BIO 002 Midterm 2
Antibodies are immunoglobin proteins produced by the immune system in response to foreign molecules, especially those on the surface of an invading microorganism. 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 the variable light (VL) and heavy chain (VH)
Photosynthesis takes place in two stages: Which of the following are true?
-Energy from sunlight is captured and transiently stored as chemical-bond energy in specialized molecules called activated carriers -All of the oxygen (O2) in the air we breathe is generated by the splitting of water molecules during the first stage of photosynthesis -In the second stage, the activated carriers are used to hep drive the carbon fixation process, in which sugars are manufactured from carbon dioxide gas (CO2)
Which of the following is true about Griffith's and Avery-MacLeod-McCarty's experiment?
-Griffith showed that heat-killed, infectious bacteria can transform harmless, living bacteria into pathogenic ones. -Griffith found that a substance present in the pathogenic S strain could permanently change, or transform, the nonlethal R strain into the deadly S strain. -showed that the "transforming principle" that would permanently change the harmless R-strain pneumococci into the pathogenic S strain is DNA - demonstrated showed that DNA is the genetic material -Showed that enzymes that destroys proteins and RNA did not affect the ability of the extract to transform bacteria, while enzymes that destroy DNA inactivated it
Which of the following are examples of general protein function? Select all that may apply.
-Transport Proteins -Receptor Proteins -Gene Regulatory Proteins NOT GLOBULAR PROTEINS
What part of the chromatin fiber does the remodeling complex directly attach to? Select all that apply. [recall the demonstration!]
-attaches to histone octamer -attaches to the DNA wrapped around histone octamer
Select all that apply. Which of the following statements are true? [multiple apply]
-competitive inhibitors block enzyme activity by competing directly with the substrate for the enzyme's attention -competitive inhibitors do not change the Vmax of a reaction
Enzymes can encourage a reaction in several ways. Choose all that apply
-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
Which of the following combination of number of carbons and double bonds of a phospholipid yield the highest mobility?
14 carbons with two double bonds
Which of the following would yield the most highly mobile phospholipid (listed as number of carbons and number of double bonds, respectively)?
15 carbons with two double bonds
If an isotope S-32 has 16 protons and 16 neutrons, how many protons, and electrons will the isotope S-35 have, respectively?
16; 19; 16
How many hydrogen bonds form between adenine and thymine? How many hydrogen bonds form between guanine and cytosine?
2 H bonds, 3 H bonds
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
Most types of molecules in the cell have asymmetric (chiral) carbons. Consequently there is the potential to have two different molecules that look much the same but are mirror images of each other and therefore not equivalent. These special types of isomers are called stereoisomers. Which of the four carbons circled in Figure 2-37 is the asymmetric carbon that determines whether the amino acid (threonine in this case) is a D or an L stereoisomer?
3-Two of the carbon atoms of threonine are asymmetric but convention it is the alpha carbon that determines whether the amino acid is the D or L isomer
Hershey and Chase used radiolabeled macromolecules to identify the material that contains heritable information. What radioactive material was used to track DNA during this experiment?
32P
Because there are four different monomer building blocks that can be used to assemble RNA polymers, the number of possible sequence combinations that can be created for an RNA molecule made of 100 nucleotides is
4^100
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 histone 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?
Acetyl groups Methyl groups Phosphate groups NOT adenine bases
During photosynthesis, energy from sunlight is captured and transiently stored as chemical-bond energy in specialized molecules called?
Activated carriers
Integrin proteins, which link intracellular actin filaments to extracellular matrix protein, belong to which class of plasma membrane proteins?
Anchors
Membrane proteins, like membrane lipids, can move laterally by exchanging positions with other membrane components. Which type of membrane protein is expected to be the least mobile?
Anchors
Which amino acids have side chains that are positively charged?
Arginine Lysine Histidine NOT aspartic acid
Label each segment in the image below. The red arrows represent _____, while the green coils represent______. The blue and yellow clouds are the secondary structures are called _______.
Beta sheets, alpha helix, functional domain
The best way to know if an organic molecule has been reduced is to see if there was an increase in the number of __________ bonds.
C-H
During respiration, energy is retrieved from the high-energy bonds found in certain organic molecules. Which of the following in addition to energy are the ultimate products of respiration?
CO2; H20
Fill in the blank.___ is an enzyme that cuts polypeptide chains, carries a tightly bound zinc ion in its active site. During the cleavage of a peptide bond , the zinc ion forms a transient bond with one of the substrate atoms, thereby assisting the hydrolysis reaction. [Check the meaning of the words!]
Carboxypeptidase
Select the answer that best fits the blank. The __ bind to newly synthesized or partially folded chains and helping them to fold along the most energetically favorable pathway.
Chaperone proteins
The energy used by the cell to generate specific biological molecules and highly ordered structures is stored in the form of
Chemical bonds
Which of the following membrane lipids does not contain a fatty acid tail?
