UNIT 3 - Structure and Function Flashcards
Describe the structure of the following biological molecules: proteins, carbohydrates, lipids, and nucleic acids.
Proteins - Amino Acids in peptide bonds
Carbohydrates - saccharides in a or b bonds to form polysaccharides
Lipids - hydrophilic or polar head attached to a non-polar (hydrophobic) hydrocarbon chain
nucleic acids - consist of nucleotides (Adenine, uracil, guanine, cytosine, and thymine)
What is the R group in an amino acid basic structure?
The R group in an amino acid structure is denotes the amino acid side chain. This is where amino acids differ as each individual amino acid has a unique side chain or R-group.
Explain why proline is not common in α-helices, but can be found frequently in collagen.
Proline is the least flexible amino acid because of the attachment of the side chain to the alpha-amino group and so it is too rigid and does not “bend” or fit with other amino acid side chains to allow the formation of a helix structure. In alpha helices, the side chains of the amino acids all point out from the axis and the structure of proline cannot accommodate this. Proline is found in collagen though because of the abundance of glycine which has the smallest side chain. The presence of many glycine residues would allow for proline to fit into this type of helical structure.
Identify the six most abundant amino acids in proteins.
leu, ala, gly, ser, val, and glu.
Why it is important to know the protein sequence in addition to the DNA sequence of a particular gene?
It is important to know the protein sequence in addition to the DNA sequence of a particular gene because it reveals information about the protein structure that is not possible with nucleic acid sequencing alone. One example is the positioning of disulphide bonds in proteins. In addition to this, many proteins are modified after they are synthesized. This modification can include cleavage of the protein to form the “mature” protein, or the addition of carbohydrates, phosphate groups, or acetyl groups to amino acid side chains.
Wool consists of α-keratin. Pure wool sweaters exposed to hot water shrink alarmingly. After shrinkage, it is virtually impossible to stretch the sweater back to its original shape. What do you think is the biochemical cause of this phenomenon?
The biochemical cause of this phenomenon is that the α-keratins are a large group of proteins which range from horn and fingernails (high cysteine content) to wool, hair, and skin (low cysteine content). The latter group is characterized by extensive α-helix formation. When wool is processed (“spun”), the fibres are teased to an elongated shape. Exposure to steam or hot water will cause the processed fibres to revert to their original, tightly H-bonded α-helices. Test whether and how much α-helices stretch by experimenting with a strand of your hair.
Describe the hydrogen-bonding pattern of an α-helix.
The C=O bond of the first amino acid to the fifth amino acid N-H bond
List the advantages of multiple subunits in proteins.
There are two major advantages of multiple subunits in proteins. The first is that having subunits that are assembled rather than one large polypeptide facilitates repair of a defective protein. It is easier and more efficient to repair one subunit rather than one very large protein. The second advantage is that having subunits rather than one large polypeptide allows better manipulation and regulation of the protein. This is true for enzymes. Since each subunit has an active site, having subunits makes it easier to increase the size of the enzyme through association of subunits instead of increasing the length of the polypeptide. In addition, the presence of subunits allows for more effective regulation of enzyme activity.
Explain how cooperativity between hemoglobin and oxygen is achieved.
Hemoglobin binds oxygen by the iron of the heme group in one of the subunits. The heme iron is attached to a histadine side chain. This binding changes the conformation of that subunit as well as the other subunits of the hemoglobin protein which facilitates more binding of oxygen. This cooperativity allows hemoglobin to bind oxygen readily in areas of the body where oxygen is abundant and take that oxygen to areas of low oxygen. When oxygen is low the hemoglobin releases the oxygen.
Describe the energy and entropy changes that occur during protein folding.
Experiments have shown that proteins fold to their native conformations quickly through directed pathways. The increase in conformational stability of the folded protein results in a decrease in free energy. A protein that is folding proceeds from high-energy, high-entropy to low-energy, low-entropy as the number of possible conformations that the folding protein can assume decreases. This energy-entropy relationship is referred to as the “folding funnel.”
