Ch2 LOs

Question 1

2.1: Explain the relationship between atoms and molecules.

Answer 1

Atoms are the fundamental unit of an element, made of protons, neutrons, and electrons. Molecules are structures made of two or more atoms held together by covalent bonds.

Question 2

2.2: Explain what electronegativity means.

Answer 2

Electronegativity is the tendency of an atom’s nucleus to attract the shared electrons in a covalent bond.

Question 3

2.2: Explain how electronegativity influences the electron positions in a covalent bond.

Answer 3

The electrons are closer to whichever atom has the most electronegativity.

Question 4

2.2: Explain how electronegativity influences the partial charges on atoms in a covalent bond.

Answer 4

The more electronegative atom has a partial negative and the other atom would have a partial positive charge.

Question 5

2.3: Compare hydrogen bonds and covalent bonds in terms of the mechanisms and strength of attraction between the atoms involved.

Answer 5

A hydrogen bond is an attraction between a partial positive charge on a hydrogen atom and a partial negative on another atom. A covalent bond is an attraction between two atoms based on shared electrons.

Hydrogen bonds are not as nearly strong as covalent bonds.

Question 6

2.6: what is an acid?

Answer 6

An ion or molecule that releases a proton.

Question 7

2.6: What is a base?

Answer 7

An ion or molecule that acquires a proton.

Question 8

2.6: What is PH? The scale?

Answer 8

Quantifies the concentration or protons in a solution.
14- Basic
7- Neutral
0- Acidic

Question 9

3.1: Compare the structure of DNA and RNA.

Answer 9

DNA Primary: sequence of nucleotides
RNA Primary: nucleotides

DNA Secondary: Double helix (H bonding)
RNA Secondary: stem and loop (not all RNA has a secondary structure)

RNA tertiary: several stem-and-loop sections twist and fold across each other to form a new 3-dimensional shape.

Question 10

3.1: Compare the chemical composition of DNA and RNA.

Answer 10

Ribonucleotides contain ribose while deoxyribonucleotides contain deoxyribose. The two molecules are identical except for what might seem like a tiny difference—an OH on the 2′ carbon of ribose versus an H bonded to the 2′ carbon of deoxyribose.

Question 11

3.1: Compare the location and function of DNA and RNA.

Answer 11

• DNA holds in coded form and create an mRNA copy. In contrast, RNAs can adopt a wide variety of shapes and have groups of atoms that can participate in an important array of chemical reactions.
  -The C-OH group on the 2′ carbon of a ribonucleotide can participate in a lot more chemical reactions than the C-H group on the 2′ carbon of a deoxyribonucleotide.

Question 12

3.2: Define complementary base pairing, and explain its connection to the observation that DNA strands are antiparallel.

Question 13

4.1: Explain how the genetic code relates transcription to translation.

Answer 13

During translation, the translation machinery “reads” the nucleotides in an mRNA in groups of 3 (codon).

Question 14

4.1 Why is the genetic code redundant?

Answer 14

The code is redundant, meaning that many amino acids are coded for by more than one codon.

Question 15

4.1: Why is the genetic code conservative?

Answer 15

The code is conservative, meaning that changes in the third position of a codon are less likely to change which amino acid is added to a protein than changes in the first or second positions.

Question 16

4.1: Why os the code unambiguous?

Answer 16

Meaning that each codon specifies exactly one amino acid or punctuation mark

Question 17

4.2: On diagrams of translation initiation, translation elongation, and translation termination, label the small and large ribosomal subunits, mRNA, tRNA, rRNA, reading frame, start codon, stop codon, release factor, and tRNA binding sites (E, A, and P). Circle and label the locations where codon- anticodon recognition and peptide bond formation occur.

Question 18

4.2: What is tRNA and which parts are labeled?

Answer 18

-Key to bridging the RNA protein language barrier
-The attachment site, which always has the nucleotide sequence CCA, is where amino acids bind so they can be carried by the tRNA.
-The anticodon is a sequence of three bases at the other end of the tRNA. The specific sequence labeled UAC in this figure, shown here in the 3′ to 5′ direction, is complementary to an AUG codon in an mRNA.

Question 19

4.2: How many tRNAs are there?

Answer 19

So for each of the 20 amino acids, there is a different tRNA with a different anticodon.

Question 20

4.2: Ribosomes

Answer 20

Protein-making machines.

Question 21

4.2: RNA subunits

Answer 21

A large subunit and a small subunit. The boundary between the two subunits is defined by where the pink mRNA strand is shown on the cartoon model. When translation is not occurring, the subunits are separate. However, when translation is occurring, the subunits are bound together to form a single structure.

Question 22

4.2: A site

Answer 22

where amino acid-charged tRNAs enter the ribosome. If the anticodon of a tRNA binds to the exposed codon in the mRNA, the tRNA and mRNA bind together.

Question 23

4.2: Charged vs uncharged tRNA

Answer 23

A “charged tRNA” is a transfer RNA molecule that has an amino acid attached to it, making it ready to deliver that specific amino acid to the ribosome during protein synthesis, while an “uncharged tRNA” is a tRNA molecule that does not have an amino acid attached and therefore cannot participate in protein translation.

