Bio1350

What is the smallest distance two points can be separated and still resolved using light microscopy/what is the minimum resolvable distance by the unaided eye? electron microscopy?

200 nm

Which of the following ratios of nucleotides is constant for DNA?

A + G = T + C

Endoplasmic Reticulum

A cell structure that forms a maze of passageways in which proteins and other materials are carried from one part of the cell to another.

Rough ER

A network of interconnected membranous sacs in a eukaryotic cell's cytoplasm; covered with ribosomes that make membrane proteins and secretory proteins.

Answer the following questions using the figure below. A. Which parts of a nucleotide are involved in a phosphodiester bond? B. Which functional group is free at the 5' end? Which functional group is free at the 3' end?

A. DNA - the five-carbon sugar is deoxyribose, which has a hydrogen attached to the 2' carbon. B. The phosphodiester bond links the phosphate group of one nucleotide to the 3' carbon on another nucleotide. C. 5' end: the phosphate group attached to the 5' carbon in the first nucleotide of the strand sticks out. 3' end: the 3' hydroxyl of the last nucleotide in the strand sticks out.

Which of the following statements is FALSE regarding GTP-binding proteins?

Activation of the GTP-binding protein involves addition of a phosphate group to its bound guanine nucleotide.

The figure below shows a ribose sugar. The part of the ribose sugar where a new ribonucleotide will attach in an RNA molecule is pointed to by arrow _____.

Arrow 4 is correct. RNA and DNA are synthesized in the 5' to 3' direction (the next ribonucleotide would be added to the end with the 3' carbon in ribose in the diagram).

Has double membrane

B. Microtubules, actin filaments, and intermediate filaments are three types of protein filaments and tubules (fibers), not membrane-bound organelles, that comprise the cytoskeleton. E. The endoplasmic reticulum does not have a double membrane.

Prokaryotic Cells

do not have a nucleus or other membrane-bound organelles

attraction between fully charged groups (ionic bond) or partially charged groups on polar molecules

electrostatic attractions

stacked sheets and interconnected network of membrane tubules that modifies and sorts membrane and secreted proteins

endoplasmic reticulum

Cells that are specialized for the secretion of proteins are likely to have which of the following features?

enlarged endoplasmic reticulum

interconnected network of membrane tubules that is contiguous with the outer nuclear membrane. Involved in the synthesis of lipids and proteins destined for secretion..

golgi apparatus

RNA in cells differs from DNA in that ______.

it is single-stranded and can fold up into a variety of structures.

Two spots that are separated by 0.3 μm can theoretically be resolved using:

light microscopy and electron microscopy.

organelles that degrade molecules

lysosomes and peroxsomes

What unit of length would you generally use to measure a typical plant or animal cell?

micrometers

"power house" of the cell where the most important cellular energy molecule, adenosine triphosphate (ATP), is produced; enclosed in two membranes and contain DNA that encodes some of their proteins and RNAs

mitochondria

Match each polymeric macromolecule to its monomeric subunits. Note: not all options will be used. carbohydrate ribonucleic acid deoxyribonucleic acid protein

monosaccharide adenine, uracil, cytosine, guanine adenine, thymine, cytosine, guanine amino acid

The __________ __________ is made up of two concentric membranes and is continuous with the membrane of the endoplasmic reticulum.

nuclear envelope

typically the most prominent organelle; encloses genetic material in a double membrane

nucleus

Use the dropdown menus to complete the following statements about the DNA double helix. In each individual strand of DNA, nucleotides are linked by [ Select ] through a [ Select ] . The two DNA strands in a double helix are held together by [ Select ] between the bases. The DNA backbone is [ Select ] due to the presence of [ Select ] .

phosphodiester bonds condensation reaction hydrogen bonds negatively charged phosphate groups

protein-containing lipid bilayer that encloses all living cells

plasma membrane

The correctly folded three-dimensional configuration of a protein is determined primarily by the ______.

primary sequence of its amino acids.