Antibodies are proteins that recognize and help to inactivate foreign proteins (called antigens). Why do such antibodies rarely react to denatured proteins? A few antibodies do recognize denatured proteins. How can this occur?
Antibodies bind to the surface of an antigen. Therefore, part of the “recognition” is the specific arrangement of amino acids at a particular spot on the surface of an antigen. Denaturation destroys the spatial arrangement of amino acids which form the surface of a protein.
However, in two instances antibodies may bind to denatured antigens. In the first case, the antibody may have been raised toward a denatured antigen; this type of bonding would occur in laboratory situations more commonly than in vivo. In the second case, the area of recognition on an antigen may be held together, at least partially, by disulphide bonds. Disulphide bonds are covalent bonds and will not break under the conditions of temperature, pH, solvent, and agitation which will dissociate H-bonds and hydrophobic interactions.
What information is provided by comparing the sequences of proteins from different organisms?
If its a secreted or membrane protein, what its possible binding sites are, and what it could bind, evolutionary traits and commonalities, useful for predictions of protein function,
How is a phylogenetic tree constructed?
A phylogenetic tree is constructed by:
1. classifying the organisms under study according to similarities (e.g., are they mammals, insects, reptiles, etc.).
2. noting the amino acid sequence of a protein common to all of the organisms.
3. Grouping the organisms according to common alterations in an amino acid sequence.
4. An organism that contains a subtle change in the sequence may be considered ancestral to other organisms in the group.
Describe the forces that stabilize proteins.
The forces that stabilize proteins are:
1. Hydrophobic effect – stabilizes proteins by causing nonpolar groups to minimize their association with water.
2. Electrostatic interactions, such as Van der Waals forces, hydrogen bonding, and ionic associations stabilize proteins by allowing side chains to bond or associate.
3. Chemical cross-linking through the formation of disulphide bonds or by the cross-linking of metal ions to a protein add stability to the folding of the protein.
List and describe two functions of proteins.
enzymes and transport proteins
What is an invariant region and what does in mean in terms of enzymes?
An invariant region is a section of primary structure that is identical or conserved across all species. For enzymes, this is usually in the catalytic region.
What is a prion?
A prion is an infectious protein that is responsible for mad cow disease and Creutzfeldt-Jacob disease. Infection with a prion causes misfolding of the PrP protein which is found in the brain. The misfolded PrP does two things: it 1) causes aggregations called amyloid plaques that damage nerve cells in the brain and 2) causes more of the PrP proteins in the brain to misfold as well.
What difficulties can you see in producing proteins by inserting the mammalian genes into bacterial hosts?
The proteins produced by mammalian genes inserted into bacterial hosts will lack sugar groups, and so may not be as effective as the authentic proteins. This is because bacteria cannot glycosylate proteins like mammalian cells do.
In an isolated nucleotide/ribonucleotide, the nitrogenous base is positioned directly over the sugar ring. What prevents H-bonding between the two?
There are no polar hydrogen atoms nor oxygen atoms on the side of the ribose ring which is closer to the base. Therefore no H-bonding is possible.
List and describe the major features of the Watson-Crick model of DNA structure.
major and minor grooves, double helix, anti-parallel right-handed helix, with conjugate base pairs
What are the structural differences between DNA and RNA?
OH on the 2 carbon present in RNA, Uracil replaces Thymine in RNA, and RNA is single stranded where most DNA is double stranded
Would you expect DNA and RNA to be water-soluble? Explain.
With both an anion (phosphate) and a sugar on every monomer unit, DNA and RNA are readily hydrated; therefore, solubility is not a problem.
Why would you expect RNA viruses to have double stranded RNA? While many RNA viruses are double stranded, not all are. What comments can you make on this latter class of viruses in light of your first answer?
Double strand promotes longevity as it protects from chemical attack. single strand makes for faster mutations
It was stated that (A + G) always equals (T + C) for duplex DNA. Is this restriction also true for single strands of DNA? Justify your answer.
The restriction is true for double stranded DNA because every purine is H-bonded to a pyrimidine. Therefore, the sum of the purines (A + G) must equal the sum of the pyrimidines (T + C). There is no such restriction for each individual strand of DNA.
