biol 329 exam 1 all HW, iclicker, and PAL questions

Which statement is false about the events/conclusions from studies during the mid-1800s surrounding the discovery of cells?

1. Cells came to be known as the smallest building block of living organisms

2. New cells can form spontaneously from the remnants of ruptured cells

3. Light microscopy was essential in demonstrating the commonalities between plant and animal tissues

4. New cells arise from the growth and division of previously existing cells

New cells can form spontaneously from the remnants of ruptured cells

Select the observable characteristic that best distinguishes archaea from bacteria

1. Can metabolize inorganic substances

2. Are found in extremely harsh environments

3. Thrive in anaerobic conditions

4. Are photosynthetic organisms

Are found in extremely harsh environments

1. Cytosol

2. Golgi apparatus

3. Plasma membrane

4. Endoplasmic reticulum

5. Nuclear envelope

6. Transport vesicles

7. Mitochondrion

Eukaryotic cells are bigger and more elaborate than prokaryotic cells. By definition, all eukaryotic cells have a _____1_____, usually the most prominent organelle. Another organelle found in essentially all eukaryotic cells is the _____2_____, which generates the chemical energy for the cell. In contrast, the _____3_____ is a type of organelle found only in the cells of plants and algae; it performs photosynthesis. If we were to strip away the plasma membrane from a eukaryotic cell and remove all of its membrane-enclosed organelles, we would be left with the _____4_____, which contains many long, fine filaments of protein that are responsible for cell shape and structure, and thereby form the cell’s _____5_____.

Eukaryotic cells are bigger and more elaborate than prokaryotic cells. By definition, all eukaryotic cells have a nucleus, usually the most prominent organelle. Another organelle found in essentially all eukaryotic cells is the mitochondrion, which generates the chemical energy for the cell. In contrast, the chloroplast is a type of organelle found only in the cells of plants and algae; it performs photosynthesis. If we were to strip away the plasma membrane from a eukaryotic cell and remove all of its membrane-enclosed organelles, we would be left with the cytosol, which contains many long, fine filaments of protein that are responsible for cell shape and structure, and thereby form the cell’s cytoskeleton.

Changes in DNA sequences from one generation to the next may result in offspring that are altered in fitness compared with their parents. The process of change and selection over the course of many generations is the basis of

1. Evolution

2. Mutation

3. Heredity

4. reproduction

Evolution

What is the smallest distance two points can be separated and still resolved using light microscopy?

1. 20nm

2. 0.2 um

3. 2 um

4. 200 um

0.2 um

Given what you know about the differences between prokaryotic cells and eukaryotic cells, SELECT ALL of the following biological processes which are “suitable” for study using E. coli as the model organism.

1. How mitochondria get distributed to cells during cell division

2. Formation of the endoplasmic reticulum

3. DNA replication

4. How the actin cytoskeleton contributes to cell shape

5. How cells decode their genetic instructions to make proteins

3. DNA replication

   5. how cells decode their genetic instructions to make proteins

Prokaryotic cells do not possess

1. A nucleus

2. Replication machinery

3. Ribosomes

4. Membrane bilayers

A nucleus

Mitochondria contain their own genome, can duplicate, and divide on a different time line from the rest of the cell. Nevertheless, mitochondria cannot function for long when isolated from the cell because they are

1. Viruses

2. Parasites

3. Endosymbionts

4. Anaerobes

Endosymbionts

The world of prokaryotes is divided into two domains (bacteria and archaea), each as different from the other as from eukaryotes. Select the observable characteristic that best distinguishes archaea from bacteria.

1. Can metabolize inorganic substances

2. Are found in extremely harsh environments

3. Thrive in anaerobic conditions

4. Are photosynthetic organisms

The world of prokaryotes is divided into two domains (bacteria and archaea), each as different from the other as from eukaryotes. Select the observable characteristic that best distinguishes archaea from bacteria.

Can metabolize inorganic substances

Are found in extremely harsh environments

Thrive in anaerobic conditions

Are photosynthetic organisms

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?

1. DNA

2. Cell

3. Protein

4. Organelle

Cell

a cell’s genome…

contains all of a cell’s DNA

Whereas ionic bonds form a(n) _____1_____, covalent bonds between atoms form a(n) _____2_____. These covalent bonds have a characteristic bond _____3_____ and become stronger and more rigid when two electrons are shared in a(n) _____4_____. Equal sharing of electrons yields a(n) _____5_____ covalent bond. If one atom participating in the bond has a stronger affinity for the electron, this produces a partial negative charge on one atom and a partial positive charge on the other. These _____6_____ covalent bonds should not be confused with the weaker _____7_____ bonds that are critical for the three-dimensional structure of biological molecules and for interactions between these molecules.