Question 24

4.2: P site

Answer 24

Where peptide bond formation takes place.

Question 25

4.2: E site

Answer 25

Exit site.

Question 26

4.3: Use a copy of the genetic code to predict the sequence of the amino acids produced from a given mRNA or double-stranded DNA fragment. Identify the template and non-template (coding) strand. Identify the start and stop codon.

Answer 26

Where tRNAs sit once the amino acid they were carrying has been added to the growing protein. The now-uncharged tRNA exits the ribosome from this site.

Question 27

4.2: Translation Elongation process

Answer 27

Each tRNA involved in building a protein moves through the ribosome by first entering the A site, moving to the P site, and exiting from the E site. A charged tRNA enters a ribosome and leaves uncharged.

Question 28

4.2: Translation termination

Answer 28

- once stop codon is reached, translation is stopped because there is no tRNA that binds to it. -Instead, a protein that has essentially the same shape as a tRNA interacts with the stop codon and binds to it. This protein is called the release factor.

Question 29

4.2: How is it possible for the release factor to be a protein but still bind to the 3 ribonucleotides in a stop codon?

Answer 29

The R-groups at the base of the tRNA-shaped release factor form hydrogen bonds and other interactions with the ribonucleotides of the stop codon.

Question 30

4.2: Ribozyme

Answer 30

An RNA molecule that catalyzes a chemical reaction, analogous to enzymes, which are protein catalysts.

Question 31

4.4: Discuss the structure and functions of the main players in translation (tRNAs and ribosomes)

Question 32

4.5: On diagrams of transcription initiation and transcription elongation, label the template and coding strands, initiation complex, promoter site, RNA polymerase, ribonucleotides, the direction of RNA polymerase movement, and direction of RNA synthesis.

Question 33

4.5: Template strand

Answer 33

The strand in a DNA double helix that is “read” by RNA polymerase during transcription.

Question 34

4.5: coding strand

Answer 34

The strand in a DNA double helix that matches the sequence of bases in the RNA product of transcription, except that the DNA contains thymine (T) and the RNA contains uracil (U).

Question 35

4.5: Promoter

Answer 35

The regulatory sequence in a gene where RNA polymerase initiates transcription.

Question 36

4.5: RNA polymerase

Answer 36

An enzyme that catalyzes the formation of phosophodiester linkages between ribonucleotides, forming an RNA product that is complementary to the sequences of bases in a DNA template.

Question 37

5.1: Describe at least three functions that proteins serve in cells.

Answer 37

catalysis, transporting materials, movement, cell structure, defense, signaling and communication

Question 38

5.2: Label the four components of an amino acid and explain the role of each in terms of how the molecule functions in a protein.

Answer 38

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Question 39

5.2: Amino groups

Answer 39

act as bases and tend to pick up a proton when they are in water

Question 40

5.2: carboxyl group

Answer 40

tend to act as acids and drop a proton

Question 41

5.2: R group

Answer 41

Bonded to the central carbon. What makes each amino acid unique is the structure of its R-group.

Question 42

5.3: Predict whether the R-group on an amino acid that you haven't seen before will 1) interact with water, and 2) act as an acid (proton donor) or base (proton acceptor).

Question 43

5.4: Describe each of the four levels of protein structure and explain how each influences the protein's final size, shape, and chemical properties.

Answer 43

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Question 44

Protein Primary

Answer 44

the sequence of amino acids, linked via peptide bonds

Question 45

Protein Secondary

Answer 45

formation of ⍺-helices and β-pleated sheets, stabilized by hydrogen bonds between backbone atoms

Question 46

Protein tertiary

Answer 46

folding into a 3-D shape stabilized by hydrogen bonds, ionic bonds, S-S bridges, and hydrophobic interactions

Question 47

Protein quaternary

Answer 47

assembly of multipart proteins from folded subunits, stabilized by hydrogen bonds, ionic bonds, S-S bridges, and hydrophobic interactions

Question 48

5.5: Compare which bonds are responsible for producing a protein's 1) primary structure, 2) secondary structure (alpha-helices and beta-pleated sheets), and 3) tertiary structure.

Answer 48

Primary- peptide bonds Secondary- hydrogen bonds between backbone atoms Tertiary- H-bonds, ionic bonds, S-S bridges, hydrophobic interactions Quaternary- hydrogen bonds, ionic bonds, S-S bridges, and hydrophobic interactions

Question 49

6.1: Draw the general structure of a monosaccharide, disaccharide, and polysaccharide. Give an example of each.

Answer 49

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Question 50

6.1: Glycosidic linkage

Answer 50

A covalent bond that links monosaccharides together to form polymers.

Question 51

6.1: Glycan

Answer 51

A polymer made up of monosaccharides joined by glycosidic linkages. (Synonymous with 'polysaccharide.')

Question 52

6.1: Carbohydrates

Answer 52

A family of molecules that includes both monosaccharides and glycans.