Cholesterol
Substances that release protons when they dissolve in water are acids. Which of the following household substance is acidic?
Coffee
Which of the following is NOT a feature commonly observed in beta sheets?
Coiled-coil patterns
Energy cannot be created or destroyed, but it can be converted into other types of energy. Cells harvest some of the potential energy in the chemical bonds of foodstuffs to generate stored chemical energy in the form of activated carrier molecules, which are often employed to join two molecules together in __________ reactions.
Condensation
Plasma membrane are extremely thin and fragile, requiring an extensive support network of fibrous proteins. This network is called the ___________.
Cortex
Extracellular proteins are often stabilized by covalent cross-linkages. The most common covalent cross-linkage is ______.
Disulfide bonds
What can be used to measure the rate of lateral diffusion of a membrane protein
FRAP
Which specific motor protein generates the forces responsible for muscle contraction and most other eukaryotic cell movements? They also power the intracellular movements of organelles and macromolecules. For example, they help move chromosomes to opposite ends of the cell during mitosis
GTP
A ____ is often defined as a segment of DNA that contains the instructions for making a particular protein or RNA molecule. The total genetic information carried by all the chromosomes in a cell or organism constitutes its _____.
Gene, genome
How are cells able to emerge from the ER with an evenly scrambled set of phospholipids?
Golgi apparatus and flippases
Which scientist or team of scientists first demonstrated that cells contain some component that can be transferred to a new population of cells and permanently cause changes in the new cells?
Griffith
Which elements are chemically enert?
Helium, neon, argon
What packs the DNA into a repeating array of DNA protein particles called nucleosomes, which are further fold up into even more compact chromatin structures
Histones
What packs the DNA into a repeating array of DNA-protein particles called nucleosomes, which further fold up into even more compact chromatin structures
Histones
For the activated carriers widely used in metabolism NADH, NADPH, FADH2. What is the the group with high-energy linkage?
Hydrogen and electrons
Two or three α helices can sometimes wrap around each other to form coiled-coils. The stable wrapping of one helix around another is typically driven by __________ interactions.
Hydrophobic
Reduction
Involves the addition of electrons to an atom
The amino acids glutamine and glutamic acid are shown in Figure 2-38. They differ only in the structure of part of their side chains (circled). At pH7, what type of interactions are possible for glutamic acid but not for glutamine?
Ionic bonds
The ___ histone, called histone H1, pulls adjacent nucleosomes together into a regular repeating array and changes the path the DNA takes as it exits the nucleosome core, allowing it to form a more condensed chromatin fiber.
Linker
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
Which of the following feedback loops best describes this image show below?
Negative feedback
Which of the following is not an activated for of the carrier?
None of the above (None of these: ATP, NADH, FADH2, Acetyl CoA)
For the activated carrier ATP what is the group with high-energy linkage?
Phosphate
Protein phosphorylation involves the enzyme-catalyzed transfer of the terminal phosphate group of ATP to the hydroxyl group on a serine, threonine, or tyrosine side chain of the protein. This reaction is catalyzed by?
Protein Kinase
Which of the following type of membrane protein would not be considered an integral membrane protein?
Protein associated proteins via non-covalent linkage Integral Proteins... -transmembrane proteins -monolayer associated proteins via covalent linkage -lipid linked proteins via covalent linkage
Fluorescence recovery after photobleaching (FRAP) involves uniformly labeling components of the cell membrane—its lipids or, more often, its proteins—with some sort of fluorescent marker then bleaching it and analyzing recovery can be used to study?
Protein mobility
Which mechanism best describes the process by which a budding yeast cell designates the site of new bud formation during cell division?
Proteins are tethered to the cell cortex
DNA is an information storage molecule, whose sequences serve as a template to make
RNA
Which of the following chemical group is NOT used to construct a DNA molecule?
Six-carbon sugar
Which of the following is true about the transportation of substances across the lipid region of the cell membrane?
Small nonpolar molecules can freely dissolve across the lipid region of the cell membrane
Macromolecules in the cell can often interact transiently as a result of noncovalent interactions. These weak interactions also produce stable, highly specific interactions between molecules. Which of the following below is the most significant in determining whether the interaction will be transient or stable?
Surface complementarity between molecules
Three DNA sequence elements are needed to produce a eucaryotic chromosome that can be replicated and then segregated at mitosis. What are these?
Telomeres Centromeres Replication Origins
Which of the following statements is FALSE for a favorable binding reaction?
The concentration of the complex remains lower than the concentration of the unbound components. TRUE -The free-energy is negative for the system -The complex disassociation rate is slower than the rate for component association -The binding energy for the association is large and negative
Heterchromatin
The most highly packed
Why is the oxidation of NADPH energetically favorable?