What differences would you expect between a duplex DNA which has more A–T base pairs and a duplex DNA which has more G–C pairs?
A and T are joined by two H-bonds, while G and C are joined by three H-bonds. Therefore, the duplex with more G-C pairs will have a higher melting temperature; and it may replicate more slowly.
What are the forces that stabilize nucleic acids? What can be used to denature nucleic acids? Can nucleic acids renature?
The forces that stabilize nucleic acids are H-bonding. In addition a stabilizing force for DNA is stacking interactions between bases in a strand. Nucleic acids can be denatured by heat (to boiling) and urea. Yes, nucleic acids can renature.
Outline the role of the 2′ hydroxyl group in RNA. What is the reason this group is lacking in DNA?
More reactive, breaks down, allows better control of regulation of genes. DNA lacks to maintain longevity.
Outline the flow of genetic information in a cell.
Central dogma. The flow of genetic information is DNA to RNA to protein. DNA is transcribed to mRNA in a process called transcription which encodes the DNA to make messenger RNA and the mRNA is then used to make proteins with ribosomes in a process called translation.
List and describe the three types of RNA.
messenger RNA (mRNA): carries the code for amino acids to make proteins.
transfer RNA (tRNA): binds specific amino acids to start protein synthesis.
ribosomal RNA (rRNA): binds mRNA and tRNA and associate with proteins in ribosomes which conduct protein synthesis.
What is a plasmid
A plasmid is a small, circular, mobile genetic element that is common in bacteria. A plasmid has a small number of genes and can replicate on its own without the chromosomal DNA replicating. They can be transferred to bacteria and replicate. That is why they are used for cloning. Genes of interest can be inserted into a plasmid which is then transferred to a bacteria to make many copies of that gene
Why do ketoses have fewer chiral carbons than the equivalent aldoses?
because of their structure
What is the difference between the α anomer and the β anomer of D-glucose?
The α anomer and the β anomer of D-glucose differ in the position of the hydroxyl (OH) group at the anomeric carbon. In the α anomer, the OH substituent of the anomeric carbon is on the opposite side of the ring from the CH2OH group at the chiral centre. In the β anomer, the OH group is on the same side as the CH2OH group.
What prevents branching from both sides of a glucose unit in a polysaccharide?
In theory, nothing prevents branching from both sides of a glucose unit in a polysaccharide. Steric crowding is probably what prevents one sugar from being attached to more than three others (i.e., the branch and the two parts of the main chain). In fact, branches usually protrude from every sixth to tenth unit of the polysaccharide chain, rather than from every monosaccharide unit.
Microorganisms in the gut can hydrolyse the polysaccharides in beans, but not all humans can do so in the process of digestion. How does this fact explain the well-known production of gas that occurs after eating a meal of beans?
Microorganisms, after hydrolysing the polysaccharides to monosaccharides, will continue to process the monosaccharides before the host organism can absorb them. The end product of metabolism is frequently a gas, so that metabolism can proceed smoothly.
Why does paper (which is composed of unoriented cellulose fibres) lose its strength and structure when wet?
Water will penetrate areas of disorder in the cellulose structure. The water molecules will then disrupt some H-bonds by competing with interchain H-bonds.
Chemically, how could you hydrolyze chitin to monosaccharides?
Boiling with a base
You could hydrolyse chitin to monosaccharides by boiling it with a concentrated base. Base hydrolysis is the most efficient way to disrupt most polymeric biochemical molecules, because OH− is such an effective nucleophile.
If cellulose forms such a compact, water-excluding structure, how can ruminants (e.g., cows) hydrolyze it?
Time, chewing cud
Time is the key to ruminant use of cellulose. Humans get one pass at hydrolysing food as it passes through their systems. Ruminants process foods in a more leisurely manner (which is what they are doing while chewing the cud). Continual mechanical processing and exposure to water and enzymes will hydrolyze the cellulose molecule from the outside in.
Compare and contrast the structures and functions of cellulose, chitin, starch, and glycogen.
