Bio002 Midterm 2
What are the 4 bases present in DNA?
A, C, T, G Adenine Cytosine Thymine Guanine
Which of the following statements is false regarding the protein Bacteriorhodopsin? - Bacteriorhodopsin is a very large protein. - Bacteriorhodopsin acts as a proton pump. - The polypeptide chain crosses the lipid bilayer at 7 alpha helices. - This protein contains polar amino acid side chains at strategic locations to help guide the movement of the proton. - This protein is found in the plasma membrane of Halobacterium halobium, which lives in salt marshes.
Bacteriohodopsin is a very large protein
Which structural feature is shared by both uracil and thymine?
Both contain 2 ketone groups - Carbon of a Carbonyl group (C=O) is bound to two other non-hydrogen atoms.
What do enzyme active sites and antibody antigen-binding sites have in common?
Both have specific conformations that allow them to bind tightly (but not covalently) to their target molecules.
The energy used by the cell to generate specific biological molecules and highly ordered structures is not stored in the form of ______________. (choose all that apply). - Brownian Movement - Heat - Light Waves - Chemical Bonds
Brownian Movement, Heat, Light Waves
What does membrane fluidity allow for?
Lateral movement of membrane proteins and molecules along a monolayer Endo and exocytosis Even distribution of cell membrane upon cell division
Euchromatin
Less condensed Eukaryotic chromatin - Genes are expressed
The classic "beads-on-a-string" structure is the most decondensed chromatin structure possible and is produced experimentally. Which chromatin components are NOT retained when this structure is generated?
Linker Histones (H1)
Enzyme Protein Example
DNA polymerase
(Q039) Both glycoproteins and proteoglycans contribute to the carbohydrate layer on the surface of the cell. Which of the following statements about glycoproteins is FALSE? They can be secreted into the extracellular environment. They have only one transmembrane domain. They have long carbohydrate chains. They are recognized by lectins.
They have long carbohydrate chains
Types of Integral proteins
Transmembrane, monolayer associated, and lipid linked
(Most/All/Some/No) genes contain information to make proteins
Most Some genes code for RNA
What are the two popular activated carriers that transfer electrons
NADH and NADPH
How do NADH and NADPH differ in structure and function?
NADH and NADPH differ in the presence of a phosphate group, which NADPH has and NADH does not. NAD+ in the body is used as an oxidizing agent for many catabolic reactions (breaking down food molecules) while NADPH is used as a reducing agent for many anabolic reactions (building molecules)
What are the types of membrane proteins?
TRACIE Transporters Receptors Anchors Cell-Recognition Intercellular connection proteins Enzymes
Nuclease
breaks down nucleic acids by hydrolyzing bonds between nucleotides
Protease
breaks down proteins by hydrolyzing peptide bonds between amino acids
A peptide bonds links..
carbon and nitrogen together
Polymerase
catalyzes polymerization reactions such as the synthesis of DNA and RNA
Phosphatase
catalyzes the hydrolytic removal of a phosphate group from a molecule
Isomerase
catalyzes the rearrangement of bonds within a single molecule
The most highly condensed form of interphase chromatin is
heterochromatin
Structural Protein Example
collagen
High energy electrons in activated carriers are (tightly/loosely) associated with the atomic nucleus.
loosely, because they are readily transferable
What makes it possible for proteins to have secondary structures?
hydrogen bonds along the backbone
Whhat is an antibody made of?
light chains Fab (Fragment, antigen binding) heavy chains disulfide bonds antigen binding site
H1 histone is also called a
linker histone
Vmax (is/is not) changed in the presence of competitive inhibitors and (is/is not) changed in the presence of noncompetitive inhibitors
is not; is
In some cases, small molecules are integral to the function of enzymes, and are dubbed "coenzymes." Which of the following is a coenzyme for the enzyme carboxypeptidase?
zinc
Which bases are purines?
"Pure Silver (Ag)" Adenine Guanine
Another way of altering chromatin structure relies on the reversible chemical modification of the histones using covalent interactions. The tails of all four of the core histones are particularly subject to these covalent modifications. Which groups can be added to and removed from the tails by enzymes that reside in the nucleus? (Select all that apply) - Acetyl groups - Methyl groups - Phosphate groups - Adenine bases
- Acetyl groups - Methyl groups - Phosphate groups
How can phosphorylation be used to regulate protein activity?
- Can activate or deactivate a protein - Can allow for the binding of other molecules to the protein
What are the Chargaff rules?
1) The base composition (nucleotide sequence) of DNA varies between species 2) For each species, the percentages of A and T are roughly equal while the percentages of G and C are roughly equal.
How many base pairs are present for one full turn of the DNA double helix?
10 base pairs
How many base pairs are present in a nucelosome?
147
(Q015) Which of the following would yield the most highly mobile phospholipid (listed as number of carbons and number of double bonds, respectively)? 24 carbons with one double bond 15 carbons with two double bonds 20 carbons with two double bonds 16 carbons with no double bonds
15 carbons with two double bonds
The most common number of carbons in fatty acid hydrocarbon chains of membrane phospholipids is: (closest answer) 16. 1. 4. 27. 10.
16
Compared to mitotic chromosomes, interphase chromosomes are ________ compressed.
20 times less condensed
For a polypeptide that is "n" amino acids long, how many possible combinations are there?
20^n
The human genome is a diploid genome. However, when germ-line cells produce gametes, these specialized cells are haploid. What is the total number of chromosomes found in each of the gametes (egg or sperm) in your body?
23
Somatic cells contain how many chromosomes?
46 chromosomes which are made up of 22 pairs of chromosomes and 2 sex chromosomes
What is bacteriohodopsin
A proton pump membrane protein found in archael cells that contains retinal. - Retinal absorbs light and causes a conformational change that allows a proton to travel out of the cell.
Isoelectric Focusing
A specialized method of separating proteins by their isoelectric point using electrophoresis; the gel is modified to possess a pH gradient - molecules migrate to the pH at which they have a net charge of 0.
Nuclear Magnetic Resonance (NMR) Spectroscopy
A technique that measures the alignment of magnetic moments from certain molecular nuclei with an external magnetic field; can be used to determine the connectivity and functional groups in a molecule.
X-Ray crystallography
A technique used to study the three-dimensional structure of molecules. It depends on the diffraction of an X-ray beam by the individual atoms of a crystallized molecule.
When the hydrolysis of ATP does not produce enough energy to power an unfavorable reaction, ATP can be hydrolyzed into _____________ and ___________ instead.
AMP and Pyrophosphate - The pyrophosphate is then hydrolyzed into two inorganic phosphates.
One of the key features of living systems is the use of energy to create and maintain order. A good example is found in the folding of newly synthesized proteins. Which activated carrier molecule is used by chaperone proteins to support protein folding?
ATP
The most widely used activated carrier is
ATP
What molecule is often hydrolyzed in an energetically favorable reaction, to power unfavorable reactions?
ATP
The coupled reaction of ___ hydrolysis to ___ produces directed movement in eukaryotic cells, due to conformational changes in motor proteins
ATP, ADP
What is an enzyme
An enzyme is a protein that acts as a catalyst for ONE specific reaction
Chemical reactions carried out by living systems depend on the ability of some organisms to capture and use atoms from nonliving sources in the environment. The specific subset of these reactions that use protein to build muscle is
Anabolic
When there is an excess of nutrients available in the human body, insulin is released to stimulate the synthesis of glycogen from glucose. This is a specific example of a/an __________ process, a general process in which larger molecules are made from smaller molecules.