What type of macromolecule helps package DNA in eukaryotic chromosomes?

proteins

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

Cells require one particular monosaccharide as a starting material to synthesize nucleotide building blocks. Which of the monosaccharides below fills this important role?

ribose

large complex of RNAs and proteins that translates a messenger RNA into a polypeptide chain

ribosome

Which of the following chemical groups is NOT used to construct a DNA molecule?

six-carbon sugar

A cell with a predominance of smooth endoplasmic reticulum is most likely specialized to carry out which of the following processes?

synthesis of large quantities of lipids

The activity of a protein can be regulated by phosphorylation, a process in which a phosphate group is added to _____________.

the hydroxyl group of a serine, threonine, or tyrosine side chain.

Which of the following statements about the DNA double helix is TRUE?

the two DNA strands run antiparallel.

The secondary structure of a protein is the alpha-carbon chain backbone and ignores side chains.

true/ Primary structure is amino acid sequence; Secondary structure is the a-carbon chain backbone and reveals elements like alpha helices and beta sheets Tertiary structure is the structure with all the side-chains in place Quaternary structure relates to the structure of proteins with more than one subunit.

weak bonding interaction between any two atoms at very close distances due to their fluctuating electrical charges

van der Waals attractions

The potential energy stored in high-energy bonds is commonly harnessed when the bonds are split by the addition of __________ in a process called __________.

water; hydrolysis

Resolving power is the ability to distinguish between two objects. Resolving power is limited by the __________ of illumination

wavelength

Describe the benefits and limitations of utilizing electron microscopy to study biological systems.

Benefits: much higher sample magnification and resolution than light microscopy: nanometer range (level of molecules, atoms). Limitations: samples must be fixed, so cannot be used on live cells difficult to label specific proteins more effort to get 3D view of cell (tomography)

Which of the following is NOT a function of RNA?

C. is correct. DNA, not RNA, is the genetic material for cells. A. is incorrect. Ribosomes are macromolecular complexes for ribosomal RNAs (rRNAs) and proteins. rRNAs form the core of the ribosome and catalyze protein synthesis. B. is incorrect. MicroRNAs (miRNAs) regulate gene expression. D. is incorrect. Messenger RNAs (mRNAs) code for proteins.

Disulfide Bonds B-Sheet How disulfide bonds form Where do disulfide bonds form

C. is correct. Disulfide bonds stabilize the conformation of proteins that are destined for secretion from the cell. A. is incorrect. In a β-sheet, several segments (strands) of a polypeptide chain are adjacent to each other and held together by hydrogen bonds between their polypeptide backbones. B. is incorrect. Disulfide bonds only form under oxidizing conditions. The cytosol is a reducing environment, so intracellular proteins would not contain disulfide bonds. Proteins destined for secretion from the cell are formed in the endoplasmic reticulum (ER). The ER lumen and extracellular environments are both oxidizing, allowing disulfide bonds to form. D. is incorrect. Disulfide bonds only form between cysteine side chains (serine, threonine, and tyrosine side chains do not form disulfide bonds, but can all be phosphorylated).

Which of the following statements about the ribosome is TRUE?

C. is correct. RNA in the large ribosomal subunit acts as an enzyme catalyzing peptide bond formation. A. is incorrect. A ribosome is composed of rRNA molecules and proteins. B. is incorrect. The small subunit binds to mRNA. D. is incorrect. Each tRNA synthetase attaches a specific amino acid to the appropriate tRNA molecule using the energy of ATP hydrolysis. The formation of this high-energy bond between an amino acid and tRNA provides the energy for peptide bond formation. E. is incorrect. Translation ends when a release factor binds to stop codon, triggering hydrolysis of the polypeptide. The ribosome dissociates into its two subunits, to be recycled during another round of protein synthesis (chaperone proteins help proteins fold, often using the energy of ATP hydrolysis).