The oxidized form, NADP+, is more stable than the reduced form NADPH
Floppases
These enzyme remove specific phospholipids from the monolayer that faces the cytosol and flips them into the side of the bilayer facing the exterior spaces.
How do changes in histone modifications lead to changes in chromatin structure?
They help recruit other proteins to the chromatin
Which of the following globular proteins is used to form filaments as an intermediate step to assembly into hollow tubes?
Tubulin
Membrane undergo spontaneous rearrangement if torn. What would happen?
Vesicles form
What would happen if chromosomes did not have telomeres?
Without telomeres every cell division would mean that some amount of important genetic information would be clipped off and lost
Three phospholipids X, Y, and Z are distributed in the plasma membrane as indicated below. For which of these phospholipids does a flippase probably not exist?
Z
Protein structures have several different levels of the organization. The primary structure of a protein is its amino acid sequence. The secondary and tertiary structures are more complicated. Consider the definitions below and select the one that best fits the term " protein domain."
a protein segmental that folds indepently
All of the biological molecules listed below contain high-energy phosphate bonds. Which one is the key driver of most phosphorylation reactions and the transfer of metabolic energy? [think what the P means in this case]
adenosine-P3
A transmembrane polypeptide chain usually crosses the lipid bilayer as an_______.
alpha-helix
The primary structure of a protein is the
amino acid sequence
How does mass spectrometry help identify proteins?
by determining precise masses of peptides derived from the protein
Figure 3-30 is an energy diagram for the reaction X-> Y. Which equation below provides the correct calculation for the amount of free-energy change when X is converted to Y?
c-a
Choose the phrase that best completes this sentence. Microtubules _____________ and are required to pull duplicated chromosome to opposite of dividing cells.
can rapidly reorganize
______and ______ pathways together constitute the cell's metabolism
catabolic, anabolic
Living systems are incredibly diverse in size, shape, environment, and behavior. It is estimated that there are between 10 million and 100 million different species. Despite this wide variety of organisms, it remains difficult to define what it means to say something is alive. Which of the following can be described as the smallest living unit?
cell
The cell constantly exchanges materials by bringing nutrients in from the external environment and shuttling unwanted by-products back out. Which term describes the process by which external materials are captured inside transport vesicles and brought into the cell?
endocytosis
Which of the following is true for the unsaturated tails of lipids in membrane?
have kinks in them and lessen the interaction between adjacent fat molecules
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?
heme
When atoms are held together by _________ __________, they typically referred to as ___________.
ionic interactions, salts
Euchromtain
light packed
Which of the following statements is true?
lipids are nonpolar and will not dissolve in water
The inactivation of one X chromosome is established by the directed spreading of heterochromatin. The silent of this chromosome is _______ in the subsequent cell divisions.
maintained
Carbon 14 is an unstable isotope of carbon that decays very slowly. Compared to the common, stable carbon 12 isotope, carbon 14 has two additional
neutrons
There are 20^100 different possible sequence combinations for a protein chain with 100 amino acids. In addition, to the amino acid sequence of the protein, what other factors INCREASE the potential for diversity in these protein macromolecules?
noncovalent interactions sampled as protein folds
The __________ __________ is made up of two concentric membranes and is continuous with the membrane of the endoplasmic reticulum.
nuclear envelope
The chromosomes we typically see in images are isolated from mitotic cells. These mitotic chromosomes are in the most highly condensed form interphase cells contain chromosomes that are less densely packed and ________.
occupy discrete territories in the nucleus
Unlike what occurs when fuel is burned to make a fire. All living systems use the energy from heat-generating reactions to create and maintain_____.
order
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
Scramblases
remove randomly selected phospholipids from one half of the lipid bilayer and insert them in the other
Oxidation
removes electrons from an atom
The central dogma provides a framework for thinking about how genetic information is copied and used to produce structural and catalytic components of the cell. From the choices below, select the order of biochemical processes that best correlates with the tenets of the central dogma.
replication, transcription, translation
Mitochondria perform cellular respiration, a process that uses oxygen, generates carbon dioxide, and produces chemical energy for the cell. Which answer below indicates a correct pairing of the material "burned" and the form of energy produced during cellular respiration?
sugar, ATP
Select the option that BEST finishes the following statement: Evolution is a process
that can be understood based on the principles of mutation and selection.
Consider the apical location of a particular protein expressed in epithelial cells, illustrated in Figure Q11-49A. Which type of defect described below is the most likely to cause the redistribution of that protein around the entire cell, shown in part B of Figure 11-35?
the deletion of a junctional protein
Flippases
these enzyme remove specific phospholipids from the side of bilayer facing the exterior space and flip them into the monolayer that faces the cytosol
The process of sorting human chromosome pairs by size and morphology is called karyotyping. A modern method employed for karyotyping is called chromosome painting. How are individual chromosomes "painted"?
using fluorescent DNA molecules