Anabolic
What are the 2 types of metabolism and how are they different?
Anabolism and Catabolism Catabolism = Complex -> Simple - Releases usable energy while some energy is lost as heat - Energetically favorable (spontaneous) Anabolism = Simple -> Complex - Uses energy to create bonds between two molecules - Energetically unfavorable (nonspontaneous)
What is a ligand?
Ant molecule that is bound to a protein by noncovalent forces - Can be signals, substrates, regulatory molecules, etc.
What does an antibody use to recognize an antigen?
Antibodies use antigen-binding sites formed from several loops of polypeptide chain that protrude from the ends of variable light (VL) and heavy chain (VH)
Quaternary structure bonds
Any type of bond between R-side chains of different polypeptides.
Tertiary structure bonds
Any type of bond between the R-side chains of the polypeptide - 3-D structure is obtained here.
How can chromosomes be arranged in the nucleus?
Attached to the nuclear envelope, attached to the nuclear lamina (basically the cell cortex but for the nuclear envelope), or can be concentrated in one specific place.
What part of the chromatin fiber does the remodeling complex directly attach to? Select all that apply. Attaches to histone octamer attaches to the RNA attaches to the lipid backbone attaches to the DNA wrapped around histone octamer None of the above
Attaches to the histone octamer Attached to the DNA wrapped around the histone octamer
How are cells able to confine specific proteins to membrane domains?
Attaching them to stuctures in the ECM, attaching them to the cortex, or creating barriers called tight junctions that restrict lateral movement of proteins past the barrier
You are a virologist interested in studying the evolution of viral genomes. You are studying two newly isolated viral strains and have sequenced their genomes. You find that the genome of strain 1 contains 25% A, 55% G, 20% C, and 10% T. You report that you have isolated a virus with a single-stranded DNA genome. Based on what evidence can you make this conclusion?
Because double stranded DNA has equal amounts of A and T
Why are proteins the main "building blocks of life"?"
Because of all the different shapes they can take on
How is heterochromatin formed and propagated?
Begins with the methylation of lysine 9 on histone H3. - This methyl group then attracts heterochromatin specific proteins as well as histone modification proteins that methylate the adjacent histones on other nucleosomes, therefore propagating the heterochromatin - STOPS WHEN IT HITS A BARRIER SEQUENCE: sequence of DNA that binds a barrier protein which prevents the histone modification proteins from traveling any further.
The equilibrium constant for complex formation between molecules A and B will depend on their relative concentrations, as well as the rates at which the molecules associate and dissociate. The association rate will be larger than the dissociation rate when complex formation is favorable. The energy that drives this process is referred to as __________ energy.
Binding
In amino acids, the end carrying the amino group is called the amino terminus, or ___ and the end carrying the free carboxyl group is the carboxyl terminus, or ___.
N-terminus, C-terminus
Are all biological enzymes proteins?
No
Are enzymes changed after catalyzing a reaction?
No
Are interphase chromosomes in the nucleus arranged randomly?
No they are arranged so that they dont tangle, and through flourescent tagging, we can see that they are arranged in specific places in the nucleus.
Which property is found in nucleosides and nucleotides?
Both contain an anomeric carbon atom that is part of a β-N-glycosidic bond. - This carbon is the 1' carbon that is attached to the nitrogenous base in both nucleosides and nucleotides
Which property is shared by both GDP and AMP? Both contain the same furanose. Both contain the same charge at neutral pH. Both contain the same number of phosphate groups. Both contain the same purine. None contain the same purine.
Both contain the same furanose - Furanose refers to any 5 carbon ring carbohydrate that has 4 carbons in the ring and an oxygen, with the last carbon being held apart from the ring. -> Deoxyribose and ribose are examples of this.
How do cells create order when entropy must always increase?
Cells create order inside themselves by making its environment more disordered leading to an overall increase in entropy in the isolated system (cell + environment)
What are genes made of?
DNA
Chromosomes are made up of a complex of?
DNA and Protein
What is the structure of DNA
DNA contains 2 polynucleotide strands, made up of 4 types of nucleotides, that run antiparallel to one another in a double helix, and are bound together by hydrogen bonds between the nitrogenous bases.
What is the first level of compaction of genetic information?
DNA is wrapped tightly around 8 positively charged histone proteins (2 each of H2A, H2B, H3, and H4) forming a nucleosome. - Nucleosomes are connected by linker DNA - This is chromatin
Activated carriers (such as ATP and NADH/NADPH) serve as sources of what for biosynthetic reactions?
Energy and Chemical Groups
Biosynthesis
Energy requiring reactions -> building molecules ("synthesis)
What is the name of the catalysts used by cells to lower the activation energy of a given reaction?
Enzymes
How is the amino acid glutamate formed?
First, the OH on glutamic acid is replaced with a phosphate group, then the phosphate group is replaced by an NH3 group.
What methods are used to study membrane fluidity?
Fluorescence Recovery After Photobleaching (FRAP) Single Particle Tracking (SPT) Separation from the membrane through detergents
How do monolayer associated proteins embed themselves in the plasma membrane?
Formation of alpha helices
Stepwise condensation of linear DNA happens in five different packing processes. Which of the following four processes has a direct requirement for histone H1?
Formation of the 30-nm fiber
Which DNA base pair is represented by a purine(left) connected to a pyrimidine (right), held together by 3 hydrogen bonds? (Answer from left to right)
G-C
Reduction reactions
Gain of electrons; Loss of Oxygen; Gain of Hydrogen - Hydrogenation ( when molecules pick up electrons, they also pick up H+ or protons from the environment resulting in hydrogenation) A + e- + H+ -> AH
Oxido-reductase
General name for enzymes that catalyze reactions in which one molecule is oxidized while the other is reduced. Enzymes of this type are often called oxidases, reductases, or dehydrogenases
What are the 2 types of protein shapes?
Globular and Fibrous
Which of the following molecules would not readily cross an intact cell membrane by simple diffusion, but would require a facilitator protein? oxygen water thyroid hormone glucose fatty acids
Glucose
Nonpolar amino acids
Glycine, Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Methionine, Proline, Cysteine
Describe Griffiths experiment and what conclusion it led to
Griffiths experiment showed that genetic information originates from a specific molecule by showing that heat-killed bacteria were able to make nonlethal strains of bacteria, permanently lethal through the transfer of some molecule, but was not able to determine what that molecule was. The experiment involved injecting mice with different combinations of a lethal strain and harmless strain of S. pneumoniae into mice. When injecting the lethal strain the mice died. When injecting heat killed versions of the lethal strain, the mice lived. When injecting the mice with a combination of heat killed lethal strain and harmless strain into the mice, the mice died and the harmless strain were now pathogenic.
What do handles often contain and what is a theory for why this is?
Handles often contain nucleotides and a theory that explains this is that the early catalysts were RNA molecules (ribozymes)
Heterochromatin
Highly condensed eukaryotic chromatin - Genes are not expressed
________ are responsible for the first and most fundamental level of chromatin packing, the nucleosome.
Histones
What does Enzyme catalyzation rate depend on?
