Chapter 5: The Structure and Function of Large Biological Molecules
all living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins and nucleic acids
macromolecules: large and complex molecules
the architecture of a large biological molecule plays an essential role in its function
FORM = FUNCTION
large biological molecules have unique properties that arise from the orderly arrangement of their atoms
polymer: long molecule consisting of many similar building blocks
monomer: the repeating unit that serves as a building block of polymers
carbohydrates, proteins, and nucleic acids are polymer -- NOT LIPIDS
although each class of polymer is made up of a different type of monomer, the chemical mechanisms by which cells make and break down polymers are basically the same in all cases
enzymes: specialized macromolecules (proteins) that speed up chemical reactions such as those that make or break down polymers
dehydration reaction: occurs when two monomers covalently bond together through the loss of a water molecule to form parts of a polymer
each monomer contributes to a part of the water molecule that is formed through this reaction
this process is also called polymerization
hydrolysis: process that disassembles polymers → reverse of dehydration synthesis
uses pressure to break the bond and adding a water molecule to the free bonds
without water, those empty bonds can virtually bond with anything and become poison
however, hydrolysis does not only occur in polymer - material doesn’t have to be a polymer
variety in molecules is due to the fact that many different polymers can be created from similar or same monomers → variation occurs when the arrangement is modified
small molecules common to all organisms act as building blocks that are ordered into unique macromolecules
least variation is seen within the same organism, while the greatest variety is seen across different species
carbohydrates: sugars and the polymers of sugars
almost everything in the body can be broken down into carbohydrates because they are needed for energy
even protein can be broken down into carbs
monosaccharides: simple sugars → simplest carbohydrates
have multiples of the molecule formula CH2O
classified by the location of the carbonyl group (aldose or ketose) and the number of carbons in the carbon skeleton (ex. triose, pentose, hexose)
another source of diversity, is in the way their parts are arranged spatially around an asymmetric carbon - where the different groups are attached to a central carbon atom
most common is glucose (C6H12O6) → alpha and beta glucose only exist randomly when in water due to how the bonds bend when in water
different glucose molecules of glucose only differ by where their double bonded oxygen is located, making it either an aldose or ketose sugar
most five or six carbon monosaccharides form rings in water as a hydration shell bends the linear structure into a more stable structure
monosaccharides serve as a major fuel for cells and as raw material for building molecules
disaccharide (oligosaccharide): two monosaccharides joined by a glycosidic linkage
glycosidic linkage: covalent bond between two monosaccharides by a dehydration reaction
maltose: alpha glucose + alpha glucose
sucrose: alpha glucose + fructose
lactose: alpha glucose + galactose
Know how to draw and recognize the molecules
polysaccharides: polymers composed of many sugar monomers (carbohydrate macromolecules)
have storage and structural roles
contain a large number of monosaccharide units bonded to each other by a series of glycosidic bonds
storage:
starch (storage polysaccharide for plants) consists of glucose monomers → plant version of glycogen in animals
plants store surplus starch as granules within chloroplasts and other plastids
simplest form of starch is amylose
glycogen (storage polysaccharide in animals) → stored in liver and muscle cells (for energy)
hydrolysis of glycogen in these cells releases glucose when the demand for sugar increases
easiest to break down in our bodies
if you have fat around your liver, it means that your body turned starch into fat and formed a lining, which is not good for you
structure:
cellulose: major component in the tough walls of plant cells
polymer of glucose, like starch, but has different glycosidic bonds (has beta bonds)
the difference is based on two ring forms for glucose: alpha and beta
chitin: structural polysaccharide found in the exoskeleton of arthropods
also provides structural support for the cell walls of many fungi
differences:
structural polysaccharides are made up of beta glycosidic linkages, while storage polysaccharides are made up of alpha glycosidic linkages
Starch is helical due to alpha configuration
Cellulose is straight and unbranched due to beta configuration