Whereas ionic bonds form a(n) salt, covalent bonds between atoms form a(n) molecule. These covalent bonds have a characteristic bond length and become stronger and more rigid when two electrons are shared in a(n) double bond. Equal sharing of electrons yields a(n) nonpolar covalent bond. If one atom participating in the bond has a stronger affinity for the electron, this produces a partial negative charge on one atom and a partial positive charge on the other. These polar covalent bonds should not be confused with the weaker noncovalent bonds that are critical for the three-dimensional structure of biological molecules and for interactions between these molecules.

T/F: Atoms with unfilled outer electron shells are especially stable and are therefore less reactive

False

T/F: All proteins and RNAs pass through many unstable conformations as they are folded, finally settling on one single, preferred conformation.

True

T/F: Protons are constantly moving between water molecules, which means there is an overall equilibrium between hydroxyl ions and hydronium ions in aqueous solutions

True

Cells contain buffers that help maintain a neutral pH. Which of the following statements is NOT relevant to how buffers work?

1. Buffers are mixtures of weak acids and bases

2. Buffers can accept protons from acids

3. Buffers can donate protons to bases

4. Buffers catalyze REDOX reactions

Buffers catalyze REDOX reactions

When atoms are held together by ____, they are typically referred to as ____.

1. H bonds, molecules

2. Ionic interactions, salts

3. Ionic interactions, molecules

4. Double bonds, nonpolar

Ionic interactions, salts

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?

1. Ionic bonds

2. H bonds

3. Van der waals interactions

4. Covalent bonds

H bonds

Polar covalent bonds form when the electrons in the bond are not shared equally between the two nuclei. Which of these molecules contains polar bonds?

1. Molecular oxygen

2. Methane

3. Propane

4. Water

Water

Which subatomic particles contribute to the atomic number for any given element?

protons

The amino acids glutamine and glutamic acid are shown in the figure. 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, H, van der waals, or covalent)

ionic

Which of the following monomer building blocks is necessary to assemble selectively permeable boundaries around and inside cells?

1. Sugars

2. Fatty acids

3. Amino acids

4. Nucleotides

Fatty acids

Each nucleotide in DNA and RNA has an aromatic base. What is the principal force that keeps the bases in a polymer from interacting with water?

1. Hydrophobic interactions

2. H bonds

3. Van der waals interactions

4. Covalent bonds

Hydrophobic interactions

covalent bond between two atoms is a result of the

sharing of electrons

What do polysaccharides, proteins, and nucleic acids have in common

1. They’re polymers held together by glycosidic and peptide bonds

2. They’re all made from monomer subunits linked by ionic bonds

3. They all contain a phosphate group and are linked by phosphodiester bonds

4. They’re all made from monomer subunits linked by covalent bonds

They’re all made from monomer subunits linked by covalent bonds

Select all molecules that are considered inorganic

1. Glucose

2. Ethanol

3. Sodium chloride

4. Water

5. Cholesterol

6. Phospholipid

7. Calcium

sodium chloride, water, calcium

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

Cholesterol is an essential component of biological membranes. Although it is much smaller than the typical phospholipids and glycolipids in the membrane, it is a(n) __________ molecule, having both hydrophilic and hydrophobic regions.

1. Polar

2. Oxygen-containing

3. Hydrophobic

4. Amphipathic

Amphipathic

T/F: Amino acids possess a carboxylic acid group and an amino group. Based on this, we can conclude that amino acids are inorganic compounds

false

T/F: Condensation (aka dehydration synthesis) reactions occur in the synthesis of all the macromolecules found in cells.

true

Which arrow points to the peptide bond in this picture?

B

Which arrow points to the C-terminus of a polypeptide in this picture?

C

Match the following amino acids with their chemical properties

a. nonpolar

b, acidic

c. nonpolar

d. polar uncharged

e. basic

f. polar uncharged

g. acidic

Glutamic acid is an amino acid that has an acid R group due to the presence of a carboxyl group. This carboxyl group can donate (lose) a proton, becoming negatively charged (at which point it is often called glutamate). Which of these statements is correct?

