KEY CONCEPTS
5.1 Macromolecules are polymers, built from monomers
5.2 Carbohydrates serve as fuel and building material
5.3 Lipids are a diverse group of hydrophobic molecules
5.4 Proteins include a diversity of structures, resulting in a wide range of functions
5.5 Nucleic acids store, transmit, and help express hereditary
information
5.6 Genomics and proteomics have transformed biological inquiry and applications
This is an interactive teacher's resource for IB Biology. It illustrates the concepts of hydrolysis and condensation reactions using jmol images of molecules?
This is an interactive teacher's resource for IB Biology. It illustrates the concepts of hydrolysis and condensation reactions using jmol images of molecules?
biological molecules .
CARBOHYDRATES, FATS AND PROTEINS.
includes how large molecules are made from smaller ones, their functions, etc.
made in a very interactive way so that students can understand and clear all their concepts
Lipids (Greek: lipos, means fat or lard)
- are a heterogeneous class of naturally occurring organic substances
- have a distinguished functional group or structural features
- are insoluble in water and highly soluble in one or more of the solvents: ether, chloroform, benzene and acetone.This property sets them apart from proteins, carbohydrates,, nucleic acids and other biomolecules
- are widely distributed in the biological world
- play a wide variety of roles in plant and animal tissues
KEY CONCEPTS
10.1 Photosynthesis converts light energy to the chemical energy of food
10.2 The light reactions convert solar energy to the chemical energy of ATP and NADPH
10.3 The Calvin cycle uses the chemical energy of ATP and NADPH to reduce CO2 to sugar
10.4 Alternative mechanisms of carbon fixation have evolved in hot, arid climates
KEY CONCEPTS
14.1 Mendel used the scientific approach to identify two laws of inheritance
14.2 Probability laws govern Mendelian inheritance
14.3 Inheritance patterns are often more complex than predicted by simple Mendelian genetics
14.4 Many human traits follow Mendelian patterns of
inheritance
biological molecules .
CARBOHYDRATES, FATS AND PROTEINS.
includes how large molecules are made from smaller ones, their functions, etc.
made in a very interactive way so that students can understand and clear all their concepts
Lipids (Greek: lipos, means fat or lard)
- are a heterogeneous class of naturally occurring organic substances
- have a distinguished functional group or structural features
- are insoluble in water and highly soluble in one or more of the solvents: ether, chloroform, benzene and acetone.This property sets them apart from proteins, carbohydrates,, nucleic acids and other biomolecules
- are widely distributed in the biological world
- play a wide variety of roles in plant and animal tissues
KEY CONCEPTS
10.1 Photosynthesis converts light energy to the chemical energy of food
10.2 The light reactions convert solar energy to the chemical energy of ATP and NADPH
10.3 The Calvin cycle uses the chemical energy of ATP and NADPH to reduce CO2 to sugar
10.4 Alternative mechanisms of carbon fixation have evolved in hot, arid climates
KEY CONCEPTS
14.1 Mendel used the scientific approach to identify two laws of inheritance
14.2 Probability laws govern Mendelian inheritance
14.3 Inheritance patterns are often more complex than predicted by simple Mendelian genetics
14.4 Many human traits follow Mendelian patterns of
inheritance
Chapter 50: Sensory and Motor MechansimsAngel Vega
KEY CONCEPTS
50.1 Sensory receptors transduce stimulus energy and transmit signals to the central nervous system
50.2 The mechanoreceptors responsible for hearing and
equilibrium detect moving fluid or settling particles
50.3 The diverse visual receptors of animals depend on light-
absorbing pigments
50.4 The senses of taste and smell rely on similar sets of sensory receptors
50.5 The physical interaction of protein filaments is required for muscle function
50.6 Skeletal systems transform muscle contraction into
locomotion
Chapter 15: Chromosomal Basis of InheritanceAngel Vega
KEY CONCEPTS
15.1 Morgan showed that Mendelian inheritance has its physical
basis in the behavior of chromosomes: Scientific inquiry
15.2 Sex-linked genes exhibit unique patterns of inheritance
15.3 Linked genes tend to be inherited together because they are located near each other on the same chromosome
15.4 Alterations of chromosome number or structure cause
some genetic disorders
15.5 Some inheritance patterns are exceptions to standard
Mendelian inheritance
KEY CONCEPTS
9.1 Catabolic pathways yield energy by oxidizing organic
fuels
9.2 Glycolysis harvests chemical energy by oxidizing glucose to pyruvate
9.3 After pyruvate is oxidized, the citric acid cycle completes the energy-yielding oxidation of organic molecules
9.4 During oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis
9.5 Fermentation and anaerobic respiration enable cells to
