferencecontrast (Nomarski)
Scanning electron
microscopy (SEM)
Transmission electron
microscopy (TEM)
Electron microscopes (EMs) are used to
study subcellular structures
LMs can magnify effectively to about 1,000
times the size of the actual specimen
Super-resolution
Scientists use microscopes to visualize
cells too small to see with the naked eye
10 m
1 m
Fluorescence
Exploring microscopy
Brightfield
(stained specimen)
Exploring microscopy
Three important parameters of microscopy
Magnica;on, the ra;o of an objects image size
to its real size
Resolu;on, the measure of the clarity of the
image, or the minimum distance of two
dis;nguishable points
Contrast, visible dierences in parts of the sample
The Fundamental Units of Life
Basic features of all cells
Plasma membrane
Semiuid substance called cytosol
Chromosomes (carry genes)
Ribosomes (make proteins)
Prokaryo/c cells are characterized by having
No nucleus
DNA in an unbound region called the nucleoid
No membranebound organelles
Cytoplasm by bound the plasma membrane
Prokaryo;c Cells
Fimbriae
Nucleoid
Ribosomes
Plasma
membrane
Bacterial
chromosome
Cell wall
Capsule
(a) A typical
rod-shaped
bacterium
Flagella
0.5 m
(b) A thin section
through the
bacterium Bacillus
coagulans (TEM)
Eukaryo;c Cells
Eukaryo/c cells are characterized by having
DNA in a nucleus that is bounded by a membranous nuclear
envelope
Membranebound organelles
Cytoplasm in the region between the plasma membrane and
nucleus
Eukaryo;c cells are generally much larger than prokaryo;c cells
The plasma membrane is a selec;ve barrier that allows sucient
passage of oxygen, nutrients, and waste to service the volume of
every cell
The general structure of a biological membrane is a double layer of
phospholipids
Panoramic view of animal cell
ENDOPLASMIC RETICULUM (ER)
Flagellum
Rough Smooth
ER
ER
Nuclear
envelope
NUCLEUS
Nucleolus
Chromatin
Centrosome
Plasma
membrane
CYTOSKELETON:
Microfilaments
Intermediate filaments
Microtubules
Ribosomes
Microvilli
Golgi apparatus
Peroxisome
Mitochondrion
Lysosome
Panoramic view of plant cell
Nuclear
envelope
NUCLEUS Nucleolus
Chromatin
Rough
endoplasmic
reticulum
Smooth
endoplasmic
reticulum
Ribosomes
Central vacuole
Golgi
apparatus
Microfilaments
Intermediate
filaments
Microtubules
CYTOSKELETON
Mitochondrion
Peroxisome
Plasma membrane
Chloroplast
Cell wall
Wall of adjacent cell
Plasmodesmata
Plant and animal cells have most of the
same organelles
Cells gene;c instruc;ons are
housed in the nucleus
8 m
5 m
Cell
Cell wall
Flagella
1 m
Protistan Cells
Plant Cells
Nucleus
Chloroplast
Nucleolus
Mitochondrion
Vacuole
Nucleus
Nucleolus
Chloroplast
Chlamydomonas
(colorized SEM)
Cells from duckweed
(colorized TEM)
Animal Cells
1 0 m
Fungal Cells
Chlamydomonas
(colorized TEM)
1 m
Cell wall
Vacuole
Buds
5 m
Cell
Nucleus
Nucleolus
Human cells from lining
of uterus (colorized TEM)
Parent
cell
Cell wall
Nucleus
Mitochondrion
Yeast cells budding
(colorized SEM)
A single yeast cell
(colorized TEM)
The nucleus
In the nucleus, DNA is organized into discrete units
called chromosomes
Each chromosome is composed of a single DNA
molecule associated with proteins
The DNA and proteins of chromosomes are together
called chroma/n
Chroma;n condenses to form discrete chromosomes
as a cell prepares to divide
The nucleolus is located within the nucleus and is the
site of ribosomal RNA (rRNA) synthesis
Gene;c instruc;ons are housed in nucleus
1 m
Nucleus
Nucleolus
Chromatin
Nuclear envelope:
Inner membrane
Outer membrane
Nuclear pore
Pores regulate the entry
and exit of molecules from
the nucleus
Surface of nuclear
envelope
Rough ER
Pore
complex
Ribosome
Chromatin
1 m
0.25 m
Close-up
of nuclear
envelope
Pore complexes (TEM)
Nuclear lamina (TEM)
Cells gene;c instruc;ons are
housed in the nucleus
Nucleus contains most of the DNA in a eukaryo;c cell
The nucleus contains most of the cells genes and is
usually the most conspicuous organelle
The nuclear envelope encloses the nucleus, separa;ng
it from the cytoplasm
The nuclear membrane is a double membrane; each
membrane consists of a lipid bilayer
The shape of the nucleus is maintained by the nuclear
lamina
The endomembrane system regulates
protein trac
Smooth ER
Nuclear
envelope
Rough ER
ER lumen
Cisternae
Ribosomes
Transport vesicle
Transitional ER