1. At equilibrium, all glutamic acid R groups will be negatively charged

2. At equilibrium, some glutamic acid R groups will be negatively charged, but others will be uncharged

3. At equilibrium, all glutamic acid R groups will be uncharged

At equilibrium, some glutamic acid R groups will be negatively charged, but others will be uncharged

The R group of glutamic acid has a pKa of 4.1. In normal cell pH of 7, glutamic acid will therefore tend to 

1. Lose a proton

2. Gain a proton

Lose a proton

Not all cellular compartments have the same pH (eg lysosomes are known for their acidic environment). In some organisms, the pH in lysosomes can be as low as 4.0. In these organisms, glutamic acid R groups will be more likely to

1. Gain a proton, becoming uncharged

2. Lose a proton, becoming uncharged

3. Lose a proton, becoming charged

Gain a proton, becoming uncharged

DNA phosphodiester backbone is negatively charged. Which amino acids should be present in the DNA backbone-binding domains of DNA-binding proteins in order for these proteins to form electrostatic attraction with the DNA molecule? (hind: think about amino acid chemical properties)

1. Aspartic acid

2. Lysine

3. Serine

4. Asparagine

5. Valine

6. Arginine

Lysine, Arginine

Match the amino acids with their names

1. proline

2. alanine

3. tyrosine

4. aspartic acid

5. serine

6. glutamine

a. alanine

b. proline

c. aspartic acid

d. tyrosine

e. arginine

f. glutamine

g. serine

In this image the red ribbon represents a polypeptide chain. Which level of protein structure is stabilized by the H bond illustrated in the image?

tertiary

Enzymes facilitate reactions in living systems. Figure 3-2 presents an energy diagram for the reaction X → Y. The solid line in the energy diagram represents changes in energy as the reactant is converted to product under standard conditions. The dashed line shows changes observed when the same reaction takes place in the presence of a dedicated enzyme. Which equation below indicates how the presence of an enzyme affects the activation energy of the reaction (catalyzed versus uncatalyzed)?

d-a versus b-a

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.

1. Dissociation

2. Association

3. Binding

4. Releasing

Binding

ΔG° indicates the change in the standard free energy as a reactant is converted to product. Given what you know about these values, which reaction below is the most favorable?

the most negative one

The energy used by the cell to generate specific biological molecules and highly ordered structures is stored in the form of

1. Brownian motion

2. Heat

3. Light waves

4. Chemical bonds

Chemical bonds

When elemental sodium is added to water, the sodium atoms ionize spontaneously. Uncharged Na becomes Na+. this means that the Na atoms have been

1. Protonated

2. Oxidized

3. Hydrogenated

4. Reduced

Oxidized

A chemical reaction is defined as spontaneous if there is a net loss of free energy during the reaction process. However, spontaneous reactions do not always occur rapidly. Favorable biological reactions require ____ to selectively speed up reactions and meet the demands of the cell

1. Heat

2. ATP

3. Ions

4. Enzymes

Enzymes

Seed oils are often dehydrogenated and added back into processed foods. The new fatty acids have an increased number of C-C double bonds. The dehydrogenation reaction could also be described as a(n) _____ reaction

1. Isomerization

2. Oxidation

3. Reduction

4. Protonation

Oxidation

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 reaction that break down nutrients in food can be described as

1. Metabolic

2. Catabolic

3. Anabolic

4. Biosynthetic

Catabolic

Figure 3-1 is an energy diagram for the reaction X → Y. Which equation below provides the correct calculation for the free-energy change when X is converted to Y?

c-a

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

1. ATP, phosphorylation

2. Water, hydrolysis

3. Hydroxide, hydration

4. Acetate, acetylation

Water, hydrolysis

During respiration, energy is retrieved from the high-energy bonds found in certain organic molecules. Which of the following (in a addition to energy) are the ultimate products of respiration

1. CO2, H2O

2. CH3, H2O

3. CH2OH, O2

4. CO2, O2

CO2, H2O

Even though cellular macromolecules contain many carbon and hydrogen atoms, they are not all spontaneously converted into CO2 and H2O. this absence of spontaneous combustion is due to the fact that biological molecules are relatively ____, and an input of energy is required to reach lower energy states

1. Large

2. Polar

3. Stable

4. Unstable

Stable

Oxidation is a favorable process in an aerobic environment, which is the reason cells can 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____

1. CO2, photosynthesis

2. CH3, combustion

3. CO2, respiration

4. CO, reduction

CO2, photosynthesis

The synthesis of glutamine from glutamic acid requires the production of an activated intermediate followed by a condensation step that completes the process. Both amino acids are shown in figure 3-4. In the condensation step, _______ is displaced by ________.

