(Unit 1) Chapter 5: The Structure and Function of Large Biological Molecules Flashcards
The critically important large molecules of all living things fall into just ___ main classes:
Four
Carbohydrates, lipids, proteins, and nucleic acids
What are called macromolecules? Why?
Carbohydrates, proteins, nucleic acids
On molecular scale, they are huge (e.x. 1 protein may have a mass of well over 100,000 daltons)
Define:
Polymer
A long molecule consisting of many similar or identical building blocks linked by covalent bonds
Define:
Monomers
The smaller molecules and repeating units that serve as the building blocks of a polymer
How are monomers connected?
Through condensation reaction, specifically a dehydration reaction
How does a dehydration reaction work?
A type of condensation reaction where two molecules are covalently bonded to each other through loss of a water molecule (thus dehydration)
Define:
Enzymes
Specialized macromolecules that speed up chemical reactions in cells
How are polymers disassembled to monomers?
Hydrolysis
Define:
Hydrolysis
A process that is essentially the reverse of dehydration reaction, thus bonds are broken b the addition of water
Where does the word polymer come from?
Greek polys (many) and meris (part)
Where does the word hydrolysis come from?
Greek hydro (water) and lysis (break)
Carbohydrates include both ______ and ________ of ______
Sugar
Polymers
Sugars
What are simple sugars known as?
Monosaccharides
What are disaccharides?
Double sugars, consisting of two monosaccharides joined by a covalent bond
Define:
Polysaccharides
Polymers composed of many sugar building blocks
Where does the word monosaccharides come from?
Greek mono (single) and sacchar (sugar)
What is general formula for a monosaccharide?
Some multiple of the unit CH2O
List the sources of diversity for simple sugars (3)
The location of the carbonyl group (ketoses or aldoses)
The size of the carbon skeleton
The spatial arrangement of their parts around asymmetric carbons
Define:
Asymmetric carbon
A carbon attached to four different atoms or groups of atoms
For sugars, how long do the carbon skeleton range from? What are they called?
3 to 7 carbons
Trioses (3-carbon), pentoses (5-carbon), hexoses (6-carbon)
Glyceraldehyde and Dihydroxyacetone are:
Trioses, glyceraldehyde is an aldose while dihydroxyacetone is a ketone
Ribose and Ribulose are:
Pentoses, ribose is an aldose while ribulose is a ketone
Glucose and Fructose are:
Hexoses, glucose is an aldose while fructose is a ketone
What is the difference between glucose and galactose?
Only differ in the placement of parts (hydroxyl group and hydrogen) around asymmetric carbons
Monosaccharides are major _________ for cells; How do cells extract energy from glucose?
Nutrients
Through cellular respiration
Define:
Disaccharide
Consists of two monosaccharides joined by a glycosidic linkage
Define:
Glycosidic linkage
A covalent bond formed between two monosaccharides by a dehydration reaction
What are examples of disaccharides? (List the monosaccharides in their formation in brackets) (3)
Maltose (glucose and glucose), sucrose (glucose and fructose), lactose (glucose and galactose)
Where is maltose present?
Where is sucrose present?
Where is lactose present?
Known as malt sugar, used in brewing beer
Known as table sugar
Present in milk
In aqueous solutions, glucose molecules, as well as most other sugars form what?
Rings
In abbreviated ring structure, what do the corners of the ring represent?
Carbons
Define:
Polysaccharide
A macromolecule, polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages
What type of linkage is between the two glucose molecules in maltose?
1-4 glycosidic linkage
What type of linkage is between the glucose and fructose molecules in sucrose?
1-2 glycosidic linkage
Even though fructose is a hexose, it forms a ____-sided ring
Five
Plants and animals store ______ for later use in the form of:
Sugars
Storage polysaccharides
What storage polysaccharides do plants use?
Starch, a polymer of glucose monomers
Where do plants store starch?
As granules within cellular structures known as plastids, which include chloroplasts
How are glucose monomers in starch joined?
1-4 glycosidic linkage
What storage polysaccharides do animals use?
Glycogen, a polymer of glucose that is like amylopectin but more extensively branched
Where do humans and other vertebrates store glycogen?