How fast and how often enzyme collides with its substrate - Increase in substrate concentration increases catalyzation rate - Increase in temperature increases catalyzation rate How fast the products form and diffuse away
Secondary structure bonds
Hydrogen bonds between the atoms of the polypeptide backbone
ATPase
Hydrolyzes ATP. Many proteins have an energy-harnessing ATPase activity as part of their function, including motor proteins such as myosin and membrane transport proteins such as the sodium pump
When a cell that already has an inactivated X chromosome, divides, does the selection of which X chromosome will be inactivated take place again?
No. All descendants that originate from a cell that already has one of the X chromosomes deactivated, will have that same X chromosome deactivated.
Is the same X-chromosome inactivated in all the normal cells of a female tissue?
No. Females are therefore known as a mosaic because the selection of which X chromosome will be inactivated in each cell of the entire female body, is random, except for those that originate from other cells that already have an inactivated chromosome.
Are genes normally present in heterochromatin?
No. If they are they do not get expressed because they are inaccessible by transcriptional proteins.
What is the difference between competitive and noncompetitive inhibition?
Noncompetitive inhibition cannot be overcome by increasing substrate concentration while competitive inhibition can be.
If the reaction X-> Y is followed by the sequential energetically favorable reaction Y-> Z, is the equilibrium constant for the X-> Y reaction changed? Why or why not?
It is not because the equilibrium concentrations is kept constant since as the Y disappears, more X is converted to Y keeping the concentration ratio of product to reactant constant.
Ligase
Joins two molecules together; DNA ligase joins two DNA strands together end-to-end
What is the relationship between KM and the strength of binding b/w substrate and enzyme?
Large KM = Weak binding because it take a larger concentration of the substrate to reach half of the enzymes max saturation Small KM = Strong binding because it takes less concentration of substrate to reach half of the enzymes max saturation
Membrane fluidity is affected by what 2 properties of lipid molecules?
Length of fatty acid tails - Longer tails make bilayer more rigid while shorter tails make the membrane less rigid. Saturation of fatty acid tails - unsaturated fatty acid tails (tails with double bonds) make the membrane more fluid while saturated fatty acid tails make the membrane more rigid because the tails pack together
Localized regions of membrane lipids that contain proteins involved in cell signaling are known as, [These are also known by other names too] homeoviscous adaptations. membrane leaflets. islands of hydropathy. hopanoids. lipid rafts.
Lipid rafts
Glycolipids
Lipids in the plasma membrane that have carbohydrates as their polar heads (oligosaccharides) - Only present in the noncytosolic layer of the plasma membrane
Oxidation reactions
Loss of electrons; Gain of Oxygen; Loss of Hydrogen - Dehydrogenation
(Q006) Which of the following statements is TRUE? Phospholipids will spontaneously form liposomes in nonpolar solvents. In eukaryotes, all membrane-enclosed organelles are surrounded by one lipid bilayer. Membrane lipids diffuse within the plane of the membrane. Membrane lipids frequently flip-flop between one monolayer and the other.
Membrane lipids diffuse within the plane of the membrane.
What is metabolic disequilibrium and why is it important?
Metabolic disequilibrium refers to the ability of cells to keep themselves in a state of constant disequilibrium by either removing products or adding reactants. If cells reach equilibrium they will die as there is no input of energy.
FRAP
Method involving irreversible straining an area with a fluorescent marker, then photobleaching a small area and seeing how long it takes for non-bleached/non-fluorescent proteins to travel into the bleached area. - Revealed that most membranes are about as viscous as olive oil.
Single Particle Tracking
Method that involves the trackign of a single or small bath of proteins in the membrane by tagging with gold
Separation from Membrane
Method that uses detergents to isolate and purify a protein from the membrane, then placing the protein in an artificial membrane to study its behavior. - Proteins diffuse laterally more rapidly in artifical membranes due to lack of membrane crowding and cellular attachments.
How is the rate of catalysis of enzymes measured?
Michaelis Constant
What is the second level of compaction of genetic information?
Nucleosomes are further packed together by the H1 histone, which changes the angle of the DNA to allow for compaction, into 30 nm wide chromatin fibers.
What is the difference between a nucleotide and a nucleoside?
Nucleotides have the base, sugar, and phosphate Nucleosides are only the base and the sugar.
What are activated carriers?
Organic molecules that can contain READILY TRANSFERRABLE high energy bonds or high energy electrons, that store chemical energy used to power nonfavorable reactions
Seed oils are often dehydrogenated and added back into processed foods. The new fatty acids have an increased number of carbon-carbon double bonds. The dehydrogenation reaction could also be described as a/an __________ reaction.
Oxidation
Your body extracts energy from the food you ingest by catalyzing reactions that essentially "burn" the food molecules in a stepwise fashion. What is another way to describe this process?
Oxidation
Which of the following is the most common phospholipid in cell membranes? Phosphatidylcholine Phosphatidylethanolamine Phosphatidylinositol Phosphatidylserine None of the above
Phosphatidylcholine
Phosphatidylinositols
Phospholipids that trasmit extracellular signals intracellularly - Only present in the cytosolic layer of the plasma membrane
Plants can produce O2 from H2O despite it being an unfavorable chemical reaction. How are plants able to do this?
Plants absorb light which provides energy to convert H2O into O2
Protein Domain
Segment of a polypeptide chain that can fold independently into a compact and stable structure made up of one or more alpha helices or B sheets. - The different protein domains of a protein usually have specific functions.
Chromatography
Separates the protein into fractions, most commonly based on binding affinity. (affinity) Determinines precise masses of peptides derived from the protein. (mass)
What are intrinsically disordered sequences?
Sequences in a polypeptide that link protein domains to each other and have other processes - They lack any definite structure and are very flexible - Can increase the number of interactions between the domains of a protein.
What stabilizes the extremely fragile cell membrane in animal cells?
The cortex: A meshwork of fibrous proteins connected to the membrane indirectly by transmembrane proteins. - Other functions include: strengthens the cell, functions in selective intake of materials, change the shape of the cell actively and can restrain the lateral movement of membrane proteins.
Where is the membrane bilayer made?
The cytosolic monolayer of the endoplasmic reticulums membrane
Why is ATP hydrolysis coupled to the movement of motor proteins?
The energy released by ATP hydrolysis creates an energy barrier high enough that the reverse reaction cannot happen without an input of energy, therefore keeping the motor proteins moving unidirectionally and not backwards.
When there is a very large tear in the plasma membrane, what will happen?
The plasma membrane will spontaneously split and form liposomes. They will do this because if there is a very large tear, the phospholipids cannot rearrange to close such a large gap and would instead seek the more energetically favorable structure by associating into liposomes.
What is X-inactivation?
The process by which one of the X chromosomes in female cells, is inactivated by extremely large amounts of methylation. None of the genes on the Barr body are expressed.
How do proteins fold?
Through noncovalent bonds; hydrogen bonds, electrostatic attractions and van der Waals interactions hydrophobic interactions havea central role in determining shape when in an aqueous environment; polarity
Which bases are pyrimidines?
Thymine and Cytosine
Activated carriers are made up of what 2 parts?