1. OH, NH3

2. ADP, NH2

3. ATP, NH3

4. Phosphate, NH3
   

   

Phosphate, NH3

For the reaction Y → X at standard conditions with [Y] = 1 M and [X] = 1 M, ΔG is initially a large negative number. As the reaction proceeds, [Y] decreases and [X] increases until the system reaches equilibrium. How do the values of ΔG and ΔG° change as the reaction equilibrates?

1. ΔG becomes less negative and ΔG° stays the same

2. ΔG becomes positive and ΔG° becomes positive.

3. ΔG stays the same and ΔG° becomes less negative.

4. ΔG reaches zero and ΔG° becomes more negative.

ΔG becomes less negative and ΔG° stays the same

Activated carriers are small molecules that can diffuse rapidly and be used to drive biosynthetic reactions in the cell. Their energy is stored in a readily transferable form such as high-energy electrons or chemical groups. Which of the molecules below donates a chemical group rather than electrons?

1. FADH2

2. NADH

3. NADPH

4. ATP

ATP

In the case of a simple conversion reaction such as X → Y, which value of ΔG° is associated with a larger concentration of X than Y at equilibrium? (Hint: How is ΔG° related to K?)

1. ΔG° = –5

2. ΔG° = –1

3. ΔG° = –0

4. ΔG° = 1

ΔG° = 1

All 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

1. glucose-P

2. creatine-P

3. acetyl-P

4. adenosine-P3

adenosine-P3

The synthesis of glutamine from glutamic acid requires the production of an activated intermediate followed by a condensation step that completes the process. Both amino acids are shown in Figure 3-4. Which molecule is added to glutamic acid in the activation step?

1. Phosphate

2. NH3

3. ATP

4. ADP

Phosphate

∆G= ∆G°+RT ln⁡〖([products])/([reactants])〗

Calculate the ΔG for ATP hydrolysis under real cell conditions:

•R= 1.987 cal/mol x K

•T= 310.15K (=37C)

•ΔG° =-7.3cal/mol

•[ADP]= 10-3 mol/L

•[P]= 10-2 mol/L

•[ATP]= 10-2 mol/L

1. 1426.3

2. -1426.3

3. 0

4. 14.26

-1426.3

If the ΔG for glucose + ATP -> glocose-6-phosphate + ADP reaction without an enzyme is -4 kcal/mol, what will be the ΔG of the same reaction when it is catalyzed by an enzyme?

1. More negative than -4

2. -4  

3. Less negative than -4

4. Impossible to tell

-4

The following are the ΔG° of hydrolysis of certain compounds. Which of these reactions would you use to drive ATP synthesis?  

a. ΔG° = -1.5 kcal/mol 

B. ΔG° = -4 kcal/mol

C.  ΔG° = -15 kcal/mol

ΔG° = -15 kcal/mol

What kind of covalent bonds will an oxygen and two hydrogens form

1. Single polar

2. Single nonpolar

3. Double polar double nonpolar

Single polar

Given that many interactions between enzymes in cells need to be transient, which of the bonds do you expect to predominate between an enzyme and its substrates? Select all that apply

1. Covalent

2. H bonds

3. Van der waals

H bonds, Van der Waals

What kind of bonds/interactions form between the two DNA strands (red oval)

1. Covalent bond

2. Electrostatic attraction

3. H bonds

4. Hydrophobic force

5. Van der waals

H bonds

between the negatively charged DNA backbone and the positively charged arginine residue in histones (blue circle)

1. Covalent bond

2. Electrostatic attraction

3. H bonds

4. Hydrophobic force

5. van der waals

Electrostatic attraction

Carboxyl group is acidic and will therefore lose (donate) its proton at physiological pH. In cells, carboxyl groups will therefore be

1. Uncharged

2. Positively charged

3. Negatively charged

Negatively charged

When two nucleotides are joined together to form a phosphodiester bond, one water molecule (and two phosphates) are released. Therefore, this is a

1. Condensation reaction

2. Hydrolysis reaction

3. None of the above

Condensation reaction

The green amino acid is a buly amino acid that introduces turns in polypeptides. It is likely a

1. Glycine

2. Cysteine

3. Proline

Proline

Silk is a natural protein fiber produced by moth larvae during pupation. One of the major structural components of silk is the protein fibrouin, which gives silk its strength and prevents it from stretching. Which secondary structure do you predict to be abundant in fibroin?