Cellulose and chitin = structural
glycogen and starch = energy storage
Cellulose and chitin are both structural polysaccharides which mean that they function to provide strength and rigidity.
Cellulose is a linear polymer of up to 15, 000 glucose residues that provides strength to plant cells due to its highly cohesive and hydrogen-bonded structure.
Chitin is the principal structural component of the exoskeletons of invertebrates. It is also found in the cell walls of most fungi and many algae.
Starch and glycogen are both composed of glucose residues and are storage polysaccharides that function as an energy source.
Starch is composed of α-amylose and amylopectin
Starch is the primary energy reserve for plants.
Glycogen is the primary energy reserve for animals.
What common biochemical structure is found in cartilage and hyaluronic acid? Where are cartilage and hyaluronic acid found in the body? Why do they have such different physical properties?
They are Glycoproteins. Flexibility is determined by hydration.
Hyaluronic acid one is more hydrating
Cartilage is the least hydrated and therefore most stiff
If lysozyme is so effective in cleaving the heteropolysaccharide of the bacterial cell wall, why isn’t it used clinically to fight bacterial infection?
Lysozyme is fairly indiscriminate in cleaving polysaccharides. It cleaves the host’s polysaccharides as well as the bacterial cell wall polysaccharides.
Outline the structure of peptidoglycan.
The structure of peptidoglycan is composed of linear chains of alternating β(1 → 4)-linked N-acetylglucosamine and N-acetylmuramic acid. The lactic group of N-acetylmuramic acid forms an amide bond with a D-amino acid-containing tetrapeptide to form the peptidoglycan repeating unit (e.g., L-Ala-D-isoglutamyl-L-Lys-D-Ala in the bacterium Staphylococcus aureus.
What is the mechanism of penicillin’s action on the bacterial cell wall?
binds to enzymes that would grow the bacterial cell wall, preventing the bacterial cell wall from being built, which means the bacteria isn’t protected from the hypotonic environment and the cell lyses.
List the five classes of lipid, and outline their functions.
Fatty acids: composed of carboxyl groups linked to an aliphatic hydro carbon tail
Triacylglycerols: energy storage
glycerophospholipids: major composition of cell membranes
sphingolipids: membrane component used in cell-to-cell recognition and hormone receptors
steroids: component of an animal cell membrane that provides rigidity
What are the names of the predominant fatty acids? How many carbons do they have?
palmitic
oleic
linoleic
stearic acids
18 carbons
Distinguish between unsaturated and saturated fatty acids.
Unsaturated fatty acids contain double bonds and saturated fatty acids are fully saturated with hydrogen and therefore do not contain double C=C bonds. As a result saturated fatty acids have the least amount of steric interference and a higher melting point.
What is the role of phospholipases?
hydrolyze glycerophospholipids of the cell membrane
What are the three types of steroid hormones? What responses do they evoke?
glucocorticoids: e.g., cortisol; affect metabolism and inflammation
aldosterone: regulates the excretion of salt and water by the kidneys
androgens and estrogens: affect sexual development and function.
List the six functions of a membrane according to the textbook.
The six functions of lipid bilayers (membranes) are:
Obtain food for energy for the cell.
Export materials out of the cell.
Maintain osmotic balance.
Create gradients for secondary transport.
Provide an electromotive force for nerve signalling.
Store energy in electrochemical gradients for ATP production (oxidative phosphorylation or photosynthesis).
List and describe the four types of membrane proteins.
integral, peripheral, associated, anchored
Distinguish between passive and active transport, and indicate whether energy is required for each of these processes.
Passive does not require energy and allows certain molecules to flow freely with a concentration gradient
Active requires energy and can conduct antiport, symport, or uniport
Define the terms “vitamin” and “cofactor.”
vitamin = organic compound the body usually can’t make essential for normal growth and nutrition.
cofactor is a non-protein compound or metallic ion that is essential for the activity of an enzyme. Vitamins can be cofactors.
Vitamins?
water soluble = b vitamin
all other letters = fat soluble
A vision
B rna and dna synthesis
D absorption of calcium
K blood clotting