Transferrable group and the handle
What phenomenon allowed the harmless strain in Griffiths experiment to become PERMANENTLY pathogenic?
Transformation: The ability of bacteria to uptake and integrate DNA from their surroundings into their own genome when under extreme stress.
Since the cell membrane is packed with lipids, in order for nutrients to cross the membrane and reach the cytoplasm, what kinds of macromolecules facilitate such processes that are located in the membrane? - Transporter proteins. - Water molecules bound to nutrients through hydrogen bonds. - Glucose molecules that provide the energy for transportation.
Transporter proteins
Enzymes catalyze the forward and backward reactions the same amount T/F
True
Histones are the one of the most evolutionarily conserved proteins of ALL eukaryotic proteins T/F
True
Transmembrane proteins must have a hydrophobic portion on the inside of the bilayer and hydrophilic portions EVERYWHERE else T/F
True
lysozyme
a natural antibiotic that severs polysaccharide chains of bacterial cell walls, causing bacteria lysing
How do changes in histone modifications lead to changes in chromatin structure?
They help recruit other proteins to the chromatin. These proteins then function to change the structure of the chromatin such as the histone modification proteins part of the heterochromatin specific proteins recruited by methylation of Lysine 9 on H3.
(Q028) Which of the following best describes the mechanism by which chromatin-remodeling complexes "loosen" the DNA wrapped around the core histones?
They use energy derived from ATP hydrolysis to change the relative position of the DNA and the core histone octamer.
Building a peptide from amino acids is a(n) ______________ reaction. It ______________ energy.
anabolic; requires the input of
Membranes contain several classes of lipids, such as phospholipids, sphingolipids, sterols, etc. In spite of their many differences, they all easily react with bases but not with acids. can be easily hydrolyzed. are readily soluble in water at 37C. are soluble in nonpolar solvents. can be reduced by strong reducing agents such as sodium.
are soluble in nonpolar solvents
Uncharged polar amino acids
asparagine, glutamine, serine, threonine, tyrosine
What are association and disassociation rates equal to?
association rate is equal to the concentration of reactant 1 MULTIPLIED by the concentration of reactant 2 because the reactant molecules must collide in order to react.
With respect to the outer and inner faces of the lipid bilayer of the cell membrane, the composition of proteins is, [Kaltura Video segment explains all] highly random and varies throughout the cell. a mirror image. identical. asymmetrical. not identical but symmetrical.
asymmetrical
What are chromatin-remodeling complexes and how are they used to regulate chromosome structure?
chromatin-remodeling complexes are protein machines that can modify the compactness of chromatin by moving the position of nucleosomes, through the HYDROLYSIS OF ATP. - Regulate chromosome structure by making specific regions of chromatin, tighter or looser to allow or restrict access to genes in the DNA - Moving JUST the nucleosomes make certain sequences on the DNA more or less accessible
ATP hydrolysis can be coupled with a __________ reaction through 2 steps: activation and condensation.
condensation reaction 1st step: OH group on the molecule that will undergo condensation is replaced by the phosphate group released upon hydrolysis of ATP 2nd Step: Phosphoanhydride bond holding the phosphate to the molecule is broken and the energy released is used to replace the phosphate group with some other moelcule.
The bonding of various macromolecules to a protein can be required for the protein to function correctly. A photoreceptor protein, rhodopsin, which is the light-sensitive protein made by the rod cells in the retina, detects light by means of a small molecule, retinal, which is attached to the protein by a ___ to a lysine side chain
covalent bond
Studies conducted with a lysozyme mutant that contains an Asp→Asn change at position 52 and a Glu→Gln change at position 35 exhibited almost a complete loss in enzymatic activity. What is the most likely explanation for the decrease in enzyme activity in the mutant?
absence of negative charges in the active site The negatively charged amino acids aspartic acid and glutamic acid are required to attack the sugar bonds being cleaved by lysozyme. Replacing these with side chains that are the same length and are polar, but uncharged, would most probably affect only the catalysis, not the binding of substrate or the stability of the protein.
Changes in Free energy are_______
additive
Similarly to Hess's Law for Changes in enthalpy, changes in free energy for sequential reactions are _______________.
additive
The process of generating monoclonal antibodies is labor-intensive and expensive. An alternative is to use polyclonal antibodies. A subpopulation of purified polyclonal antibodies that recognize a particular antigen can be isolated by chromatography. Which type of chromatography is used for this purpose?
affinity
Energy required by the cell is generated in the form of ATP. ATP is hydrolyzed to power many of the cellular processes, increasing the pool of ADP. As the relative amount of ADP molecules increases, they can bind to glycolytic enzymes, which will lead to the production of more ATP. The best way to describe this mechanism of regulation is
allosteric activation
What is a characteristic of all molecules that are embedded in the plasma membrane?
amphipathic
(Q027) Methylation and acetylation are common changes made to histone H3, and the specific combination of these changes is sometimes referred to as the "histone code." Which of the following patterns will probably lead to gene silencing?
lysine 9 methylation
Membrane orientation is _____________ even through movement of membrane in vesicles.
maintained
The inactivation of one X chromosome is established by the directed spreading of heterochromatin. The silent state of this chromosome is __________ in the subsequent cell divisions.
maintained
Genetic information is stored in the ___________ of ___________ cells as __________
nucleus; eukaryotic; chromosomes
When genes are expressed _________ of the nucleotide sequence is transcribed into RNA molecules, ___________ of which are translated to proteins.
part; many
Membrane domains
functionally specialized regions on the membrane that contain specific proteins
Which of the following methods would be the most suitable to assess the relative purity of a protein in a sample you have prepared?
gel electrophoresis
Which of the following methods would be the most suitable to assess whether your protein exists as a monomer or in a complex?
gel-filtration chromatography
(Q026) The N-terminal tail of histone H3 can be extensively modified, and depending on the number, location, and combination of these modifications, these changes may promote the formation of heterochromatin. What is the result of heterochromatin formation?
gene silencing
The complete set of information in an organism's DNA is called its
genome
Which of the following molecules would not readily cross an intact cell membrane by simple diffusion, but would require a facilitator protein? oxygen water thyroid hormone glucose fatty acids
glucose
Cell surfaces are coated with_________
glycoproteins
Transport Protein Example
hemoglobin
The condensation reaction that connects monomers to make macromolecules is coupled with the hydrolysis of ATP by first converting the monomer to a ________________.
high energy intermediate - Similar to synthesis of glutamine
In eukaryotic chromosomes, the DNA is tightly folded by binding to a set of _________ and ___________ _____________. This complex of DNA and protein is called __________.
histones; nonhistone proteins; chromatin
Example of gene regulatory proteins
homeodomain proteins
Some proteins have alpha-helices, some have beta-sheets, and still others have a combination of both. What makes it possible for proteins to have these common structural elements?
hydrogen bonds along the protein backbone
Lysozyme is an enzyme that specifically recognizes and breaks exterior bacterial polysaccharides, which renders it an effective antibacterial agent. Into what classification of enzymes does lysozyme fall?
hydrolase
Many integral membrane proteins have not been analyzed by X-ray crystallography.However, transmembrane segments can be inferred using computer analysis of the aminoacid sequence of the protein. This technique is known as lipid rafting. lipid analysis. SDS-PAGE. hydropathic analysis. homeoviscous adaptation.