DNA replication is considered semiconservative because

During DNA replication, each parental DNA strand serves as a template to produce a new strand of DNA and the resulting daughter helices include one parental and one newly synthesized DNA strand.

Which of the following influences the shape of a folded protein?

Electrostatic attractions, hydrogen bonds, van der Waals attractions, and hydrophobic interactions are all weak, noncovalent interactions that influence the shape of a folded protein.

Which of the following statements about α helices is FALSE?

Hydrogen bonds form between the C=O and N-H of amino acids in adjacent polypeptide chains.

Smooth ER

Makes lipids

Which of the following is a monosaccharide?(Chemical Formula)

Monosaccharides have the chemical formula: (CH20)n where n is 3, 4, 5 or 6.

Which of the following statements about the genetic code is CORRECT?

Most amino acids can be specified by more than one codon. The genetic code is redundant because it is a 3-base code (a 'codon') that specifies amino acids. Since there are 64 possible variations in a 3-base code of 4 nucleotides, most amino acids are encoded by multiple codons (64 combinations: 4x4x4 = 64). A. is incorrect. Each codon specifies only one amino acid. C. is incorrect. The START codon AUG does code for methionine and, consequently, nearly all polypeptides begin with methionine. However, methionine can also be found within a polypeptide. D. is incorrect. The three STOP codons do not code for an amino acid (61 codons code for amino acids).

Which of the following classes of amino acids is buried within the folded structure of the protein?

Nonpolar amino acids are hydrophobic and are in the interior of proteins.

Choose the statement which correctly describes the directionality of DNA and RNA polymerization.

Polymerization of DNA and RNA always occurs in the 5' to 3' direction.

Ribosomes find the start site of translation by _________.

Ribosomes will scan along the mRNA from the 5′ end until it recognizes the AUG codon (start codon), the translational start site, which leads to the binding of an initiator tRNA.

Which of the following statements best explains how a modern transmission electron microscope (TEM) can achieve a resolution of about 2.0 nanometers, whereas a standard light microscope has a maximum resolution of about 200 nanometers?

The wavelengths of electron beams are much shorter than the wavelengths of visible light.

Some proteins have α helices, some have β sheets, and still others have a combination of both. What makes it possible for proteins to have these common structural elements?

The α helix and β sheet are formed by hydrogen bonding between C=O and N-H in the polypeptide backbone.

weak bonding interaction between any two atoms at very close distances due to their fluctuating electrical charges

Van Der Waals

Select the definition which best describes the term protein domain.

a protein segment that folds independently that generally have a specific function

The primary structure of a protein is the _______.

amino acid sequence.

chemical bond formed by the sharing of electrons between two atoms

covalent bonds

system of protein filaments that includes microfilaments, microtubules and intermediate filaments

cytoskeleton

portion of cytoplasm that is not contained within intracellular membranes; concentrated aqueous gel containing many large and small molecules; site of many chemical reactions, including most protein synthesis

cytosol

Indicate whether the statements below are TRUE or FALSE. If a statement is false, explain why it is false. A. The chemistry of life is carried out and coordinated primarily by the action of small molecules, which are also more abundant than macromolecules in cells. B. Carbon-based compounds make up the vast majority of molecules found in cells. C. A disaccharide consists of a sugar covalently linked to another molecule such as an amino acid or a nucleotide. D. A disaccharide is the longest macromolecule in human cells.

A. FALSE. Although small molecules are important in many processes, the chemical reactions in living systems are regulated by the coordinated action of large polymeric molecules (macromolecules). I Macromolecules are abundant in cells (proteins = 15%, DNA and RNA = 7%, polysaccharides = 2%, inorganic ions and small molecules = 4%, water = 70%). See figure below. B. TRUE C. FALSE. A disaccharide consists of two sugar molecules that undergo a condensation reaction to form a covalent bond (known as a glycosidic linkage). D. FALSE. The longest macromolecule in human cells is a nucleic acid, chromosome 1. A single strand of DNA is incredibly long - it would be approximately 3 inches long if it were stretched out. DNA is highly compacted in cells with the help of histone proteins.