produce ATP without the use of oxygen
9.6 Glycolysis and the citric acid cycle connect to many other metabolic pathways
KEY CONCEPTS
4.1 Organic chemistry is the study of carbon compounds
4.2 Carbon atoms can form diverse molecules by bonding to four other atoms
4.3 A few chemical groups are key to molecular function
KEY CONCEPTS
6.1 Biologists use microscopes and the tools of biochemistry to
study cells
6.2 Eukaryotic cells have internal membranes that
compartmentalize their functions
6.3 The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes
6.4 The endomembrane system regulates protein traffic and
performs metabolic functions in the cell
6.5 Mitochondria and chloroplasts change energy from one form to another
6.6 The cytoskeleton is a network of fibers that organizes structures and activities in the cell
6.7 Extracellular components and connections between cells help coordinate cellular activities
KEY CONCEPTS
11.1 External signals are converted to responses within the cell
11.2 Reception: A signaling molecule binds to a receptor protein, causing it to change shape
11.3 Transduction: Cascades of molecular interactions relay
signals from receptors to target molecules in the cell
11.4 Response: Cell signaling leads to regulation of transcription or cytoplasmic activities
11.5 Apoptosis integrates multiple cell-signaling pathways
KEY CONCEPTS
13.1 Offspring acquire genes from parents by inheriting
chromosomes
13.2 Fertilization and meiosis alternate in sexual life cycles
13.3 Meiosis reduces the number of chromosome sets from diploid to haploid
13.4 Genetic variation produced in sexual life cycles contributes to evolution
KEY CONCEPTS
43.1 In innate immunity, recognition and response rely on traits
common to groups of pathogens
43.2 In adaptive immunity, receptors provide pathogen-specific
recognition
43.3 Adaptive immunity defends against infection of body fluids and body cells
43.4 Disruptions in immune system function can elicit or exacerbate disease
KEY CONCEPTS
18.1 Bacteria often respond to environmental change by
regulating transcription
18.2 Eukaryotic gene expression is regulated at many stages
18.3 Noncoding RNAs play multiple roles in controlling gene
expression
18.4 A program of differential gene expression leads to the different cell types in a multicellular organism
18.5 Cancer results from genetic changes that affect cell cycle control
KEY CONCEPTS
48.1 Neuron structure and organization reflect function in information transfer
48.2 Ion pumps and ion channels establish the resting potential of a neuron
48.3 Action potentials are the signals conducted by axons
48.4 Neurons communicate with other cells at synapses
KEY CONCEPTS
12.1 Most cell division results in genetically identical daughter cells
12.2 The mitotic phase alternates with interphase in the cell cycle
12.3 The eukaryotic cell cycle is regulated by a molecular
control system
Chapter 16: Molecular Basis of InheritanceAngel Vega
KEY CONCEPTS
16.1 DNA is the genetic material
16.2 Many proteins work together in
DNA replication and repair
16.3 A chromosome consists of a DNA molecule packed together with proteins
KEY CONCEPTS
45.1 Hormones and other signaling molecules bind to target
receptors, triggering specific response pathways
45.2 Feedback regulation and coordination with the nervous system are common in endocrine signaling
45.3 Endocrine glands respond to diverse stimuli in regulating homeostasis, development,
and behavior
Bio chapter 2: A Chemical Connection to BiologyAngel Vega
KEY CONCEPTS
2.1 Matter consists of chemical elements in pure form and
in combinations called compounds
2.2 An element’s properties depend on the structure of its atoms
2.3 The formation and function of molecules depend on chemical bonding between atoms
2.4 Chemical reactions make and break chemical bonds
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Cancer cell metabolism: special Reference to Lactate Pathway
Bio Chapter 5: Macromolecules
1. Chapter 5: The Macromolecules of Life
• Within cells, small organic molecules are joined together to
form larger molecules
• Macromolecules are large molecules composed of thousands
of covalently connected atoms
• A polymer is a long molecule consisting of many similar
building blocks called monomers
e.g. proteins
2. Three of the four classes of life’s organic molecules are
polymers:
– Carbohydrates e.g. starch
– Proteins e.g. enzymes
– Nucleic acids e.g. DNA
Not really a polymer, but large
– Lipids e.g fats
3. The Synthesis and Breakdown of
Polymers
• Monomers form larger molecules by condensation
reactions called dehydration reactions (two
monomers bond through loss of a water)
• Polymers are disassembled to monomers by
hydrolysis, a reaction that is essentially the reverse
of the dehydration reaction
4. Figure 5.2
(a) Dehydration reaction: synthesizing a polymer
1 2 3
1 2 3 4
1 2 3 4
Dehydration removes a water
molecule, forming a new bond.