hydropathic analysis
The likely number of and locations of transmembrane segments of integral membrane proteins is inferred by hydropathic analysis. western blot. affinity labeling. X-ray crystallography. SDS-PAGE.
hydropathic analysis
The 5' end of DNA contains _____________ while the 3' end contains ______________
phosphate group; Hydroxide
TECHNIQUE: Inactivation of a fluorescent dye in a very concentrated spot on a cell so that the fluidity of membranes can be subsequently visualized is called, liposome formation. ferritin-conjugated lectins. the freeze-fracture technique. SDS-PAGE. photobleaching.
photobleaching
Cell-cell communication in plants takes place via specialized structures called cell wall pores. desmids. gap junctions. connexons. plasmodesmata.
plasmodesmata
The four histones that make up the octamer are proteins, with a high proportion of ___ amino acids, which help the histones bind tightly to the ___ sugar-phosphate backbone of DNA
positively charged; negatively charged
The secondary structures of a protein are the_____
regular, repeated folds present in a lowest energy conformation.
what is a protein backbone made up of?
repeating -N-C-C- sequence found in every amino acid one end has an amino group: N-terminus one end has the carboxyl group: C-terminus coming off the backbone are amino acid side chains, which are not involved in forming peptide bonds
Antibody production is an indispensable part of our immune response, but it is not the only defense our bodies have. Which of the following is observed during an infection that is NOT a result of antibody-antigen interactions?
systematic temperature increase
In a DNA double helix,
the two DNA strands run antiparallel
The correct folding of proteins is necessary to maintain healthy cells and tissues. The presence of unfolded proteins are associated with some neurodegenerative disorders as Alzheimer's disease, Huntington's disease, and Creutzfeldt-Jakob disease (the specific faulty protein is different for each disease). What happens to these disease-causing, unfolded proteins?
they form protein aggregates
The hydrolysis of ATP to AMP and Pyrophosphate produces __________ as much energy as hydrolysis of ATP to ADP and P.
twice
Activated carrier activation is an energetically ______________ process that is often coupled with an energetically ______________ process that powers it
unfavorable; favorable - Such as the oxidation of food molecules.
What is the second law of thermodynamics?
The entropy of an isolated system always increases
What is Michaelis Constant?
KM = The concentration of substrate at which the enzyme is functioning at half its maximum speed. Concentration at 1/2 Vmax
If you have a strand of DNA in which 20% of the bases are adenine, what percentage of guanine do you have?
30%
Electrophoresis
A mixture of proteins is loaded on a polymer gel and subjected to an electrical field, where they are separated by electrical charge
Negatively charged amino acids:
Aspartic acid, Glutamic acid
Extracellular proteins are often stabilized by covalent cross-linkages. The most common covalent cross-linkage is ______.
disulfide bond
(Q027) In the photosynthetic archaean Halobacterium halobium, a membrane transport protein called bacteriorhodopsin captures energy from sunlight and uses it to pump protons out of the cell. The resulting proton gradient serves as an energy store that can later be tapped to generate ATP. Which statement best describes how bacteriorhodopsin operates? - The absorption of sunlight triggers a contraction of the β barrel that acts as the protein's central channel, squeezing a proton out of the cell. - The absorption of sunlight triggers a shift in the conformation of the protein's seven, membrane-spanning α helices, allowing a proton to leave the cell. - The absorption of sunlight triggers a restructuring of bacteriorhodopsin's otherwise unstructured core to form the channel through which a proton can exit the cell. - The absorption of sunlight triggers the activation of an enzyme that generates ATP.
- The absorption of sunlight triggers a shift in the conformation of the protein's seven, membrane-spanning α helices, allowing a proton to leave the cell.
What do molecular chaperones do?
- They assist polypeptide folding by helping the folding process follow the most energetically favorable pathway. - They interact directly with the RNA - They help streamline the protein-folding process by making it a more efficient and reliable process inside the cell. - They can isolate proteins from other components of the cells until folding is complete. They cannot interact with unfolded polypeptides in a way that changes the final fold of the protein
Select all that apply. One of the two X chromosomes is inactivated in the cells of mammalian females by heterochromatin formation. What would happen if the X-inactivation did not occur? - Women would make double the amount of proteins encoded by the X chromosome - It would cause a genetic disorder such as downs syndrome - Females genetic makeup would be more closely related to males - There would be no change
- Women would make double the amount of proteins encoded by the X chromosome - It would cause a genetic disorder such as downs syndrome Trisomy 21 is caused by extra chromosome information, therefore having an extra X chromosome is similar to trisomy.
Hydrolysis of ATP has approximately what free energy change?
-13 kcal/mol
What are the 3 specialized sequences found in DNA, and how many of each are there?
1) Replication origins: There are multiple origins of replication along the eukaryotic chromosome. This sequence of DNA allows for the binding of specialized proteins to initiate DNA replication. 2) Telomers: There are 2 telomeres, one at each end of every chromosome. Telomeres are noncoding repeating sequences that cap the DNA at both ends and serve to prevent the breakdown of any genes since DNA gets shorter with each replication. - Also classify the DNA as intact, so the cell does not destroy it. 3) Centromere: There is 1 centromere in each chromosome. Centromeres are regions of HIGHLY condensed chromatin which serve as the location where duplicated chromosomes split during mitosis
How many hydrogen bonds form between A and T versus C and G?
A and T form 2 hydrogen bonds C and G form 3
Motor proteins use the energy in ATP to transport organelles, rearrange elements of the cytoskeleton during cell migration, and move chromosomes during cell division. Which of the following mechanisms is sufficient to ensure the unidirectional movement of a motor protein along its substrate?
A conformational change is coupled to ATP hydrolysis.
Karyotype
A display of all the chromosomes in a cell paired up, by number.
Fully folded proteins typically have polar side chains on their surfaces, where electrostatic attractions and hydrogen bonds can form between the polar group on the amino acid and the polar molecules in the solvent. In contrast, some proteins have a polar side chain in their hydrophobic interior. Which of the following would NOT occur to help accommodate an internal, polar side chain?
A hydrogen bond forms between a polar side chain and an aromatic side chain.
What is a metabolic pathway?
A metabolic pathway is a series of reactions in which the products of one are the reactants of the next, where each reaction can be catalyzed by a different enzyme.
Phosphorylation can be used to either activate or deactivate a protein. How?
Addition of the phosphate group can change the conformational structure of the protein because, phosphate carry 2 negative charges which can attract positively charged amino acids from the other end of the protein, therefore changing its shape. - This shape change may lead to better/improved substrate binding or can be used to turn off a molecule.
When can a cell enter M Phase?