Certain hydroxyl groups on cellulose monomers can hydrogen-bond with hydrogen on parallel cellulose monomers
enzymes that digest starch by hydrolyzing alpha linkages can’t hydrolyze beta linkages in cellulose → different arrangements, won’t fit in enzyme
the cellulose in human food passes through the digestive tract as “insoluble fiber”
some microbes use enzymes to digest enzymes → without this enzyme cellulose physically can’t be brown down in any body
many herbivores have symbiotic relationships with these microbes, which is why they can process cellulose much better than people can
individual glucose molecules (mini carbs) are macromolecules, but not polysaccharides
lipids: the one class of large biological molecules that does not include true polymers, and are generally not big enough to be considered macromolecules
the unifying feature of lipids is that they mix poorly, if at all, with water
due to its molecular structure → consists mostly of hydrocarbon regions, which are nonpolar, and thus does not mix well with water
although fats are not polymers, they are large molecules assembled from dehydration reactions
fats are constructed from two types of smaller molecules: glycerol and fatty acids
glycerol is a three-carbon alcohol with a hydroxyl group (OH) attached to each carbon
fatty acids consist of a carboxyl group attached to a long carbon skeleton
formed through dehydration synthesis
in a fat, three fatty acid chains are joined to glycerol by an ester linkage (esterification), creating a triacylglycerol or triglyceride
fatty acids in a fat can be all the same or of two or three different kinds
this is why fats are not polymers because they do not always have the same monomer and are made up of two or more different molecules put together
saturated fatty acids: have the maximum number of hydrogen atoms possible and no double bonds
form fats that are unhealthy for the body in large quantities → must control consumption
usually solid at room temperature
most animal fats are saturated
unsaturated fatty acids: have one or more double bond
there are unbonded hydrogens in its structure, which means that it can bond to anything on these H
polyunsaturated lipids: have more than one double bond (very healthy for you)
usually liquid or oil at room temperature due to “kinks” in fatty acid chains (due to cis structure) that cause the fat molecules to not be able to pack close together
plant fats and fish fats are usually unsaturated
hydrogenation: the process of converting unsaturated fats to saturated fat by adding hydrogen
hydrogenating vegetable oils also creates unsaturated fats with trans double bonds (very unhealthy and extremely hard to get rid of)
to become a trans fat, a hydrogen or OH on a carbon will switch sides under pressure or heat and become a trans fat
trans fats start as a cis fat, then the H or OH switches under high pressure or heat
to be a trans fat, the fat must be unsaturated for the double bond to be there
these trans fats may contribute more than saturated fats to cardiovascular disease
the major function of fats is energy storage
humans and other mammals store their long-term food reserves in adipose cells
adipose tissue also cushions vital organs and insulates the body
plants store starches in seeds → compact method, good for immobile beings
a diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits
not guaranteed diseases because factors such as genetics and environment, etc, also contribute
fats are also good because they are needed by your body -- ex. insulation and neurons
if fat coat on neurons disintegrates, the neurons can’t communicate with body probably
this is what happens in Parkinson’s disease → neurons can’t communicate with muscles
phospholipids are essential for cells because they are major constituents of cell membranes
phospholipids have two fatty acid chains and a phosphate group attached to a glycerol
they two fatty acid tails are hydrophobic, but the phosphate groups and its attachments form a hydrophilic head
they have one bent tail and one straight tail to allow the cell membrane to remain semi-permeable
if both were straight, the lipids would be too close together, not allowing anything to pass in or out of cell membranes, and if they were both bent, they would be too far apart, causing a lack of control
bent tail is an unsaturated fatty acid (due to kink of cis bond), and straight tail is saturated
the head of the phospholipid is charged, which allows it to form bonds with other molecules
when phospholipids are added to water, they self-assemble into double-layered sheets called bilayers
at the surface of a cell, phospholipids are also arranged in a bilayer, with the hydrophobic tails pointing towards the interior
this forms a boundary between the cell and its external environment