Short polymer Unlinked monomer
H2O
Longer polymer
H2O
(b) Hydrolysis: breaking down a polymer
Hydrolysis adds a water
molecule, breaking a bond.
1 2 3
5. Concept 5.2: Carbohydrates serve
as fuel and building material
• Carbohydrates include sugars and the polymers of sugars
• The simplest carbohydrates are monosaccharides, or single
sugars
• Carbohydrate macromolecules are polysaccharides, polymers
composed of many sugar building blocks
• Monosaccharides have molecular formulas that are usually
multiples of CH2O
• Glucose is the most common monosaccharide
• Monosaccharides are classified by location of the carbonyl
group and by number of carbons in the carbon skeleton
7. Figure 5.4
(a) Linear and ring forms
(b) Abbreviated ring structure
Be able to number the ring of glucose and ribose correctly!
8. LE 5-5
Glucose
Maltose
Fructose Sucrose
Glucose Glucose
Dehydration
reaction in the
synthesis of maltose
Dehydration
reaction in the
synthesis of sucrose
1–4
glycosidic
linkage
1–2
glycosidic
linkage
•A disaccharide is formed when a dehydration reaction joins two monosaccharides
•This covalent bond is called a glycosidic linkage
Be able to construct maltose, sucrose, and lactose if given
glucose, galactose, and fructose.
Alpha 1,4
Alpha 1,2
10. Polysaccharides
• Polysaccharides, the polymers of sugars, have
storage and structural roles
• The structure and function of a polysaccharide are
determined by its sugar monomers and the positions
of glycosidic linkages
• Starch, a storage polysaccharide of plants, consists
entirely of glucose monomers
• Plants store surplus starch as granules within
chloroplasts and other plastids
11. LE 5-6a
Chloroplast Starch
1 µm
Amylose
Starch: a plant polysaccharide
Amylopectin
α-14 linked glucose α 14 linked glucose
And α 16 branching
12. LE 5-6b
Mitochondria Glycogen granules
0.5 µm
Glycogen
Glycogen: an animal polysaccharide
•Glycogen is a storage
polysaccharide in
animals
•Humans and other
vertebrates store
glycogen mainly in liver
and muscle cells
•Same branching as
amylopectin except
more frequent and
shorter branches
13. LE 5-7
α Glucose
α and β glucose ring structures
β Glucose
Starch: 1–4 linkage of α glucose monomers.
Cellulose: 1–4 linkage of β glucose monomers.