After chromosomes have been duplicated
Positively charged amino acids
Aginine, Lysine, Histidine
Metabolism
All of the chemical reactions that occur in an organism
A glycolipid molecule may do which of the following? Lateral diffusion on the plane of the membrane Flexion of its fatty acid tails Rotation about its axis All of the these None of the these
All of these
The flexibility of the membrane and its capacity for expansion allow the cell to do which of the following? All of the these None of the these Grow Change shape Move
All of these
Which of the following is a major class of membrane lipid molecules? All of the these. phospholipids sterols glycolipids None of the above
All of these
Evaluate the ways in which proteins work to keep a membrane selectively permeable. - All of the these are true - Many membrane bound proteins are transporters, each with a specific mechanism to allow for entrance of a molecule into the cell - Many membrane bound proteins are channels, each with a hydrophobic pore across the membrane which allows for diffusion across the membrane - Certain cells can immobilize certain membrane proteins by attaching them to intracellular or extracellular macro molecules - The attached sugar chains on some proteins that are attached to lipids not only act to lubricate the cells, but are also involved in cell-cell recognitions
All of these are true
Which of the following are possible functions of plasma membrane proteins? All of these are true. Transporters Anchors Receptors Enzymes
All of these are true.
What is true about allostery?
Allosteric regulators are often products of other chemical reactions in the same biochemical pathway.
Standard free energy change allows what to be calculated? what is the equation used?
Allows the calculation of free energy change for a reaction with different concentrations of product and reactant. ΔG = ΔG° + RT ln [Product]/[Reactant]
What is the significance of the ability of histone modifications being able to serve as docking sites for regulatory proteins?
By allowing the binding of certain regulatory proteins, the histone modification allows for different patterns and combinations of modifications + regulatory proteins to mean different things to the cell. - Since histone tails can receive multiple modifications, a wide variety of combinations of proteins and modifications are possible.
The biosynthetic pathway for the two amino acids E and H is shown schematically in Figure 4-33. You are able to show that E inhibits enzyme V, and H inhibits enzyme X. Which biosynthetic product is most likely the inhibitor of enzyme T? (see figure 4-33)
C
Oxidation is a favorable process in an aerobic environment, which is the reason cells are able to derive energy from the oxidation of macromolecules. Once carbon has been oxidized to __________, its most stable form, it can only cycle back into the organic portion of the carbon cycle through __________.
CO2; Photosynthesis
THINK BEYOND: A colleague gives you two membrane fractions from a plant cell lysate. One contains the plasma membrane fraction, the other the mitochondrial fraction. The tubes are not labeled, but you run the samples anyway, looking at the macromolecule composition of the samples. You know for certain that the second sample contains the mitochondrial fraction simply because it contains insignificant amounts of, carbohydrates. specifically phospholipids. lipids. protein. None of the above
Carbohydrates
Kinase
Catalyzes the addition of phosphate groups to molecules. Protein kinases are an important group of kinases that attach phosphate groups to proteins
Histone Methylation
Causes chromatin to condense forming HETEROCHROMATIN. - Most commonly occurs on the 9th lysine of the H3 histone of the nucleosome. - Can occur to lysine (K) or Arginine (R)
Histone Phosphorylation
Causes chromatin to loosen forming EUCHROMATIN since the addition of phosphate groups to histone tails make them slightly negative, repelling the negatively charged DNA molecule, making it more accessible. - Can occur on serine, Threonine, and Tyrosine
Histone Acetylation
Causes chromatin to loosen forming EUCHROMATIN since the addition of the acetyl groups to histone tails make them slightly negative, repelling the negatively charged DNA molecule, making it more accessible. - Can occur on Arginine, Lysine, Threonine, Serine, and Histidine
What are the functions of the plasma membrane that are assisted by membrane proteins?
Cell communication cell motility and growth import/export of molecules
What are some things that chromatin remodeling proteins can do?
Change the position of DNA wrapped around nucleotides Make DNA more accessible Make DNA less accessible Slide nucleosomes along DNA
In non animal cells, how is membrane fluidity controlled?
Changing of phospholipid fatty acid tail length and saturation
A prokaryotic organism is isolated from a hydrothermal vent, where it has been observed to be thriving. Based on your knowledge of the plasma membrane, what would you not expect to find Long-tail fatty acids. Saturated fatty acids. cholesterol. fatty acids with polar heads. none of the these answers
Cholesterol
What is the fourth level of compaction of genetic information?
Chromatin composed looped domains are tightly compressed to form a compressed chromosome characteristic of the mitotic chromosome.
What is the third level of compaction of genetic information?
Chromatin fibers form loops around the chromosome scaffold, forming 300 nm structures called looped domains.
What are the 2 mechanisms by which cells are able to regulate chromosome structure?
Chromatin- Remodeling complexes Reversible Histone Modification
What methods separate or isolate proteins?
Chromatography Electrophoresis Isoelectric Focusing
What is a common method for cells drive a reaction with a positive ΔG?
Couple the reaction to another reaction with a negative ΔG
(Q034) In the 1940s, proteins were thought to be the more likely molecules to house genetic information. What was the primary reason that DNA was not originally believed to be the genetic material?
DNA was found to have only 4 types of building blocks, while proteins had 20.
What did Avery, Macleod, and McCarty's experiment reveal?
DNA was the molecule that caused the permanent transformation in griffiths earlier experiment. - No one believed this.
How are integral proteins extracted from the membrane?
Detergent molecules that destroy the membrane - amphipathic molcules that form partial micelles around the protein and the bilayers hydrophobic regions.
(Q015) Which of the following questions would NOT be answered by using karyotyping? Is the individual genetically female or male? Do any of the chromosomes contain pieces that belong to other chromosomes? Does the individual have an extra chromosome? Do any chromosomes contain point mutations?
Do any chromosome contain point mutations?
What are the classes of general proteins and what are their functions?
Enzymes : Catalyze covalent bond breakage or formation (tryptophan synthetase, pepsin, ribulose bisphosphate carboxylase, DNA polymerase, protein kinase) Structural Proteins: Provide mechanical support to cells or tissues (collagen, elastin, tubulin, keratin) Transport Proteins: Carry small molecules or ions (hemoglobin, glucose carriers, transferrin, bacteriorhodopsin) Motor Proteins: Generate movement in cells and tissues (myosin, kinesin, dynein) Storage Proteins: Store amino acids or ions (ferritin, ovalbymin, caesin) Signal Proteins: Carry extracellular signals from cell to cell (insulin, netrin, nerve growth factor, epidermal growth factor) Receptor Proteins: Detect signals and transmit them to the cells response machinery (rhodopsin, insulin receptor, acetylcholine receptor) Gene Regulatory Proteins: Bind to DNA to switch genes on or off (lactose repressor, homeodomain proteins)
How is symmetric growth of the ER bilayer ensured?
Enzymes called SCRAMBLASES catalyzes the transfer of a random phospholipid from one half of the bilayer to the other
How do enzymes catalyze reactions?
Enzymes lower the activation energy required for a reaction by holding their substrate in a way that makes the high energy transition state acquirable at lower energy levels, WITHOUT changing the temperature. - DONT change the energy of the reactants or the products of the reaction. (i.e. DONT change the temperature of the cell) - Bind to and chemically alter the substrates
Signal Protein Example
Epidermal Growth Factor
What are the 2 main chromatin structures?
Euchromatin and Heterochromatin
How is cholesterol distributed across the membrane bilayer
Evenly distributed across both layers.
The rule that oxidation reactions release energy and reduction reactions require energy is true of all reactions. T/F
False. This is only true for cells because the unique environment of cells permits this.
How does the cell cortex differ in red blood cells vs other cells in animals?