steroids: lipids characterized by a carbon skeleton consisting of four fused rings
steroid backbone: 3 cyclohexanes (one with a double bond), 1 pentane
cholesterol: type of steroid that is a component in animal cell membranes and a precursor from which other steroids are synthesized
high levels of cholesterol in the blood may contribute to cardiovascular disease
proteins account for more than 50% of the dry mass of most cells
some proteins speed up chemical reactions → enzymes
enzymes reduce the amount of initial energy for the reaction to happen so that it SEEMS to be occurring faster
enzymatic proteins regulate metabolism by acting as catalysts
ALL ENZYMES ARE PROTEINS BUT NOT ALL PROTEINS ARE ENZYMES
enzymes have specific shapes and need specific conditions to work and be effective
other protein functions include defense, storage, transport, cellular communication, movement, and structural support
proteins are all constructed from the same set of 20 amino acids, linked in unbranched polymers
peptide bond: bond between amino acids forming a polymer
polypeptide: unbranched polymers of amino acids
protein: biologically functional molecule made up of polypeptides, each folded and coiled into a specific three-dimensional structure
almost all proteins can be broken down into urea when they are not needed anymore, so that it can be released from the body as urine
water soluble proteins are easier to break down into urea than other proteins
enzymatic proteins:
selective acceleration of chemical reactions
ex. digestive enzymes catalyze the hydrolysis of bonds in food molecules
storage proteins:
storage of amino acids
ex. Casein, the protein of milk, is the major source of amino acids for baby mammals
defensive proteins:
protection against disease
ex. antibodies inactivate and help destroy viruses and bacteria → tell white blood cells which dangerous cells need to be destroyed
transport proteins:
transport of substances
ex. hemoglobin is a protein transports oxygen around the body
hormonal proteins:
coordination of an organism’s activities → helps cells, organs, and organ systems talk to each other
ex. insulin, secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar within the body → insulin unlocks channels in cells to allow glucose in (does not go into cells or break down glucose on its own)
contractile and motor proteins:
used for movement
ex. responsible for the undulations of cilia and flagella / actin and myosin proteins are responsible for the contraction of muscles
receptor proteins:
response of cell to chemical stimuli
ex. receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells
structural proteins:
used for support
ex. Keratin is the protein of hair, horns, feather, and other skin appendages
amino acids: organic molecules with amino (N-terminus) and carboxyl groups (C-terminus)
amino acids differ in their properties due to differing side chains, called R groups
non-polar side chains (hydrophobic)
electrically charged side chains (acid and base) (hydrophilic)
polar side chains (hydrophilic)
amino acids are linked by covalent bonds called peptide bonds
form of dehydration synthesis
OH from C-terminus of amino #1 and H from N-terminus of amino #2 form water and create a straight bond between the remaining C and N
3 amino acids = tripeptide , 4+ amino acids = polypeptide
each polypeptide has a unique linear sequence of amino acids, with a carboxyl end and an amino end
the specific activities of proteins result from their intricate three-dimensional architecture
as soon as polypeptide chains are formed, they have to be formed into a specific structure and taken to where it is to be used, if not, then spliceosomes come along and cut up the bonds so that the amino acids can be used again and recycled
B-cells remember how to build the antibodies (versions of the virus that still has the same protein but without the ability to multiply) - B-cells memorize the shape of the virus to quickly make the antibodies when they encounter the virus again
a functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape
the sequence of amino acids determines a protein’s three-dimensional structure and its structure determines how the protein works
the function of a protein usually depends on its ability to recognize and bind to some other molecule
proteins share three superimposed levels of structure → primary, secondary, and tertiary structure
primary structure:
a protein’s unique sequence of amino acids
like the order of letters in a long word
determined by inherited genetic information: DNA → RNA → polypeptide (this is how our body comes up with unique characteristics)
secondary structure:
consists of coils and folds in the polypeptide chain