•Like starch, cellulose is a
polymer of glucose, but the
glycosidic linkages differ
•The difference is based on
two ring forms for glucose:
alpha (α) and beta (β)
•Note placement of hydroxyls
on monomeric units in the
different polymers
14. • Polymers with alpha glucose are helical
• Polymers with beta glucose are straight
• In straight structures, H atoms on one strand can bond with
OH groups on other strands
• Parallel cellulose molecules held together this way are
grouped into microfibrils, which form strong building
materials for plants
17. •Enzymes that digest starch by hydrolyzing alpha linkages can’t hydrolyze
beta linkages in cellulose
•Cellulose in human food passes through the digestive tract as insoluble
fiber
•Some microbes use enzymes to digest cellulose
•Many herbivores, from cows to termites, have symbiotic relationships
with these microbes
18. •Chitin, another structural polysaccharide, is found in the exoskeleton
of arthropods (Beta linkage)
•Chitin also provides structural support for the cell walls of many
fungi
•Chitin can be used as surgical thread
19. Concept 5.3: Lipids
• Lipids are the one class of large biological molecules
that do not form true polymers
• The unifying feature of lipids is having little or no
affinity for water
• Lipids are hydrophobic because they consist mostly of
hydrocarbons, which form nonpolar covalent bonds
• The most biologically important lipids are fats,
phospholipids, and steroids
20. Dehydration reaction in the synthesis of a fat
Glycerol
Fatty acid
(palmitic acid)
•Fats are constructed from two types of smaller molecules: glycerol
and fatty acids
•Glycerol is a three-carbon alcohol with a hydroxyl group attached to
each carbon
•A fatty acid consists of a carboxyl group attached to a long carbon
skeleton
Fats
21. Ester linkage
Fat molecule (triacylglycerol)
In a fat, three fatty acids are joined to glycerol by an ester linkage,
creating a triacylglycerol, or triglyceride
22. •Fatty acids vary in length (number of
carbons) and in the number and locations of
double bonds
•Saturated fatty acids have the maximum
number of hydrogen atoms possible and no
double bonds
•Most animal fats are saturated; plant and
fish fats are generally unsaturated
•Saturated fats are solid at room
temperature
•A diet rich in saturated fats may contribute
to cardiovascular disease through plaque
deposits
23. Figure 5.10
(a) Saturated fat (b) Unsaturated fat
Structural
formula
of a saturated
fat molecule
Space-filling
model of
stearic acid,
a saturated
fatty acid
Structural
formula of an
unsaturated
fat molecule
Space-filling
model of oleic
acid, an
unsaturated
fatty acid Cis double
bond causes
bending.
24. Structural formula Space-filling model Phospholipid symbol
Hydrophilic
head
Hydrophobic
tails
Fatty acids
Choline
Phosphate
Glycerol
HydrophobictailsHydrophilicheadPhospholipids In a phospholipid, two
fatty acids and a
phosphate group are
attached to glycerol
The two fatty acid tails
are hydrophobic, but the
phosphate group and its
attachments form a
hydrophilic head
26. • Steroids are lipids characterized by a carbon
skeleton consisting of four fused rings
• Cholesterol, an important steroid, is a component in
animal cell membranes
27. 1. Lipids cannot be considered
polymers because
a. they contain polar covalent bonds.
b. their structure includes carbon rings.
c. they can be artificially created.
d. their monomers are connected via ionic
bonds.
e. they are not composed of monomer
subunits.
28. 1. Lipids cannot be considered
polymers because
a. they contain polar covalent bonds.
b. their structure includes carbon rings.
c. they can be artificially created.
d. their monomers are connected via ionic
bonds.
e. they are not composed of monomer
subunits.
30. Figure 5.13a
Enzymatic proteins
Function: Selective acceleration of
chemical reactions
Example: Digestive enzymes catalyze the
hydrolysis of bonds in food molecules.
Enzyme
Storage proteins
Function: Storage of amino acids
Examples: Casein, the protein of milk, is the
major source of amino acids for baby
mammals. Plants have storage proteins in
their seeds. Ovalbumin is the protein of egg
white, used as an amino acid source for the
developing embryo.
Ovalbumin Amino acids
for embryo
Defensive proteins
Function: Protection against disease
Example: Antibodies inactivate and help
destroy viruses and bacteria.
Virus
Antibodies
Bacterium
Transport proteins
Function: Transport of substances
Examples: Hemoglobin, the iron-containing
protein of vertebrate blood, transports
oxygen from the lungs to other parts of the
body. Other proteins transport molecules
across membranes, as shown here.
Transport
protein
Cell membrane
31. Figure 5.13b
Function: Coordination of an organism’s
activities
Example: Insulin, a hormone secreted by the
pancreas, causes other tissues to take up
glucose, thus regulating blood sugar,
concentration.
High
blood sugar
Insulin
secreted
Hormonal proteins
Normal
blood sugar
Function: Response of cell to chemical
stimuli
Example: Receptors built into the
membrane of a nerve cell detect
signaling molecules released by other
nerve cells.
Receptor proteins
Signaling
molecules
Receptor
protein
Function: Movement
Examples: Motor proteins are responsible
for the undulations of cilia and flagella.
Actin and myosin proteins are responsible
for the contraction of muscles.