In red blood cells the cortex is very simple and made up of the fibrous proteins spectrin which maintains the concave shape of red blood cells. In other animal cells the cell cortex is much more complicated including actin and myosin.
What is a Barr Body?
Inactive X chromosome
What are the 2 classes of membrane proteins?
Integral and Peripheral - Integral proteins are proteins embedded in the plasma membrane - Peripheral proteins are associated to the plasma membrane through attachment to integral proteins
DNA Hybridization
Process that paints chromosomes different colors using sets of fluorescent dyes which bind to chromosome specific DNA sequences. - Mainly distinguishes between DNA that is rich in A-T pairs and DNA that is G-C pair, rich. - Creates a predictable pattern of bands along the chromosome which allow it to be identified according to the pattern and color of these bands.
Most genes contain information to make ________
Proteins
Genes code for:
Proteins and RNA
Which of the following are ways in which protein lateral mobility can be restricted in the plasma membrane? [Multiple answers] Proteins can be tethered to the cell cortex inside the cell. Proteins can be tethered to the extracellular matrix molecules outside the cell. Proteins can be tethered to proteins on the surface of another cell. Diffusion barriers can restrict proteins to a particular membrane domain. None of the above
Proteins can be tethered to the cell cortex inside the cell. Proteins can be tethered to the extracellular matrix molecules outside the cell. Proteins can be tethered to proteins on the surface of another cell. Diffusion barriers can restrict proteins to a particular membrane domain.
(Q034) Which mechanism best describes the process by which an antigen-presenting cell triggers an adaptive immune response? Proteins are tethered to the cell cortex. Proteins are tethered to the extracellular matrix. Proteins interact with the proteins on the surface of another cell. Protein movement is limited by the presence of a diffusion barrier.
Proteins interact with the proteins on the surface of another cell
What is the difference between purines and pyrimidines?
Purines are composed of 2 rings while pyrimidines only contain 1.
The DNA from two different species can often be distinguished by a difference in the
Ratio of A + T to G + C
Nonspontaneous Reaction
Reaction in which there is a gain in free energy (ΔG > 0) and requires a constant input of energy to proceed. - Energetically unfavorable
Spontaneous Reaction
Reaction in which there is a loss of free energy (ΔG < 0) and once started, proceeds without any additional input of energy. - Energetically favorable
Redox reactions
Reactions that involve the transfer of electrons - Can be a complete transfer of electrons or can exist in a covalent bond where electrons are only partially transferred
In animal cells, how is membrane fluidity controlled?
Regulation of cholesterol concentration in membrane - Cholesterol makes the membrane more rigid --> High concentration = very rigid
Explain Hershey and Chase's experiment and what conclusion it led to.
Revealed, through the flourescent tagging of proteins and DNA in the T2 bacteriophage, that DNA IS THE MOLECULE OF INHERITANCE. Flourescently tagged DNA and protein of the T2 bacteriophage (made up only of DNA and protein), then studied what was injected into bacterial cells upon the viruses infection. Found that the DNA was injected into the bacteria upon infection.
Reversible Histone Modification
Reversible, COVALENT, addition/removal of chemical groups (such as phosphate, methyl, and acetyl) to the histone tails in a nucleosome that change its affinity for DNA, for other histones, or can serve as docking sites for regulatory proteins. - Regulate chromosome structure because by changing its affinity, for example making it less attracted to DNA, makes the DNA more accessible and less compact.
Example of Receptor Protein
Rhodopsin, acetylcholine receptor
Floppases
Specific membrane proteins that selectively transfer phospholipids from the cytosolic layer to the noncytosolic layer of the bilayer
Flippases
Specific memembrane proteins that selectively transfer phospholipids from the noncytosolic layer to the cytosolic layer of the bilayer
Each type of chromatin structure is established and maintained by different sets of histone tail modifications that attract distinct sets of non-histone proteins. For instance heterochromatin-specific modifications allow heterochromatin to form and to spread with the help of heterochromatin-specific proteins (non-histone proteins). What is the purpose of the barrier DNA sequence in this context?
Stops the proliferation of heterochromatin structure
What is the ultimate/ primary source of energy?
The Sun because plants convert the energy from the sun to chemical energy which animals consume.
What is cell memory?
The ability of differentiated cells to maintain their identity throughout all of their descendants.
The cell wants to keep (more/less) of NAD+ than NADH and (more/less) of NADPH than NADP+.
The cell wants to keep MORE of NAD+ and MORE of NADPH
The nucleolus contains what?
The chromosomes and their specific genes that encode ribosomal RNA. - This is where rRNA is synthesized which combine with proteins to form ribosomes.
What is the glycocalyx and what is its function?
The glycocalyx is the surface of carbohydrates that encompass the cell from glycoproteins and glycolipids. - Functions in cell to cell recognition in that the oligosaccharides which make up the glycocalyx are able to bind to the membrane proteins lectin on other cells. - Also forms a coating around the cell protecting it from mechanical damage and giving it a slimy coating.
Fred Griffith studied two strains of Streptococcus pneumonia, one that causes a lethal infection when injected into mice, and a second that is harmless. He observed that pathogenic bacteria that have been killed by heating can no longer cause an infection. But when these heat-killed bacteria are mixed with live, harmless bacteria, this mixture is capable of infecting and killing a mouse. What did Griffith conclude from this experiment?
The heat-killed pathogenic bacteria, permanently, "transformed" the harmless strain into a lethal one.
Two cells with different cell-surface markers are fused in the presence of polyethylene glycol (PEG). The cells are then placed at 0°C. What do you expect to observe about the individual cell markers? - Only one marker will disperse, while the other remains stationary. - The markers will be endocytosed by the fused cell and then redistributed as fused markers. - The markers will evenly disperse throughout both membranes. - Both sets of markers will not mix but will migrate to opposite poles from one another. - The markers will essentially remain where they are, with little migration.
The markers will essentially remain where they are with little migration
You discover that a cell extract has a very high concentration of cholesterol. What could you infer from the discovery? The membranes of the cells are very rigid. The membranes of the cells have more proteins. The membranes of the cells are fragmented. No answer text provided.
The membranes of the cells are very rigid
What is equilibrium constant K?
The ratio of product to reactant concentration for a particular reaction at equilibrium. - The HIGHER the K, the MORE NEGATIVE ΔG For reactions with only 1 reactant K = [product]/[reactant] For reactions with 2 substrates, K = [Product]/([reactant_1][reactant_2])
You use fluorescent tags to identify certain membrane proteins and try to observe their cellular functions. However, there are no fluorescent signals. What do you think is going on? The tags may have altered the proteins' structures and no longer associate with the membrane. The membrane is too fluidic and signals move too fast. The membrane has other proteins that transport this protein of interest out of the cell.
The tags may have altered the proteins' structures and no longer associate with the membrane.
How can sequential reactions allow unfavorable reactions to occur?
Unfavorable reactions can occur when there is a favorable reaction right after it that uses the products as its reactants and has a negative enough ΔG that it makes the overall ΔG negative. - "Siphons" the products of the unfavorable reaction by quickly converting the products of the unfavorable reaction to products of the favorable reaction, making the amount of reactant concentration of the unfavorable reaction always higher than the product concentration, therefore lowering the ΔG of the unfavorable reaction.