result from hydrogen bonds between repeating constituents of the polypeptide backbone
can have alpha helix and beta pleated sheets together but held together loosely
tertiary structure:
overall shape of a polypeptide is determined by interactions among various side chains (R groups), rather than interactions between backbone constituents
interactions include hydrogen bonds, ionic bonds, hydrophobic interactions, and LDF
strong covalent bonds called disulfide bridges may reinforce the protein’s structure
more compressed together, forms a specific shape
quaternary structure:
results when a protein consists of two or more polypeptide chains
combinations of tertiary structures
Ex. collagen (3 polypeptides coiled) and hemoglobin (4 polypeptides - two alpha, two beta)
Factors Affecting Protein Structure
changed primary structure, pH, salt concentration, temperature, other environmental factors
denaturation: loss of a protein’s native structure
if a protein does not have its ideal conditions, it will become denatured, but if you return it to ideal conditions, it will return back to functioning normally
it is hard to predict a protein’s structure from its primary structure
most proteins probably go through several stages on their way to a stable structure
diseases such as Alzheimer’s, Parkinson’s, and mad cow disease are associated with misfolded proteins
the amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene
genes consist of DNA, a nucleic acid made of monomers called nucleotides
DNA is a carboxylic acid and a polymer (monomer made up of nitrogenous base, pentose sugar, and acid group)
there are two types of nucleic acid → deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
DNA provides directions for its own replication
DNA directs synthesis of messenger RNA (mRNA), and through mRNA, controls protein synthesis
This process is called gene expression
recessive and dominant genes are determined by their coiling → in the double helix, recessive genes will remain tight close to the dominant genes so that only the dominant gene is expressed / copied
the dominant gene unwinds to be read, copied, and transformed into RNA
Stages of Synthesis:
Synthesis of mRNA
mRNA made out of freed bases in the nucleus (DNA code determines code of RNA)
mRNA exits nucleus
Movement of mRNA in cytoplasm
Ribosome takes mRNA and reads the code
tRNA brings amino acids read from the “recipe” to the ribosome
Synthesis of Protein
tRNA carries amino acids to ribosomes
A chain of amino acids is formed
Protein is formed out of amino acids
each gene along a DNA molecule directs synthesis of a messenger RNA (mRNA)
the mRNA molecule interacts with the cell’s protein-synthesizing machinery to direction production of a polypeptide
the flow of genetic information can be summarized as DNA → RNA → polypeptide
nucleic acids are polymers called polynucleotides → same as saying DNA
each polynucleotide is made of monomers called nucleotides
each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups
free floating nucleotides will have three phosphate groups
if it is part of DNA, it will have one phosphate group
in DNA sugar is deoxyribose, in RNA the sugar is ribose
nucleoside: portion of a nucleotide without the phosphate group
SO nucleotide = nucleoside + phosphate group
nucleotides are linked together by a phosphodiester linkage to build a polynucleotide
phosphodiester linkage consists of a phosphate group that links the sugar of two nucleotides
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
DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a double helix
on almost all genes, only one side of the DNA is the actual gene, while the other side is just there for protection → only one strand might have the gene to be read
the backbone of DNA run in opposite 5’ → 3’ directions from each other, an arrangement referred to as antiparallel
5’ and 3’ come from which direction the carbons in the pentose sugar is pointing
the strands are also complementary to each other → makes it possible to generate two identical copies of each DNA molecule in a cell preparing to divide
RNA is single-stranded, meaning that it has more variable forms
complementary pairing can also occur between two RNA molecules or between parts of the same molecule
in RNA, thymine is replace with uracil (U)
once the structure of DNA and its relationship to amino acid sequence was understood, biologists sought to “decode” genes by learning their base sequences
the first chemical techniques for DNA sequencing were developed in the 1970s and refined over the next 20 years
it is enlightening to sequence the full complement of DNA in an organism’s genome
the rapid development of faster and less expensive methods of sequencing was a side effect of the Human Genome Project