Mainly in liver and muscle cells
True or False:
Glycogen stores are depleted in about a day
True, unless they are replenished by consumption of food
Organisms build strong materials from:
Structural polysaccharides
The polysaccharide _________ is a major component of the tough walls that enclose plant cells. On a global scale, plants produce almost __^__ kg (___ _______ tons) per year
Cellulose
10^14
100 billion
What is the difference between starch and cellulose? (2)
In starch, glucose monomers are in alpha formation (they are in beta formation in cellulose)
Starch molecule is mostly helical while cellulose molecules are straight
What is the difference between alpha and beta glucose?
In alpha glucose, the hydroxyl group on carbon 1 is positioned below the plane of the ring
In beta glucose, the hydroxyl group on carbon 1 is positioned above the plane of the ring
True or False:
Cellulose is sometimes branched
False, cellulose is never branched
The hydrogen bonding between some hydroxyl groups of cellulose, parallel cellulose molecules held together this way are grouped into units called:
Microfibrils
Enzymes that digest starch by ___________its alpha linkages are unable to hydrolyze the beta linkages of _________ because of the distinctly different shapes of these two molecules
Hydrolyzing
Cellulose
On food packages, what does “insoluble fiber” mainly refer to?
Cellulose
Some ___________ can digest cellulose
Prokaryotes
Cows harbour cellulose-digesting prokaryotes in its _____, the first compartment in its _______
Rumen
Stomach
Define:
Chitin
The carbohydrate used by arthropods (insects, spiders, crustaceans, and related animals) to build their exoskeleton)
Define:
Exoskeleton
A hard case the surrounds the soft parts of an animal
True of False:
Pure chitin is hard
False, pure chitin is leathery but becomes hardened when encrusted with calcium carbonate (a salt)
True or False:
Chitin is found in fungi, who use it instead of cellulose
True
Describe the structure of chitin monomer
Similar to glucose monomer of cellulose except that it also has nitrogen containing appendage
Compounds called Lipids are group together due to one important trait:
They mix poorly, if at all, with water
What is fat constructed from?
Two kinds of smaller molecules: glycerol and fatty acids
Define:
Glycerol
An alcohol with three carbons, each bearing a hydroxyl group
Describe the structure of a fatty acid
Has a long carbon skeleton, usually 16 or 18 in length
The carbon at one end of the chain is part of a carboxyl group
In making a fat, ______ fatty acid molecules each join to glycerol by an ____________. The resulting fat is called a _______________
Three
Ester linkage
Triacylglycerol
Define:
Ester linkage
A bond between a hydroxyl group and a carboxyl group
What is a triacylglycerol also called?
Triglyceride
True or False:
Fatty acids vary in length and in the number and locations of double bonds
True
If there are no double bonds between carbon atoms in the chain of a fatty acid, what is it known as?
Saturated fatty acid (as it is saturated with hydrogen)
If there is one or more double bonds in the chain of a fatty acid, what is it known as?
Unsaturated fatty acid
The fatty acid will have a kink in the chain wherever:
There is a cis double bond
Fat made from saturated fatty acids is called:
Saturated fat
The lack of double bonds in saturated fats and flexibility allow the fat molecules to pack tightly in an _________ ___,
Saturated fat
Saturated animal fats are _____ at room temperature
Solid
Why are unsaturated fats (e.x. fish and plant fats) liquid at room temperature?
The kinks due to cis double bonds prevent molecules from packing together closely
Hydrogenating unsaturated fats can also produce fats with _____ double bonds
Trans
True or False:
Diet rich in saturated fats is one of several factors that may contribute to cardiovascular disease known as atherosclerosis
True
Why are fats useful? (3)
Fats can store more than twice as much energy as starch
Can cushion vital organs such as kidneys
Can also insulate the body
Describe the structure of a phospholipid (3)
Only two fatty acids attached to glycerol
The third hydroxyl group of glycerol is joined to a phosphate group (has negative charge)
Additional small molecules (usually charged or polar) can be linked to the phosphate group to form a variety of phospholipids
True of False:
The two ends of phospholipids are both hydrophobic
False, hydrocarbon tails are hydrophobic while phosphate group and attachments form a hydrophilic head
When phospholipids are added to water, what happens?