1. Alpha helix

2. Beta helix

3. Random coil

Beta helix

What levels of protein structure are determined (at least partially) by hydrogen bonds? Select all that apply

1. Primary

2. Secondary

3. Tertiary

4. Quaternary

Secondary

Tertiary

Quaternary

The _____ law of thermodynamics states that energy can neither be created nor destroyed

1. First

2. Second

3. Third

4. Fourth

First

carries out protein synth in the cytoplasm

ribosome

composed of different membranes that are suspended in the cytoplasm within a euk cell which divide the cell into functional and structural compartments (organelles)

endomembrane system

break down carbohydrates to produce adenosine triphosphate (ATP)

mitochondria

Cell theory was articulated by these three people

Schleiden, schwann, virchow

Who observed microscopic organisms that he called animicules

van leeuwenhoek

who disproved spontaneous generation with the curved flask

pasteur

The nucleus contains ___, which diffuses DNA, protein, and some RNA, and creates chromosomes

chromatin

Plant cell wall is composed of these three things

Cellulose, hemicellulose, lignin

Describe the differences between the prokaryotic domains

1. Bacteria: peptidoglycan in cell walls, ester linked membrane lipids

2. Archaea: extreme enviros, ether linked lipids

Which is not a unifying feature of cells

1. Self regulate

2. Carry out a variety of chemical reactions

3. Reproduce only by mitosis

4. Have a surrounding plasma membrane

5. None of the above

Reproduce only by mitosis

1. Which is a key difference between prok and euk

   1. Euk have membrane bound organelles

   2. Prok have linear DNA and euk have circular DNA

   3. Euk are always uinicellular, prok can be multi or uni

   4. Euk undergo simple fission, prok undergo mitosis and meiosis

Euk have membrane bound organelles

1. What does the nucleus confine to keep them separated from other cell components

   1. Lysosomes

   2. Peroxisomes

   3. Ribosomes

   4. Chromosomes

   5. Centrosomes

Chromosomes

what allows for specialization in multicellular euk

1. Different cell types

2. Evolution

3. Absence of cell to cell communication

4. Simple body plans

5. Differential gene expression

Differential gene expression

which is key difference between bacteria and archaea

1. Bacteria have a plasma membrane lipids similar to eukaryotes while Archaea contain branching phospholipids

2. Bacteria have DNA replication like eukaryotes while Archaea have unique enzymes in DNA replication

3. Bacteria include many types of extremophiles while archaea are present in every conceivable habitat

4. Bacteria have ether bonds that connect lipids to glycerol while archaea have ester bonds that connect lipids to glycerol

5. Bacteria contain branching phospholipids while archaea have plasma membrane lipids like eukaryotes

Bacteria have a plasma membrane lipids similar to eukaryotes while Archaea contain branching phospholipids

weak noncovalent interaction due to fluctuating electrical charges when atoms are close

van der waals (temporary dipole/dispersion)

Noncovalent interaction that forces together hydrophobic portions of dissolved molecules

Hydrophobic force

Force that draws together oppositely charged atoms

Electrostatic attraction

Hydrocarbons are composed of repeating ____ bonds

Nonpolar covalent

Disaccharides are formed from two monosaccharides via ____ and can be split back into simple sugars via _____

condensation/dehydration, hydrolysis

Nitrogenous bases with a double ring structure

Purines (A and G)

Nitrogenous bases with a single ring structure

Pyrimidines (C, T, U)

Amino acid monomers are connected via a ____ bond, Nucleotide monomers are connected via a ____ bond

Peptide, phosphodiester

Draw the structure of the seven functional groups and explain their properties

Hydroxyl (-OH) → Polar, forms hydrogen bonds, increases solubility.

Carbonyl (C=O) → Found in ketones and aldehydes, reactive.

Carboxyl (-COOH) → Acidic, donates H⁺, found in amino acids.

Amino (-NH₂) → Basic, accepts H⁺, forms peptide bonds.

Sulfhydryl (-SH) → Forms disulfide bonds (stabilizes proteins).

Phosphate (-PO₄³⁻) → Highly charged, involved in energy transfer (ATP).

Methyl (-CH₃) → Nonpolar, affects gene expression (epigenetics

Define and contrast protein primary, secondary, tertiary, and quaternary structure

1. Primary- linear sequence of amino acids

2. Secondary- H bonds for a helices and B sheets

3. Tertiary- R group interactions form 3D shape

4. Quaternary- multiple polypeptides form a protein

Describe the functions of nucleic acids in the cells, provide examples

1. DNA stores genetic information

2. RNA helps in protein synthesis

3. ATP carries energy