Many genomes have been sequenced, generating large sets of data
all living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins and nucleic acids
macromolecules: large and complex molecules
the architecture of a large biological molecule plays an essential role in its function
FORM = FUNCTION
large biological molecules have unique properties that arise from the orderly arrangement of their atoms
polymer: long molecule consisting of many similar building blocks
monomer: the repeating unit that serves as a building block of polymers
carbohydrates, proteins, and nucleic acids are polymer -- NOT LIPIDS
although each class of polymer is made up of a different type of monomer, the chemical mechanisms by which cells make and break down polymers are basically the same in all cases
enzymes: specialized macromolecules (proteins) that speed up chemical reactions such as those that make or break down polymers
dehydration reaction: occurs when two monomers covalently bond together through the loss of a water molecule to form parts of a polymer
each monomer contributes to a part of the water molecule that is formed through this reaction
this process is also called polymerization
hydrolysis: process that disassembles polymers → reverse of dehydration synthesis
uses pressure to break the bond and adding a water molecule to the free bonds
without water, those empty bonds can virtually bond with anything and become poison
however, hydrolysis does not only occur in polymer - material doesn’t have to be a polymer
variety in molecules is due to the fact that many different polymers can be created from similar or same monomers → variation occurs when the arrangement is modified
small molecules common to all organisms act as building blocks that are ordered into unique macromolecules
least variation is seen within the same organism, while the greatest variety is seen across different species
carbohydrates: sugars and the polymers of sugars
almost everything in the body can be broken down into carbohydrates because they are needed for energy
even protein can be broken down into carbs
monosaccharides: simple sugars → simplest carbohydrates
have multiples of the molecule formula CH2O
classified by the location of the carbonyl group (aldose or ketose) and the number of carbons in the carbon skeleton (ex. triose, pentose, hexose)
another source of diversity, is in the way their parts are arranged spatially around an asymmetric carbon - where the different groups are attached to a central carbon atom
most common is glucose (C6H12O6) → alpha and beta glucose only exist randomly when in water due to how the bonds bend when in water
different glucose molecules of glucose only differ by where their double bonded oxygen is located, making it either an aldose or ketose sugar
most five or six carbon monosaccharides form rings in water as a hydration shell bends the linear structure into a more stable structure
monosaccharides serve as a major fuel for cells and as raw material for building molecules
disaccharide (oligosaccharide): two monosaccharides joined by a glycosidic linkage
glycosidic linkage: covalent bond between two monosaccharides by a dehydration reaction
maltose: alpha glucose + alpha glucose
sucrose: alpha glucose + fructose
lactose: alpha glucose + galactose
Know how to draw and recognize the molecules
polysaccharides: polymers composed of many sugar monomers (carbohydrate macromolecules)
have storage and structural roles
contain a large number of monosaccharide units bonded to each other by a series of glycosidic bonds
storage:
starch (storage polysaccharide for plants) consists of glucose monomers → plant version of glycogen in animals
plants store surplus starch as granules within chloroplasts and other plastids
simplest form of starch is amylose
glycogen (storage polysaccharide in animals) → stored in liver and muscle cells (for energy)
hydrolysis of glycogen in these cells releases glucose when the demand for sugar increases
easiest to break down in our bodies
if you have fat around your liver, it means that your body turned starch into fat and formed a lining, which is not good for you
structure:
cellulose: major component in the tough walls of plant cells
polymer of glucose, like starch, but has different glycosidic bonds (has beta bonds)
the difference is based on two ring forms for glucose: alpha and beta
chitin: structural polysaccharide found in the exoskeleton of arthropods
also provides structural support for the cell walls of many fungi
differences:
structural polysaccharides are made up of beta glycosidic linkages, while storage polysaccharides are made up of alpha glycosidic linkages
Starch is helical due to alpha configuration
Cellulose is straight and unbranched due to beta configuration