They assemble into a bilayer that shield the hydrophobic sections away from water
True or False:
At the surface of the cell, phospholipids are arranged in a similar bilayer
True
Is it true that cells could not exist without phospholipids?
True
Define:
Steroid
Lipids that are characterized by a carbon skeleton consisting of four fused rings
What is cholesterol?
A common component of animal cell membranes, also the precursor from which other steroids are synthesized in vertebrates
Where is cholesterol synthesized in vertebrates?
In the liver
Where does the word protein come from?
Greek proteios (first place)
Name the types of proteins (8)
Enzymatic proteins Structural proteins Storage proteins Transport proteins Hormonal proteins Receptor proteins Contractile and motor proteins Defensive proteins
State the function and example of:
Enzymatic proteins
Selective acceleration of chemical reactions Digestive enzymes (catalyse hydrolysis of polymers in food)
State the function and example (3) of:
Structural proteins
Support
Collagen and elastin provide fibrous framework in animal connective tissues
Keratin is protein of hair, horns, feathers and other skin appendages
State the function and example (2) of:
Storage proteins
Storage of amino acids
Ovalalbumin is the protein of egg white (used as amino acid source for developing embryos)
Casein, protein in milk, is major source of amino acids for baby mammals
State the function and example of:
Transport proteins
Transport of other substances
Hemoglobin transports oxygen from lungs to other parts of other body
State the function and example of:
Hormonal proteins
Coordination of an organism’s activities
Insulin (hormone secreted by pancreas) helps regulate the concentration of sugar in the blood of vertebrates
State the function and example (2) of:
Contractile and motor proteins
Movement
Actin and myosin are responsible for contraction of muscles
State the function and example of:
Receptor proteins
Response of cell to chemical stimuli
Receptors built into nerve cells detect chemical signals released by other nerve cells
State the function and example of:
Defensive proteins
Protection against disease
Antibodies combat bacteria and viruses
Life would not be possible without _______, most of which are ________
Enzymes
Proteins
Define:
Catalysts
Chemical agents that selectively speed up chemical reactions without being consumed by the reaction
What are polymers of amino acids known as?
Polypeptides
A protein consists of ___ or ____ ____________, each ______ and ______ into a specific three-dimensional structure
One
More polypeptides
Folded
Coiled
What are amino acids?
Organic molecules possessing both carboxyl and amino groups
What is the asymmetric carbon in the middle of an amino acid known as?
Alpha-carbon
How many types of amino acids are there?
20
What are the three types of amino acids?
Nonpolar, polar, and electrically charged
Which amino acids are nonpolar? (9)
Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline
Which amino acids are polar? (6)
Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine
What are the types of electrically charged amino acids? (2)
Acidic and Basic
Which amino acids are electrically charged? (5)
Aspartic acid, Glutamic acid, Lysine, Arginine, Histidine
Which electrically charged amino acids are acidic?
Aspartic acid and Glutamic acid
Which electrically charged amino acids are basic?