Indicate whether the following statements are TRUE or FALSE. If a statement is false, explain why it is false. A. A large number of noncovalent interactions enable protein-protein and protein-ligand interactions. B. Covalent bonds between cysteine residues can stabilize the conformation of secreted proteins. C. Once properly folded, a protein's conformation does not change.

A. TRUE. Protein-protein and protein-ligand interactions require many weak non-covalent interactions (e.g., electrostatic interactions, hydrogen bonds, hydrophobic interactions) B. TRUE. Disulfide bonds are covalent bonds between cysteine residues that can stabilize the conformation of secreted proteins (require an oxidizing environment like the ER lumen and extracellular environment. Cannot form in the reducing environment of the cytosol). C. FALSE. Proteins can have active and inactive conformations. Protein activity can be regulated through allostery: conformational change induced by the binding of a ligand.

A. What type of bonds hold the two DNA strands together? Which part of the nucleotides are engaged in these interactions? B. Complementary base-pairing: adenine pairs with thymine and guanine pairs with cytosine. How are the complementary base pairs similar? How does this influence the structure of the DNA helix? C. Are the two DNA strands arranged in a parallel or antiparallel orientation? How do you know? D. One strand of a DNA helix has the following sequence: 5′-GCATTCGTGGGTAG-3′. Provide the sequence of the complementary strand and label the 5′ and 3′ ends.

A. The two DNA strands are held together by hydrogen bonds between the bases in the nucleotides of the different strands. B. A smaller pyrimidine always pairs with a bulkier purine. This ensures that the base-pairs have the same width. C. The two DNA strands in a double helix are arranged in an antiparallel orientation because the 5' and 3' ends of each DNA strand are oriented in opposite directions in the DNA double helix. D. 5′-CTACCCACGAATGC-3′ *Remember: nucleic acid sequences are always written 5' to 3' by convention.

Indicate whether the following statements are TRUE or FALSE. If a statement is false, explain why it is false. A. Condensation reactions occur in the synthesis of all the macromolecules found in cells. B. A large number of noncovalent interactions is required to hold two regions of a polypeptide chain together in a stable conformation. C. A single polypeptide tends to adopt three or four distinctly different conformations with unique geometries.

A. True B. True C. False. There is a single most stable fold for every polypeptide. The fold adopted has the single, lowest free-energy value.

Given what you know about the differences between prokaryotic cells and eukaryotic cells, use the dropdown menus to choose whether the following biological processes are "suitable" or "unsuitable" for study using the bacterium E. coli as the model organism. Make sure that you are able to justify each answer.

A. Unsuitable because prokaryotes do not have organelles. B. Suitable because all living organisms have DNA as their genetic material. C. Unsuitable because prokaryotes do not have organelles—mitochondria are thought to be derived from early aerobic bacteria, and may be instead suitable for studying the mechanism for consuming oxygen to generate ATP.

Enzymes

A. is TRUE. Enzymes catalyze chemical reactions while remaining unchanged themselves, allowing them to undertake repeated rounds of catalysis. B. is TRUE. The levels of different enzymes provide specificity (selectivity) as to which chemical reactions occur in the cell. C. is TRUE. Enzymes can catalyze an energetically unfavorable reaction by coupling it to a reaction that is more energetically favorable. D is FALSE. Enzymes do not alter the relative energies of the reactants and products (i.e., they do not alter whether a reaction is energetically favorable or unfavorable). E. is TRUE. Enzymes reduce the activation energy for a reaction, making it more likely for the reaction to occur. All chemical reactions catalyzed by enzymes involve an overall reduction in energy state.

The eukaryotic chromosomes are organized inside the nucleus with a huge compaction ratio of several thousand-fold. What is responsible for such tight packaging?