Certain hydroxyl groups on cellulose monomers can hydrogen-bond with hydrogen on parallel cellulose monomers
enzymes that digest starch by hydrolyzing alpha linkages can’t hydrolyze beta linkages in cellulose → different arrangements, won’t fit in enzyme
the cellulose in human food passes through the digestive tract as “insoluble fiber”
some microbes use enzymes to digest enzymes → without this enzyme cellulose physically can’t be brown down in any body
many herbivores have symbiotic relationships with these microbes, which is why they can process cellulose much better than people can
individual glucose molecules (mini carbs) are macromolecules, but not polysaccharides
lipids: the one class of large biological molecules that does not include true polymers, and are generally not big enough to be considered macromolecules
the unifying feature of lipids is that they mix poorly, if at all, with water
due to its molecular structure → consists mostly of hydrocarbon regions, which are nonpolar, and thus does not mix well with water
although fats are not polymers, they are large molecules assembled from dehydration reactions
fats are constructed from two types of smaller molecules: glycerol and fatty acids
glycerol is a three-carbon alcohol with a hydroxyl group (OH) attached to each carbon
fatty acids consist of a carboxyl group attached to a long carbon skeleton
formed through dehydration synthesis
in a fat, three fatty acid chains are joined to glycerol by an ester linkage (esterification), creating a triacylglycerol or triglyceride
fatty acids in a fat can be all the same or of two or three different kinds
this is why fats are not polymers because they do not always have the same monomer and are made up of two or more different molecules put together
saturated fatty acids: have the maximum number of hydrogen atoms possible and no double bonds
form fats that are unhealthy for the body in large quantities → must control consumption
usually solid at room temperature
most animal fats are saturated
unsaturated fatty acids: have one or more double bond
there are unbonded hydrogens in its structure, which means that it can bond to anything on these H
polyunsaturated lipids: have more than one double bond (very healthy for you)
usually liquid or oil at room temperature due to “kinks” in fatty acid chains (due to cis structure) that cause the fat molecules to not be able to pack close together
plant fats and fish fats are usually unsaturated
hydrogenation: the process of converting unsaturated fats to saturated fat by adding hydrogen
hydrogenating vegetable oils also creates unsaturated fats with trans double bonds (very unhealthy and extremely hard to get rid of)
to become a trans fat, a hydrogen or OH on a carbon will switch sides under pressure or heat and become a trans fat
trans fats start as a cis fat, then the H or OH switches under high pressure or heat
to be a trans fat, the fat must be unsaturated for the double bond to be there
these trans fats may contribute more than saturated fats to cardiovascular disease
the major function of fats is energy storage
humans and other mammals store their long-term food reserves in adipose cells
adipose tissue also cushions vital organs and insulates the body
plants store starches in seeds → compact method, good for immobile beings
a diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits
not guaranteed diseases because factors such as genetics and environment, etc, also contribute
fats are also good because they are needed by your body -- ex. insulation and neurons
if fat coat on neurons disintegrates, the neurons can’t communicate with body probably
this is what happens in Parkinson’s disease → neurons can’t communicate with muscles
phospholipids are essential for cells because they are major constituents of cell membranes
phospholipids have two fatty acid chains and a phosphate group attached to a glycerol
they two fatty acid tails are hydrophobic, but the phosphate groups and its attachments form a hydrophilic head
they have one bent tail and one straight tail to allow the cell membrane to remain semi-permeable
if both were straight, the lipids would be too close together, not allowing anything to pass in or out of cell membranes, and if they were both bent, they would be too far apart, causing a lack of control
bent tail is an unsaturated fatty acid (due to kink of cis bond), and straight tail is saturated
the head of the phospholipid is charged, which allows it to form bonds with other molecules
when phospholipids are added to water, they self-assemble into double-layered sheets called bilayers
at the surface of a cell, phospholipids are also arranged in a bilayer, with the hydrophobic tails pointing towards the interior
this forms a boundary between the cell and its external environment