Lysine, Arginine, and Histidine
Name the amino acid:
Gly or G
Glycine
Name the amino acid:
Ala or A
Alanine
Name the amino acid:
Val or V
Valine
Name the amino acid:
Leu or L
Leucine
Name the amino acid:
Ile or I
Isoleucine
Name the amino acid:
Met or M
Methionine
Name the amino acid:
Phe or F
Phenylalanine
Name the amino acid:
Trp or W
Tryptophan
Name the amino acid:
Pro or P
Proline
Name the amino acid:
Ser or S
Serine
Name the amino acid:
Thr or T
Theonine
Name the amino acid:
Cys or C
Cysteine
Name the amino acid:
Tyr or Y
Tyrosine
Name the amino acid:
Asn or N
Asparagine
Name the amino acid:
Gln or Q
Glutamine
Name the amino acid:
Asp or D
Aspartic acid
Name the amino acid:
Glu or E
Glutamic acid
Name the amino acid:
Lys or K
Lysine
Name the amino acid:
Arg or R
Arginine
Name the amino acid:
His or H
Histidine
Name the abbreviations of amino acid:
Glycine
Gly or G
Name the abbreviations of amino acid:
Alanine
Ala or A
Name the abbreviations of amino acid:
Valine
Val or V
Name the abbreviations of amino acid:
Leucine
Leu or L
Name the abbreviations of amino acid:
Isoleucine
Ile or I
Name the abbreviations of amino acid:
Methionine
Met or M
Name the abbreviations of amino acid:
Phenylalanine
Phe or F
Name the abbreviations of amino acid:
Tryptophan
Trp or W
Name the abbreviations of amino acid:
Proline
Pro or P
Name the abbreviations of amino acid:
Serine
Ser or S
Name the abbreviations of amino acid:
Threonine
Thr or T
Name the abbreviations of amino acid:
Cysteine
Cys or C
Name the abbreviations of amino acid:
Tyrosine
Tyr or Y
Name the abbreviations of amino acid:
Asparagine
Asn or N
Name the abbreviations of amino acid:
Glutamine
Gln or Q
Name the abbreviations of amino acid:
Aspartic acid
Asp or D
Name the abbreviations of amino acid:
Glutamic acid
Glu or E
Name the abbreviations of amino acid:
Lysine
Lys or K
Name the abbreviations of amino acid:
Arginine
Arg or R
Name the abbreviations of amino acid:
Histidine
His or H
Name the amino acid with R group of:
H-
Glycine
Name the amino acid with R group of:
CH3-
Alanine
Name the amino acid with R group of:
(CH3)2CH-
Valine
Name the amino acid with R group of:
(CH3)2CHCH2-
Leucine
Name the amino acid with R group of:
CH3CH2CH(CH3)-
Isoleucine
Name the amino acid with R group of:
CH3SCH2CH2-
Methionine
Name the amino acid with R group of:
C6H5CH2-
Phenylalanine
Name the amino acid with R group of:
C8H8NHCH2-
Tryptophan
Name the amino acid with R group of:
-CH2CH2CH2
Proline
Name the amino acid with R group of:
HOCH2-
Serine
Name the amino acid with R group of:
(OHCH3)CH-
Threonine
Name the amino acid with R group of:
HSCH2-
Cysteine
Name the amino acid with R group of:
HOC6H4CH2-
Tyrosine
Name the amino acid with R group of:
H2NC(O)CH2-
Asparagine
Name the amino acid with R group of:
H2NC(O)CH2CH2-
Glutamine
Name the amino acid with R group of:
O(-)C(O)CH2-
Aspartic acid
Name the amino acid with R group of:
O(-)C(O)CH2CH2-
Glutamic acid
Name the amino acid with R group of:
H3N(+)CH2CH2CH2CH2-
Lysine
Name the amino acid with R group of:
H2NC(NH2(+))NHCH2CH2CH2-
Arginine
Name the amino acid with R group of:
C3H2NHNH(+)CH2-
Histidine
The group that differs on an amino acid is known as:
R group
When two amino acids join by a dehydration reaction, what is the resulting covalent bond called?
Peptide bond
What are the two ends of a polypeptide chain known as?
Amino end (N-terminus) Carboxyl end (C-terminus)
True or False:
A polypeptide is a protein
False, the term polypeptide is not synonymous with the term protein
A functional protein is ___ or more ____________ precisely _______, ______, and ______ into a ________ of unique shape
One Polypeptides Twisted Folded Coiled Molecule
Describe:
Globular proteins
Roughly spherical proteins
Describe:
Fibrous proteins
Proteins shaped like long fibers
What does a ribbon model show?
Shows how the single polypeptide chain folds and coils to form the functional protein
What do the yellow lines in a ribbon model represent?
Cross-linking bonds between the protein peptides that stabilizes its shape
What does a space-filling model show?
Shows more clearly the globular shape seen in many proteins, as well as the specific three-dimensional structure unique to certain proteins
What can mimic endorphins? Why?
Heroin, morphine, and other opiate drugs
They share a similar shape with endorphins
What are the four levels of protein structure?
Primary, secondary, tertiary, quaternary
Define:
Protein’s Primary Structure
The unique sequence of amino acids
Define:
Protein’s Secondary Structure
The coils or folds that contribute to the protein’s overall shape
What are the coils and folds in secondary structure of a protein a result of?
Hydrogen bonds
What are the two main types of secondary structures?