The Endoplasmic Re;culum:
Biosynthe;c Factory
The endoplasmic re/culum (ER) accounts for more
than half of the total membrane in many eukaryo;c
cells
The ER membrane is con;nuous with the nuclear
envelope
There are two dis;nct regions of ER
Smooth ER, which lacks ribosomes
Rough ER, surface is studded with ribosomes
Func4ons of Smooth & Rough ER
The smooth ER
Synthesizes lipids
Metabolizes carbohydrates
Detoxies drugs and poisons
Stores calcium ions
The rough ER
Has bound ribosomes, which secrete glycoproteins
(proteins covalently bonded to carbohydrates)
Distributes transport vesicles, proteins surrounded by
membranes
Is a membrane factory for the cell
The endomembrane system
Nucleus
Rough ER
Smooth ER
cis Golgi
trans Golgi
Plasma
membrane
The endomembrane system regulates
protein trac and performs metabolic
func;ons in the cell
Components of the endomembrane system
Nuclear envelope
Endoplasmic re;culum
Golgi apparatus
Lysosomes
Vacuoles
Plasma membrane
These components are either con;nuous or
connected via transfer by vesicles
The Golgi Apparatus
Golgi app consists of acened membranous sacs called cisternae
Func;ons of the Golgi apparatus
Modies products of the ER
Manufactures certain macromolecules
Sorts and packages materials into transport vesicles
cis face
(receiving side of
Golgi apparatus)
0.1 m
Cisternae
trans face
(shipping side of
Golgi apparatus)
TEM of Golgi apparatus
Lysosomes: Diges;ve Compartments
Nucleus
Vesicle containing
two damaged
organelles
1 m
1 m
Mitochondrion
fragment
Peroxisome
fragment
Lysosome
Digestive
enzymes
Lysosome
Lysosome
Plasma membrane
Peroxisome
Digestion
Food vacuole
Vesicle
(a) Phagocytosis
Mitochondrion
Digestion
(b) Autophagy
Lysosome is a membranous sac of hydroly;c enzymes that can digest macromolecules
Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids
Lysosomal enzymes work best in the acidic environment inside the lysosome
Lysosomes: Diges;ve Compartments
Some types of cell can engulf another cell by
phagocytosis; this forms a food vacuole
A lysosome fuses with the food vacuole and digests
the molecules
Lysosomes also use enzymes to recycle the cells own
organelles and macromolecules, a process called
autophagy
Vacuoles: Diverse Maintenance
Compartments
Food vacuoles are
formed by phagocytosis
Contrac/le vacuoles,
Central
found in many
Nucleus
vacuole
freshwater pro;sts,
Cell wall
pump excess water out
Chloroplast
5 m of cells
A plant cell or fungal cell may have one or
Central vacuoles, found
several vacuoles, derived from endoplasmic
in many mature plant
reticulum and Golgi apparatus
cells, hold organic
compounds and water
Cytosol
Mitochondria and chloroplasts change
energy from one form to another
Mitochondria are the sites of cellular respira;on, a
metabolic process that uses oxygen to generate ATP
Chloroplasts, found in plants and algae, are the sites of
photosynthesis
Peroxisomes are oxida;ve organelles
Mitochondria and chloroplasts have similari;es with
bacteria
Enveloped by a double membrane
Contain free ribosomes and circular DNA molecules
Grow and reproduce somewhat independently in cells
Mitochondria and chloroplasts change
energy from one form to another
Intermembrane space
Outer
membrane
DNA
Free
ribosomes
in the
mitochondrial
matrix
Inner
membrane
Cristae
Matrix
(a) Diagram and TEM of mitochondrion
0.1 m
Mitochondria: Chemical Energy
Conversion
Mitochondria are in nearly all eukaryo;c cells
They have a smooth outer membrane and an inner
membrane folded into cristae
The inner membrane creates two compartments:
intermembrane space and mitochondrial matrix
Some metabolic steps of cellular respira;on are catalyzed
in the mitochondrial matrix
Cristae present a large surface area for enzymes that
synthesize ATP
Chloroplasts Capture Light Energy
Ribosomes
Stroma
Inner and outer
membranes
Granum
DNA
Intermembrane space
Thylakoid
(a) Diagram and TEM of chloroplast
1 m
Chloroplasts Capture Light Energy
Chloroplasts contain the green pigment chlorophyll, as
well as enzymes and other molecules that func;on in
photosynthesis
Chloroplasts are found in leaves and other green organs
of plants and in algae
Chloroplast structure includes
Thylakoids, membranous sacs, stacked to form a
granum
Stroma, the internal uid
The chloroplast is one of a group of plant organelles,
called plas/ds