A. is correct. The various chromatin proteins, including histone and non-histone proteins, wrap and fold the DNA to achieve an astonishing compaction ratio.

According to the conventional way of writing the sequence of a peptide or a protein, which is the C-terminal amino acid in the peptide: Pro-Val-Thr-Gly-Lys-Cys-Glu?

Glutamic acid/glutamate (Glu)

Describe the major differences between immunofluorescence (IMF) and green fluorescent protein (GFP) fusion.

Immunofluorescence allows you to visualize a specific protein in dead cells. Specific: antibodies bind specifically to a particular protein (antigen). Sensitive: fluorescent molecules attached to the antibodies allow you to detect low abundance proteins. Must kill cells during preparation, so only get a "snapshot" of cell at one point in time (static view of cell). Green fluorescent protein (GFP) fusion allows you to visualize a specific protein in living cells by first fusing the gene for GFP to the gene of a specific protein and then expression the fusion protein in particular cells. Specific: GFP gene fused to the gene for a specific protein. Sensitive: GFP fluorescent allows you to detect low abundance proteins. Can use in living cells - visualize dynamic processes, change through time.

As a cell biology researcher, why might you choose to use indirect immunofluorescence microscopy (IMF) rather than conventional light microscopy?

Indirect immunofluorescence microscopy (IMF): Pros: allows you to visualize a specific protein using fluorescently linked antibodies that bind to that specific protein (antigen). The technique is sensitive because the use of fluorescently linked antibodies allows you to visualize even low abundance proteins. Because the fluorescent dye emits light, you are able to visualize objects smaller than 0.2 µm. Cons: sample preparation (fixing the cells through crosslinking and permeabilizing the membrane) requires killing the cells, so you cannot observe dynamic processes in live cells (you only get a snapshot of where specific proteins are at one point in time). Conventional light microscopy: Pros: provides a general view of the cell and cellular structures. Less involved sample preparation. Cons: does not allow you to visualize specific proteins (staining can reveal subcellular structures, but are not specific to particular proteins). It is only able to resolve details as small as 0.2 µm.

The three families of cellular macromolecules are polymerized and depolymerized by a general mechanism involving water. Which of the following statements is true regarding these macromolecules?

The addition of each monomer to the growing polymer is a condensation reaction that forms a covalent bond is accompanied by the release of one water molecule and is energetically unfavorable. The opposite reaction (depolymerization) involves hydrolysis and consumes one water molecule.

You have a segment of DNA that contains the following sequence: 5′-GGACTAGACAATAGGGACCTAGAGATTCCGAAA-3′3′-CCTGATCTGTTATCCCTGGATCTCTAAGGCTTT-5′ You know that the RNA transcribed from this segment contains the following sequence: 5′-GGACUAGACAAUAGGGACCUAGAGAUUCCGAAA-3′ Which of the following choices best describes how transcription occurs?

The bottom strand is the template strand; RNA polymerase moves along this strand from 3′ to 5′.

Which statement describes the most common relationship of the inhibitor molecule to the allosteric enzyme in feedback inhibition of enzyme activity?

The inhibitor is the final product of the metabolic pathway.

Both DNA and RNA are synthesized by covalently linking a nucleoside triphosphate to the previous nucleotide, constantly adding to a growing chain. In the case of DNA, the new strand becomes part of a stable helix. The two strands are complementary in sequence and antiparallel in directionality. What is the principal force that holds these two strands together?

hydrogen bonds

interaction that forms when a hydrogen atom is "sandwiched" between two electron-attracting atoms (usually oxygen or nitrogen)

hydrogen bonds

interaction that results from the disruptive effect of hydrophobic groups on network formed between hydrogen bonds between water molecules

hydrophobic forces

interaction that results from the disruptive effect of hydrophobic groups on network formed between hydrogen bonds between water molecules

hydrophobic interactions