Contractile and motor proteins
Function: Support
Examples: Keratin is the protein of hair,
horns, feathers, and other skin
appendages. Insects and spiders use silk
fibers to make their cocoons and webs,
respectively. Collagen and elastin proteins
provide a fibrous framework in animal
connective tissues.
Structural proteins
Muscle
tissue
30 µm
Actin MyosinActin
60 µm
Connective
tissue
Collagen
32. Amino Acid Monomers
• Amino acids are organic molecules with carboxyl
and amino groups
• Amino acids differ in their properties due to
differing side chains, called R groups
• Cells use 20 amino acids to make thousands of
proteins
Polypeptides are polymers of amino acids
A protein consists of one or more polypeptides
Polypeptides
34. Figure 5.14
Nonpolar side chains; hydrophobic
Side chain (R group)
Glycine
(Gly or G)
Alanine
(Ala or A)
Valine
(Val or V)
Leucine
(Leu or L)
Isoleucine
(Ile or I)
Proline
(Pro or P)
Tryptophan
(Trp or W)
Phenylalanine
(Phe or F)
Methionine
(Met or M)
Polar side chains; hydrophilic
Electrically charged side chains; hydrophilic
Aspartic acid
(Asp or D)
Glutamic acid
(Glu or E)
Lysine
(Lys or K)
Arginine
(Arg or R)
Histidine
(His or H)
Glutamine
(Gln or Q)
Acidic (negatively charged)
Basic (positively charged)
Asparagine
(Asn or N)
Tyrosine
(Tyr or Y)
Cysteine
(Cys or C)
Threonine
(Thr or T)
Serine
(Ser or S)
Know how to
draw:
glycine,
valine,
cysteine,
glutamine,
glutamic
acid, lysine
and put them
into dipeptide
form
35. Amino Acid Polymers
Amino acids
are linked by
peptide bonds
A polypeptide
is a polymer of
amino acids
36. Figure 5.16
(a) A ribbon model (b) A space-filling model (c) A wireframe model
Groove
Groove
Target
molecule
Different models have different uses e.g. secondary structure or amino-
acid contact sites
37. Four Levels of Protein Structure
• The primary structure of a protein is its unique
sequence of amino acids
• Secondary structure, found in most proteins,
consists of coils and folds in the polypeptide
chain
• Tertiary structure is determined by interactions
among various side chains (R groups)
• Quaternary structure results when a protein
consists of multiple polypeptide chains
39. LE 5-20d
Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone
Disulfide bridge
Ionic bond
Hydrogen
bond
Tertiary structure is
determined by interactions
between R groups, rather
than interactions between
backbone constituents
These interactions
between R groups include
hydrogen bonds, ionic
bonds, hydrophobic
interactions, and van der
Waals interactions
Strong covalent bonds
called disulfide bridges
may reinforce the protein’s
conformation
40. Sickle-Cell Disease: A Simple Change in
Primary Structure
• A slight change in primary structure can affect a
protein’s conformation and ability to function
• Sickle-cell disease, an inherited blood disorder,
results from a single amino acid substitution in the
protein hemoglobin
41. Molecules do not associate
with one another; each carries oxygen.
42. What Determines Protein Structure?
• In addition to primary structure, physical and
chemical conditions can affect structure
• Alterations in pH, salt concentration,
temperature, or other environmental factors
can cause a protein to unravel
• This loss of a protein’s native structure is
called denaturation
• A denatured protein is biologically inactive
43. The Protein-Folding Problem
• It is hard to predict a protein’s conformation from its
primary structure
• Most proteins probably go through several states on
their way to a stable conformation
• Chaperonins are protein molecules that assist the
proper folding of other proteins
44. Figure 5.21
Hollow
cylinder
Cap
Chaperonin
(fully
assembled)
Polypeptide
1 An unfolded
polypeptide
enters the
cylinder
from
one end.
2 Cap attachment
causes the
cylinder to
change shape,
creating a
hydrophilic
environment
for polypeptide
folding.
3 The cap
comes off,
and the
properly
folded
protein is
released.
