Chapter 3 Flashcards
Biological Macromolecules
alpha-helix structure (α-helix)
type of secondary protein structure formed by folding the polypeptide into a helix shape with hydrogen bonds stabilizing the structure
amino acid
a protein’s monomer; has a central carbon or alpha carbon to which an amino group, a carboxyl group, a hydrogen, and an R group or side chain is attached; the R group is different for all 20 common amino acids
beta-pleated sheet (β-pleated)
secondary structure in proteins in which hydrogen bonding forms “pleats” between atoms on the polypeptide chain’s backbone
biological macromolecule
large molecule necessary for life
that is built from smaller organic molecules
carbohydrate
biological macromolecule in which the ratio of carbon to hydrogen and to oxygen is 1:2:1; carbohydrates serve as energy sources and structural support in cells and form arthropods’ cellular exoskeleton
cellulose
polysaccharide that comprises the plants’ cell wall; provides structural support to the cell
chaperone
(also, chaperonin) protein that helps nascent protein in the folding process
chitin
type of carbohydrate that forms the outer skeleton of all arthropods that include crustaceans and insects; it also forms fungi cell walls
dehydration synthesis
(also, condensation) reaction that links monomer molecules, releasing a water molecule for each bond formed
denaturation
loss of shape in a protein as a result of changes in temperature, pH, or chemical exposure
deoxyribonucleic acid (DNA)
double-helical molecule that
carries the cell’s hereditary information
disaccharide
two sugar monomers that a glycosidic bond links
enzyme
catalyst in a biochemical reaction that is usually a complex or conjugated protein
glycogen
storage carbohydrate in animals
glycosidic bond
bond formed by a dehydration reaction
between two monosaccharides with eliminating a water molecule
hormone
chemical signaling molecule, usually protein or steroid, secreted by endocrine cells that act to control or regulate specific physiological processes
hydrolysis
reaction that causes breakdown of larger molecules into smaller molecules by utilizing water. Polymer to monomer
lipid
macromolecule that is nonpolar and insoluble in water
messenger RNA (mRNA)
RNA that carries information
from DNA to ribosomes during protein synthesis
monomer
smallest unit of larger molecules that are polymers
monosaccharide
single unit or monomer of carbohydrates
nucleic acid
biological macromolecule that carries the cell’s genetic blueprint and carries instructions for the cell’s functioning
nucleotide
monomer of nucleic acids; contains a pentose sugar, one or more phosphate groups, and a nitrogenous
base
omega fat
type of polyunsaturated fat that the body requires; numbering the carbon omega starts from the methyl end or the end that is farthest from the carboxylic end (beginning or end hence omega)
peptide bond
bond formed between two amino acids by a dehydration reaction
phosphodiester linkage
covalent chemical bond that holds together the polynucleotide chains with a phosphate group linking neighboring nucleotides’ two pentose sugars
phospholipid
membranes’ major constituent; comprised of two fatty acids and a phosphate-containing group attached to a glycerol backbone
polymer
chain of monomer residues that covalent bonds link; polymerization is the process of polymer formation from monomers by condensation
polynucleotide
long chain of nucleotides
polypeptide
long chain of amino acids that peptide bonds link
polysaccharide
long chain of monosaccharides; may be branched or unbranched
primary structure
linear sequence of amino acids in a
protein
protein
biological macromolecule comprised of one or more amino acid chains
purine
type of nitrogenous base in DNA and RNA; adenine and guanine are purines
pyrimidine
type of nitrogenous base in DNA and RNA;
cytosine, thymine, and uracil are pyrimidines
quaternary structure
association of discrete polypeptide subunits in a protein
ribonucleic acid (RNA)
single-stranded, often internally base paired, molecule that is involved in protein synthesis
ribosomal RNA (rRNA)
RNA that ensures the proper alignment of the mRNA and the ribosomes during protein synthesis and catalyzes forming the peptide linkage
saturated fatty acid
long-chain hydrocarbon with single
covalent bonds in the carbon chain; the number of hydrogen atoms attached to the carbon skeleton is maximized
secondary structure
regular structure that proteins form
by intramolecular hydrogen bonding between the oxygen atom of one amino acid residue and the hydrogen attached to the nitrogen atom of another amino acid residue
starch
storage carbohydrate in plants
steroid
type of lipid comprised of 4 fused hydrocarbon rings forming a planar structure
tertiary structure
a protein’s three-dimensional conformation, including interactions between secondary structural elements; formed from interactions between amino acid side chains
trans fat
fat formed artificially by hydrogenating oils, leading to a different arrangement of double bond(s) than those in naturally occurring lipids
transcription
process through which messenger RNA forms on a template of DNA
transfer RNA (tRNA)
RNA that carries activated amino acids to the site of protein synthesis on the ribosome
translation
process through which RNA directs the protein’s formation
triacylglycerol (also, triglyceride)
fat molecule; consists of 3 fatty acids linked to a glycerol (alcohol) molecule
unsaturated fatty acid
“long-chain hydrocarbon” that has “one or more double bonds” in the hydrocarbon chain
wax
lipid comprised of a long-chain fatty acid that is esterified to a long-chain alcohol/hydrocarbon;
Harder and less greasy. serves as a protective coating on some feathers, aquatic mammal fur, and leaves (to reduce water loss and resist infective agents)
which categories of amino acid would you expect to find on the surface of a soluble protein, and which would you expect to find in the interior?