Alpha helix and Beta pleated sheet
Describe:
Alpha helix
A delicate coil held together by hydrogen bonding between every fourth amino acid
Describe:
Beta pleated sheet
Two or more regions of the polypeptide chain lying side by side are connected by hydrogen bonds between parts of the two parallel polypeptide backbones
Define:
Protein’s Tertiary Structure
The overall shape of a polypeptide resulting from interactions between the side chains (R groups) of the various amino acids
What is one interaction that contributes to tertiary structure?
Hydrophobic interaction
Describe:
Hydrophobic interaction
Amino acids with hydrophobic side chains end up in clusters at the core of the protein, out of contact with water
In tertiary structure, the shape of a protein may be reinforce further by covalent bonds called:
Disulfide bridges
Where do disulfide bridges form?
Form where two cysteine monomers (amino acids with sulfhydryl groups on side chains) are brought close together by the folding of the protein; the sulfur of the two cysteine bond together
Define:
Protein’s Quaternary Structure
The overall protein structure that results from the aggression of these polypeptide subunits (some proteins consist of two or more polypeptide chains aggregated into one functional macromolecule)
True or False:
Even a change in the primary structure can affect a protein’s shape and ability to function
True
What is an example of the effects of the change in primary structure?
Sickle-cell disease; The substitution of valine for glutamic acid causes an exposed hydrophobic region in the secondary/tertiary structure or hemoglobin, which in turn causes crystallization into a fibre (causes the abnormal sickle shape)
Define:
Denaturation
Protein unravelling and losing its native shape
Define:
Chaperonins
Protein molecules that assist in the proper folding of other proteins
What are chaperonins also known as?
Chaperone proteins
When were the first 3-D structure for proteins worked out? For what?
1959
Hemoglobin and related protein
What first made working out 3-D structures for proteins possible?
X-ray crystallography
What is a newer method now used for working out the 3-D structure of proteins? What is different about it?
Nuclear magnetic resonance (NMR) spectroscope
Does not require protein crystallization
What is the newest approach of figuring out the 3-D structure of proteins?
Bioinformatics
Define:
Gene
A unit of inheritance that programs the amino acid sequence of a polypeptide
DNA belongs to which group of compounds?
Nucleic Acids
What are the two types of nucleic acids in living organisms? What is their function?
Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA) Enable living organisms to reproduce their complex components from one generation to the next
State the flow of DNA to proteins (3)
DNA directs the synthesis of a type of RNA known as messenger RNA (mRNA)
The mRNA moves into the cytoplasm via the nuclear pore
The mRNA interacts with the cell’s protein-synthesizing machinery to direct production of a polypeptide, which folds into all or part of a protein
Nucleic acids are macromolecules that exist as polymers called:
Polynucleotides
What are the monomers of polynucleotides called?
Nucleotide
Describe the structure of a nucleotide
Composed of three parts:
A nitrogenous base
A five-carbon sugar (pentose)
A phosphate group
What is the portion of a nucleotide without the phosphate group called?
Nucleoside
There are ___ families of nitrogenous bases:
Two
Pyrimidines and Purines
Describe:
Pyrimidines
Have six-membered ring of carbon and nitrogen atoms
Describe:
Purines
Larger, with a six membered ring fused to a five membered ring
State the pyrimidines (3)
Cytosine (C)
Thymine (T)
Uracil (U)
State the purines (2)
Adenine (A)
Guanine (G)
What sugar is connected to the nitrogenous base in the nucleotides of RNA? DNA?
RNA: Ribose
DNA: Deoxyribose
What is the difference between ribose and deoxyribose?
In deoxyribose, the second carbon in the ring lacks an oxygen atom
True or False:
RNA is composed of two polypeptide chains
False, RNA is composed of one polypeptide chain while DNA is composed of two polypeptide chains
What is the structure of DNA?
Double helix
What are the two ends of nucleotide polymers known as? Why?
5’ and 3’ ends
One end has a phosphate attached to a 5’ carbon, while the other end has a hydroxyl group on a 3’ carbon
The two sugar phosphate backbones of DNA run in ________ 5’ to 3’ directions from each other, referred to as:
Opposite
Antiparallel