Correctly folded
protein
45. LE 5-24a
Photographic film
Diffracted X-rays
X-ray
source
X-ray
beam
X-ray
diffraction pattern
Crystal
•Scientists use X-ray crystallography to determine a protein’s
conformation
•Another method is nuclear magnetic resonance (NMR) spectroscopy,
which does not require protein crystallization
47. The Roles of Nucleic Acids
• There are two types of nucleic acids:
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
• DNA provides directions for its own replication
• DNA directs synthesis of messenger RNA (mRNA) and,
through mRNA, controls protein synthesis
• Protein synthesis occurs in ribosomes
49. The Structure of Nucleic Acids
• Nucleic acids are polymers called polynucleotides
• Each polynucleotide is made of monomers called
nucleotides
• Each nucleotide consists of a nitrogenous base, a
pentose sugar, and a phosphate group
• The portion of a nucleotide without the phosphate
group is called a nucleoside
50. LE 5-26a
5′ end
3′ end
Nucleoside
Nitrogenous
base
Phosphate
group
Nucleotide
Polynucleotide, or
nucleic acid
Pentose
sugar
51. LE 5-26b
Nitrogenous bases
Pyrimidines
Purines
Pentose sugars
Cytosine
C
Thymine (in DNA)
T
Uracil (in RNA)
U
Adenine
A
Guanine
G
Deoxyribose (in DNA)
Nucleoside components
Ribose (in RNA)
Be able to
recognize
each base &
the hydrogen
bonding
pattern
between base
pairs.
When given the
bases, sugars, and a
phosphate structure,
be able to construct a
nucleotide pair.
Pyrimidines are CUT!
53. Nucleotide Polymers
• Nucleotide polymers are linked together,
building a polynucleotide
• Adjacent nucleotides are joined by covalent
bonds that form between the –OH group on the
3´ carbon of one nucleotide and the phosphate
on the 5´ carbon on the next
• These links create a backbone of sugar-
phosphate units with nitrogenous bases as
appendages
• The sequence of bases along a DNA or mRNA
polymer is unique for each gene
54. The DNA Double Helix
• A DNA molecule has two polynucleotides spiraling
around an imaginary axis, forming a double helix
• In the DNA double helix, the two backbones run in
opposite 5´ to 3´ directions from each other, an
arrangement referred to as antiparallel
• One DNA molecule includes many genes
• The nitrogenous bases in DNA form hydrogen bonds in
a complementary fashion: A always with T, and G
always with C
55. LE 5-27
Sugar-phosphate
backbone
3′ end5′ end
Base pair (joined by
hydrogen bonding)
Old strands
Nucleotide
about to be
added to a
new strand
5′ end
New
strands
3′ end
5′ end3′ end
5′ end
56. DNA and Proteins as Tape Measures of
Evolution
• The linear sequences of nucleotides in DNA molecules
are passed from parents to offspring
• Two closely related species are more similar in DNA
than are more distantly related species
• Molecular biology can be used to assess evolutionary
kinship
57. DNA and polypeptide sequences from closely related species are more similar to
each other than sequences from more distantly related species. For the remaining
questions, you will look at amino acid sequence data for the β polypeptide chain of
hemoglobin, often called β-globin. You will then interpret the data to hypothesize
whether the monkey or the gibbon is more closely related to humans.
In the alignment shown below, the letters give the sequences of the 146 amino acids
in β-globin from humans, rhesus monkeys, and gibbons. Because a complete
sequence would not fit on one line, the sequences are broken into segments. The
sequences for the three different species are aligned so that you can compare them
easily. For example, you can see that, for all three species, the first amino acid is “V”
(valine) and the 146th amino acid is “H” (histidine).
Create a cladogram for human, monkey, and gibbon based on data below.
58. The Theme of Emergent Properties in the
Chemistry of Life: A Review
• Higher levels of organization result in the emergence of new
properties
Explain the new properties for each of the 4 groups of
Biomolecules
(Hint: see page 90 for emergent properties overview)
• Organization is the key to the chemistry of life
Editor's Notes
Figure 5.2 The synthesis and breakdown of polymers
Figure 5.4 Linear and ring forms of glucose
Figure 5.6 Polysaccharides of plants and animals
Figure 5.10 Saturated and unsaturated fats and fatty acids
Answer: E
Answer: E
Figure 5.13a An overview of protein functions (part 1)
Figure 5.13b An overview of protein functions (part 2)
Figure 5.14 The 20 amino acids of proteins
Figure 5.16 Structure of a protein, the enzyme lysozyme