steroids: lipids characterized by a carbon skeleton consisting of four fused rings
steroid backbone: 3 cyclohexanes (one with a double bond), 1 pentane
cholesterol: type of steroid that is a component in animal cell membranes and a precursor from which other steroids are synthesized
high levels of cholesterol in the blood may contribute to cardiovascular disease
proteins account for more than 50% of the dry mass of most cells
some proteins speed up chemical reactions → enzymes
enzymes reduce the amount of initial energy for the reaction to happen so that it SEEMS to be occurring faster
enzymatic proteins regulate metabolism by acting as catalysts
ALL ENZYMES ARE PROTEINS BUT NOT ALL PROTEINS ARE ENZYMES
enzymes have specific shapes and need specific conditions to work and be effective
other protein functions include defense, storage, transport, cellular communication, movement, and structural support
proteins are all constructed from the same set of 20 amino acids, linked in unbranched polymers
peptide bond: bond between amino acids forming a polymer
polypeptide: unbranched polymers of amino acids
protein: biologically functional molecule made up of polypeptides, each folded and coiled into a specific three-dimensional structure
almost all proteins can be broken down into urea when they are not needed anymore, so that it can be released from the body as urine
water soluble proteins are easier to break down into urea than other proteins
enzymatic proteins:
selective acceleration of chemical reactions
ex. digestive enzymes catalyze the hydrolysis of bonds in food molecules
storage proteins:
storage of amino acids
ex. Casein, the protein of milk, is the major source of amino acids for baby mammals
defensive proteins:
protection against disease
ex. antibodies inactivate and help destroy viruses and bacteria → tell white blood cells which dangerous cells need to be destroyed
transport proteins:
transport of substances
ex. hemoglobin is a protein transports oxygen around the body
hormonal proteins:
coordination of an organism’s activities → helps cells, organs, and organ systems talk to each other
ex. insulin, secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar within the body → insulin unlocks channels in cells to allow glucose in (does not go into cells or break down glucose on its own)
contractile and motor proteins:
used for movement
ex. responsible for the undulations of cilia and flagella / actin and myosin proteins are responsible for the contraction of muscles
receptor proteins:
response of cell to chemical stimuli
ex. receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells
structural proteins:
used for support
ex. Keratin is the protein of hair, horns, feather, and other skin appendages
amino acids: organic molecules with amino (N-terminus) and carboxyl groups (C-terminus)
amino acids differ in their properties due to differing side chains, called R groups
non-polar side chains (hydrophobic)
electrically charged side chains (acid and base) (hydrophilic)
polar side chains (hydrophilic)
amino acids are linked by covalent bonds called peptide bonds
form of dehydration synthesis
OH from C-terminus of amino #1 and H from N-terminus of amino #2 form water and create a straight bond between the remaining C and N
3 amino acids = tripeptide , 4+ amino acids = polypeptide
each polypeptide has a unique linear sequence of amino acids, with a carboxyl end and an amino end
the specific activities of proteins result from their intricate three-dimensional architecture
as soon as polypeptide chains are formed, they have to be formed into a specific structure and taken to where it is to be used, if not, then spliceosomes come along and cut up the bonds so that the amino acids can be used again and recycled
B-cells remember how to build the antibodies (versions of the virus that still has the same protein but without the ability to multiply) - B-cells memorize the shape of the virus to quickly make the antibodies when they encounter the virus again
a functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape
the sequence of amino acids determines a protein’s three-dimensional structure and its structure determines how the protein works
the function of a protein usually depends on its ability to recognize and bind to some other molecule
proteins share three superimposed levels of structure → primary, secondary, and tertiary structure
primary structure:
a protein’s unique sequence of amino acids
like the order of letters in a long word
determined by inherited genetic information: DNA → RNA → polypeptide (this is how our body comes up with unique characteristics)
secondary structure:
consists of coils and folds in the polypeptide chain
result from hydrogen bonds between repeating constituents of the polypeptide backbone