What is Vmax?
V max refers to the rate of catalysis by an enzyme at which enzymes are fully saturated with substrate molecules - No real way to determine this value
The study of enzymes also includes an examination of how the activity is regulated. Molecules that can act as competitive inhibitors for a specific reaction are often similar in shape and size to the enzyme's substrate. Which variable or variables used to describe enzyme activity will remain the same in the presence and absence of a competitive inhibitor?
Vmax
Due to cell memory, when cells divide, what are they able to pass down?
When cells divide, they pass down all of their 1) HISTONE MODIFICATIONS 2) CHROMOSOME STRUCTURES (heterochromatin and euchromatin) 3) GENE EXPRESSION PATTERS
Renaturation
When the denaturing solvent is removed from a protein, it refolds spontaneously
What would happen if chromosomes did not have telomeres?
With every cell division, chromosomes would get shorter and genes at the ends of the chromosomes would be lost.
Which of the following methods cannot be used to isolate or separate proteins? Choose all that apply.
X-Ray Crystallography Nuclear Magnetic Resonance Spectroscopy (NMR) both help to discover precise folding patterns
Do enzymes form temporary covalent bonds with substrates?
Yes
Can ONE histone have more than one modification?
Yes, a histone can be modified at multiple amino acids along its tail.
Can interphase chromatins change the composition of their chromatin (ex: make euchromatin become heterochromatin) ?
Yes.
How can mass spectrometry be used to identify different proteins?
by determining precise masses of peptides derived from the protein
When cells break chemical bonds some of the energy is captured as _______ energy while the rest is lost as __________.
chemical; heat
Of the following lipids, which is found in approximately equal amounts in both the outer and inner portions of the lipid bilayer? [Review Figures in your textbook] glycolipid phosphatidylserine phophatidylethanolamine cholesterol phophatidylinositol
cholesterol
Chromosomes are made up of
chromatin
how are proteins held together?
covalent peptide bonds hold together long chains of amino acids a bond forms between a carbon of a carboxyl group shares electrons with a nitrogen from an amino group it is a condensation reaction to form a peptide bond
Disulfide bonds form between __________ side-chains
cysteine
The only chemical reactions that are possible are those that ___________ the disorder of the UNIVERSE
decrease
Two identical, folded polypeptide chains form a symmetrical complex of two protein subunits called a _____ that is held together by interactions between two identical binding sites
dimer
Chromatin remodeling can serve as ____ for regulatory proteins
docking sites
how can enzymes encourage reactions?
enzyme binds to two substrate molecules and orients them precisely to encourage a reaction to occur between them binding of substrate to enzyme rearranges electrons in the substrate, creating partial negative and positive charges that favor a reaction enzyme strains the bound substrate molecule, forcing it toward a transition state to favor a reaction
Hydrolase
enzymes that catalyze a hydrolytic cleavage reaction
Which of the following molecules would enter the cell only via a specialized transmembrane receptor? ethanol cholesterol carbon dioxide fatty acids water
ethanol
Interphase chromosomes can contain regions of both _____________ and ____________
euchromatin and heterochromatin
A living cell contains thousands of different enzymes, many of which are operating at the same time in the same small volume of the cytosol. That said, things need to be controlled properly. This can be done by ____
feedback inhibition
When a denaturant is removed, what happens to the polypeptide?
it returns to its original conformation
A prokaryotic organism is isolated from a glacier, where it was thriving. Based on your knowledge of the plasma membrane, you would expect to find a predominance of - largely saturated fatty acids. - cell wall to define the cell because the cell membrane would not be present. - largely unsaturated fatty acids. - equal amounts of saturated and unsaturated fatty acids, as long as the chain was close to 12 carbons in length. - none of the above - excessive amounts of cholesterol
largely unsaturated fatty acids
Phospholipids assemble into ___________ when they are submerged in liquid
liposomes
The more 2 substrates bind together complementarily, the ___________ negative the value of ΔG for the reaction.
more
At higher value of K, the shape of the 2 substrates are ___________ complementary, because they have _____________ binding.
more; stronger
Motor Protein Example
myosin
Starting with shredded spinach leaves, you follow a procedure that allows for separation of cellular organelles. You are specifically looking for the fraction that contains the mitochondria. To identify this fraction, you should test for the phospholipids unique to the mitochondrial membrane. polysaccharides that specifically surround the mitochondria. phospholipids unique to intracellular membranes. presence of enzymes associated with cellular respiration. general presence of enzymes that fix carbon.
presence of enzymes associated with cellular respiration.
The phosphorylation of a protein is typically associated with a change in activity, the assembly of a protein complex, or the triggering of a downstream signaling cascade. The addition of ubiquitin, a small polypeptide, is another type of covalent modification that can affect the protein function. Ubiquitylation often results in
protein degradation
What is the purpose of Histone H1?
pull nucleosomes together and pack them into a more compact chromatin fiber
(Q002) Which of the following functions of the plasma membrane is possible without membrane proteins? intercellular communication selective permeability cellular movement import/export of molecules
selective permeability
Fluorescently labeled antibodies are widely used in research to "tag" a molecule of interest, such as an antigen (see figure below). Using an unlabeled "primary" antibody (black) to bind to the target, and a labeled "secondary" antibody that binds to the primary antibody (NOT the molecule of interest) greatly improves the _________________ of the technique.
sensitivity
When a protein is phosphorylated, what possible amino acids is the phosphate group added to?
serine, threonine, tyrosine
What is the name of the molecules that enzymes bind to and chemically modify?
substrates
(Q003) Which of the following chemical groups is NOT used to construct a DNA molecule?
six carbon sugar
The net distance a molecule travels through the cytosol via diffusion is relatively short in comparison with the total distance it may need to travel. This is because movement governed by diffusion alone is a __________ process that is most effective for the dispersion of small molecules over short distances.
slow
What is the effect of the solvents used in the denaturation process?
solvents break all noncovalent interactions
The larger the values of K, the __________ the binding b/w 2 substrates by ___________ bonds.
stronger, noncovalent
Disulphide bonds provide great conformational stability to some proteins, but these proteins are usually found extra-cellularly. Why?
the cytosol contains a high concentration of reducing agents
The antigen-binding sites of antibodies are formed from several loops of polypeptide chains - what determines the antigen-binding specificity of these loops?
the length and amino acid sequnce of the loops
(Q025) Although the chromatin structure of interphase and mitotic chromosomes is very compact, DNA-binding proteins and protein complexes must be able to gain access to the DNA molecule. Chromatin-remodeling complexes provide this access by
using the energy of ATP hydrolysis to move nucleosomes.
What is the behavior of ΔG throughout a reaction?
ΔG tends to decrease in a reaction until it hits 0 at which the reaction is at equilibrium - Reactions tend to proceed until reaching equilibrium.
What equation can you use to calculate the concentration of products to reactants at equilibrium for a reaction with only 1 reactant?
ΔG° = -1.42 log K - where 1.42 = RT in kcal/mole - For every 1.42 kcal/mol diff in free energy, K is changed by a factor of 10.
β sheets are involved in the formation of amyloid fibers, which can cause various diseases. What mechanism drives the formation of amyloid fibers?
β-sheet stabilization of abnormally folded proteins