What distribution of amino acids would you expect to find in a protein embedded in a lipid bilayer?
Polar and charged amino acid residues (the remainder after peptide bond formation) are more likely to be found on the surface of soluble proteins where they can interact with water, and nonpolar (e.g., amino acid side chains) are more likely to be found in the interior where they are sequestered from water. In membrane proteins, nonpolar and hydrophobic amino acid side chains associate with the hydrophobic tails of phospholipids, while polar and charged amino acid side chains interact with the polar head groups or with the aqueous solution. However, there are exceptions. Sometimes, positively and negatively charged amino acid side chains interact with one another in the interior of a protein, and polar or charged amino acid side chains that interact with a ligand can be found in the ligand binding pocket.
A mutation occurs, and cytosine is replaced with adenine. What impact do you think this will have on the DNA structure?
Adenine is larger than cytosine and will not be able to base pair properly with the guanine on the opposing strand, causing the double helix to bulge at that position.
Dehydration synthesis leads to formation of
water and polymers
During the breakdown of polymers, which of the following reactions takes place?
hydrolysis
The following chemical reactants produce the ester ethyl ethanoate (C4H8O2): C2H6O + CH3COOH
What type of reaction occurs to make ethyl ethanoate?
condensation / dehydration synthesis
An example of a monosaccharide is
glucose (dextrose), fructose (levulose), and galactose
Cellulose and starch are examples of:
Polysaccharides
Plant cell walls contain which of the following in abundance?
Cellulose
Lactose is a disaccharide formed by the formation of a ________ bond between glucose and ________.
glycosidic; galactose
Which of the following is not an extracellular matrix role of carbohydrates?
a. protect an insect’s internal organs from external trauma
b. prevent plant cells from lysing after the plant is watered
c. maintain the shape of a fungal spore
d. provide energy for muscle movement
The carbohydrates in the extracellular matrix do not provide energy for muscle movement. The energy for muscle movement is provided by adenosine triphosphate (ATP) produced in the mitochondria of muscle cells.
saturated fats have all of the following characteristics
except:
a. they are solid at room temperature
b. they have single bonds within the carbon chain
c. they are usually obtained from animal sources
d. they tend to dissolve in water easily
D
What are the components of a phospholipid? Why are phospholipids important?
Phospholipids are a class of lipids that are a major component of all cell membranes. They can form lipid bilayers because of their amphiphilic characteristic. The structure of the phospholipid molecule generally consists of two hydrophobic fatty acid “tails” and a hydrophilic “head” consisting of a phosphate group.
Cholesterol is an integral part of plasma membranes.
Based on its structure, where is it found in the membrane?
within the tail bilayer
Phospholipids are important components of
the plasma membrane of cells
The monomers that make up proteins are called
amino acids
The α-helix and the β-pleated sheet are part of which protein structure?
secondary
Mad cow disease is an infectious disease where one misfolded protein causes all other copies of the protein to begin misfolding. This is an example of a disease impacting ____ structure.
tertiary
A nucleotide of DNA may contain ________.
deoxyribose, thymine, and a phosphate group
The building blocks of nucleic acids are
nucleotides
How does the double helix structure of DNA support its
role in encoding the genome?
Complementary base pairing creates a very stable structure.
Why are biological macromolecules considered organic?
Biological macromolecules are considered organic as they contain carbon atoms in their ring or chain structure along with other elements like nitrogen, oxygen, hydrogen, and sulfur.
What role do electrons play in dehydration synthesis
and hydrolysis?
In dehydration synthesis, the H and OH ions transfer electrons to monomers, while in hydrolysis, the electrons are taken up by H and OH ions from monomers.
Describe the similarities and differences between
glycogen and starch.
The glycogen and starch are similar as both are polymers of glucose, while they differ in the type of structure and occurrence.