can have alpha helix and beta pleated sheets together but held together loosely
tertiary structure:
overall shape of a polypeptide is determined by interactions among various side chains (R groups), rather than interactions between backbone constituents
interactions include hydrogen bonds, ionic bonds, hydrophobic interactions, and LDF
strong covalent bonds called disulfide bridges may reinforce the protein’s structure
more compressed together, forms a specific shape
quaternary structure:
results when a protein consists of two or more polypeptide chains
combinations of tertiary structures
Ex. collagen (3 polypeptides coiled) and hemoglobin (4 polypeptides - two alpha, two beta)
Factors Affecting Protein Structure
changed primary structure, pH, salt concentration, temperature, other environmental factors
denaturation: loss of a protein’s native structure
if a protein does not have its ideal conditions, it will become denatured, but if you return it to ideal conditions, it will return back to functioning normally
it is hard to predict a protein’s structure from its primary structure
most proteins probably go through several stages on their way to a stable structure
diseases such as Alzheimer’s, Parkinson’s, and mad cow disease are associated with misfolded proteins
the amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene
genes consist of DNA, a nucleic acid made of monomers called nucleotides
DNA is a carboxylic acid and a polymer (monomer made up of nitrogenous base, pentose sugar, and acid group)
there are two types of nucleic acid → deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
DNA provides directions for its own replication
DNA directs synthesis of messenger RNA (mRNA), and through mRNA, controls protein synthesis
This process is called gene expression
recessive and dominant genes are determined by their coiling → in the double helix, recessive genes will remain tight close to the dominant genes so that only the dominant gene is expressed / copied
the dominant gene unwinds to be read, copied, and transformed into RNA
Stages of Synthesis:
Synthesis of mRNA
mRNA made out of freed bases in the nucleus (DNA code determines code of RNA)
mRNA exits nucleus
Movement of mRNA in cytoplasm
Ribosome takes mRNA and reads the code
tRNA brings amino acids read from the “recipe” to the ribosome
Synthesis of Protein
tRNA carries amino acids to ribosomes
A chain of amino acids is formed
Protein is formed out of amino acids
each gene along a DNA molecule directs synthesis of a messenger RNA (mRNA)
the mRNA molecule interacts with the cell’s protein-synthesizing machinery to direction production of a polypeptide
the flow of genetic information can be summarized as DNA → RNA → polypeptide
nucleic acids are polymers called polynucleotides → same as saying DNA
each polynucleotide is made of monomers called nucleotides
each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups
free floating nucleotides will have three phosphate groups
if it is part of DNA, it will have one phosphate group
in DNA sugar is deoxyribose, in RNA the sugar is ribose
nucleoside: portion of a nucleotide without the phosphate group
SO nucleotide = nucleoside + phosphate group
nucleotides are linked together by a phosphodiester linkage to build a polynucleotide
phosphodiester linkage consists of a phosphate group that links the sugar of two nucleotides
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
DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a double helix
on almost all genes, only one side of the DNA is the actual gene, while the other side is just there for protection → only one strand might have the gene to be read
the backbone of DNA run in opposite 5’ → 3’ directions from each other, an arrangement referred to as antiparallel
5’ and 3’ come from which direction the carbons in the pentose sugar is pointing
the strands are also complementary to each other → makes it possible to generate two identical copies of each DNA molecule in a cell preparing to divide
RNA is single-stranded, meaning that it has more variable forms
complementary pairing can also occur between two RNA molecules or between parts of the same molecule
in RNA, thymine is replace with uracil (U)
once the structure of DNA and its relationship to amino acid sequence was understood, biologists sought to “decode” genes by learning their base sequences
the first chemical techniques for DNA sequencing were developed in the 1970s and refined over the next 20 years
it is enlightening to sequence the full complement of DNA in an organism’s genome
the rapid development of faster and less expensive methods of sequencing was a side effect of the Human Genome Project
Many genomes have been sequenced, generating large sets of data