Why is it impossible for humans to digest food that contains cellulose?
we lack appropriate enzymes (cellulase) to break down this complex substance, cellulose. Undigestible cellulose is the fibre which aids in the smooth working of the intestinal tract.
Explain at least three functions that lipids serve in plants and/or animals.
Fat serves as a valuable way for animals to store energy. It can also provide insulation.
Waxes can protect plant leaves and mammalian fur from getting wet.
Phospholipids and steroids are important components of animal cell membranes, as well as plant, fungal, and bacterial membranes.
Why have trans fats been banned from some restaurants? How are they created?
Trans fats are created artificially when hydrogen gas is bubbled through oils to solidify them - the double bonds of the cis conformation in the hydrocarbon chain may be converted to double bonds in the trans configuration; some restaurants are banning trans fats because they cause higher levels of LDL, or “bad” cholesterol
Why are fatty acids better than glycogen for storing large amounts of chemical energy?
Fats have a higher energy density than carbohydrates (averaging 9kcal/gram versus 4.3kcal/gram respectively); thus, on a per gram basis, more energy can be stored in fats than can be store in carbohydrates; additionally, fats are packaged into spherical globules to minimize interactions with the water-based plasma membrane, while glycogen is a large branched carbohydrate that cannot be compacted for storage
Part of cortisol’s role in the body involves passing through the plasma membrane to initiate signaling inside a cell. Describe how the structures of cortisol and the plasma membrane allow this to occur.
Cortisol is a small, generally hydrophobic molecule, while the phospholipids that create plasma membranes have hydrophilic head and hydrophobic tails - since cortisol is hydrophobic, it can interact with the sequestered tails of the phopholipids in the center of the plasma membrane; this, along with its small size, allows cortisol to move through the plasma membrane to the inside of the cell
Explain what happens if even one amino acid is substituted for another in a polypeptide chain. Provide a specific example.
When one amino acid is changed to another it may lead to the formation of the non-functional protein, which can have a deleterious effect on the body.
For example, the substitution of amino acid valine for glutamate in the sequence of the protein-coding for hemoglobin results in the formation of wrong hemoglobin structure, which gives the sickle shape to the red blood cells, which ultimately clogs the arteries and hence cause the disease called sickle cell anemia.
Describe the differences in the four protein structures.
The proteins exist in four different structural forms- primary structure, secondary structure, tertiary and quaternary structure.
The primary structure of the protein is the sequence of amino acids joined by peptide bonds in a linear fashion. When these polypeptide chains fold into helix or sheets then it is called the secondary structure of proteins. When the proteins fold into the three-dimensional structure due to side-chain interactions then it is called the tertiary structure of proteins. And when the protein is made up of many polypeptide chains or subunits, then it forms the quaternary structure.
Aquaporins are proteins embedded in the plasma membrane that allow water molecules to move between the extracellular matrix and the intracellular space.
Based on its function and location, describe the key features of the protein’s shape and the chemical characteristics of its amino acids.
Aquaporins are proteins embedded in the plasma membrane that allow water molecules to move between the extracellular matrix and the intracellular space. Based on its function and location, describe the key features of the protein’s shape and the chemical characteristics of its amino acid membrane. The top and bottom of the protein must contain charged or polar amino acids (hydrophilic) to interact with the aqueous environments. The exterior transmembrane region must contain non‐polar amino acids (hydrophobic) that can interact with the phospholipid tails. However, the inside of this channel must contain hydrophilic amino acids since they will interact with the traveling water molecule
What are the structural differences between RNA and DNA?
DNA contains the sugar deoxyribose while RNA contains a ribose sugar, and hence they have their name as DeoxyriboNucleic Acid and RiboNucleic Acid respectively. Again, the nitrogenous bases present in DNA are Adenine, thymine, cytosine, and Guanine, while RNA instead of Thymine contains uracil base. They both also differ in the number of helical strands. The DNA is double-stranded while RNA is a single-stranded molecule. Also, the molecular mass of DNA is larger than RNA.
What are the four types of RNA and how do they function?
The four types of RNA are mRNA, tRNA, rRNA and heterogeneous nuclear RNA or hn RNA. they have different functional roles in the cell.
messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and micro RNA (miRNA)
The mRNA plays an important role in carrying the information in the form of a sequence of bases from the DNA template strand to code the functional protein by a process called translation.
The rRNA along with proteins plays an important role in making the protein synthesis machinery called the ribosome.
The tRNA plays the role in the transfer of amino acids corresponding to the sequence of codons present in the mRNA and form the polypeptide chain in the ribosome.
The last hn RNA is involved in the splicing process, where the introns are removed and all exons or coding regions are joined together to form the mRNA or mature RNA, which ultimately codes for the polypeptide.