Question 53

6.1: alpha linkage

Answer 53

same side

Question 54

6.1: beta linkage

Answer 54

opposite side

Question 55

6.3: Explain how the structures of cellulose, chitin, glycogen, and starch support their functions.

Answer 55

Cellulose gives plants structural strength, because the combination of β-glycosidic linkages and hydrogen-bonded strands creates a tough, mesh-like material that is difficult for molecular machines to break down.

Question 56

7.1: Compare the monomer subunit, bond responsible for polymerization, and important biological function(s) observed in proteins, nucleic acids, and carbohydrates.

Answer 56

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Question 57

7.1: Proteins -monomer subunit -bond responsible for polymerization -important biological functions

Answer 57

-amino acids -peptide bond (formed via dehydration synthesis between the carboxyl group of one amino acid and the amino group of another) -Enzymes catalyze biochemical reactions -structural support -transport -cell signaling -immune response

Question 58

7.1: Nucleic Acids -monomer subunit -bond responsible for polymerization -important biological functions

Answer 58

- nucleotides -phosphodiester bond (links the phosphate group of one nucleotide to the hydroxyl group on the sugar of another) -store genetic info -transmit genetic info -energy transfer

Question 59

7.1: Carbohydrates -monomer subunit -bond responsible for polymerization -important biological functions

Answer 59

-monosaccharides -glycosidic bond (formed between hydroxyl groups of two monosaccharides) -energy storage -structural support -cell recognition and signaling

Question 60

7.2: Compare the primary, secondary, and tertiary structures of proteins, RNA, and DNA.

Answer 60

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Question 61

7.2: structures of protein

Answer 61

1) peptide bonds 2) a-helices and/or pleated sheets stabilized by hydrogen bonds 3) Folding into specific shapes stabilized by ionic bonds, hydrogen bonds, S-S bonds, and/or hydrophobic interactions

Question 62

7.2: structures of RNA

Answer 62

1) Phosphodiester linkages 2) loop and stem 3) specific shapes stabilized by hydrogen bonds

Question 63

7.2: structures of DNA

Answer 63

1) phosphodiester linkages 2) double helix formed from antiparallel strands stabilized by hydrogen bonds 3) supercoiling (twisting on itself)

Question 64

Defend the following three statements: 1) amino acids are much more diverse in structure and chemical properties than nucleotides, 2) in terms of diversity in shape and chemical properties, proteins > RNA > DNA, and 3) in terms of diversity in function, proteins > RNA > DNA.

Question 65

8.1: Use drawings, models, or other representations to compare the structures of fats, phospholipids, and steroids.

Answer 65

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Question 66

8.1: Fats

Answer 66

are made up of three hydrocarbon-rich molecules called fatty acids, each of which is attached to a 3-carbon molecule called glycerol.

Question 67

8.1: steroids

Answer 67

have a bulky structure containing carbon atoms arranged in four "fused rings." Steroids vary in the R-groups attached to this core structure, with the example shown here featuring an -OH group on one end and a hydrocarbon tail with 8 carbons on the other.

Question 68

8.1: Phospholipids

Answer 68

are a family of molecules that have two long hydrocarbon "tails" and a "head" that includes a phosphate group and a polar group. The polar groups in phospholipids got their name because they each contain one or more charges or partial charges. When you start analyzing different phospholipids, you'll find that each type has 1) a different polar group, and 2) hydrocarbon tails that vary in length and/or degree of saturation.

Question 69

8.1: Amphipathic Lipids

Answer 69

Polar and nonpolar - ex: cholesterol

Question 70

9.4: Given several models of membranes, predict how differences in phospholipid composition and cholesterol content will affect their relative fluidity and permeability, and explain your reasoning.

Question 71

9.1: Draw a cell membrane and label integral and peripheral proteins, carbohydrate components, and lipid components.

Answer 71

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Question 72

9.1: Peripheral membrane protein

Answer 72

A protein found on the inner or outer surface of a cell membrane.

Question 73

9.1: Transmembrane protein

Answer 73

A protein that spans the lipid bilayer of a cell membrane.

Question 74

9.2: Compare the processes of diffusion, osmosis, and facilitated diffusion, and provide biological examples that illustrate each process.

Answer 74

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Question 75

9.2: Diffusion

Answer 75

the spontaneous movement of atoms, ions, and molecules from areas of higher concentration to areas of lower concentration.

Question 76

9.2: osmosis

Answer 76

- an example of diffusion -refers specifically to the diffusion of water across membranes - from an area of higher concentration (low solute concentration) to an area of lower concentration (higher solute concentration)

Question 77

9.5: Given several ions and molecules, predict the relative rates at which they will cross a plasma membrane in the absence of membrane proteins. Explain your reasoning.

Answer 77

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Question 78

9.5: Selective permeability

Answer 78

Means that some substances can cross membranes much more readily than others.

Question 79

9.5: The ability of a substance- an atom, an ion, or a molecule- to pass through a lipid bilayer depends on two things:

Answer 79

size and charge

Question 80

9.5: which molecules can move across a cell membrane?

Answer 80

Small, nonpolar molecules like oxygen (O2) and carbon dioxide (CO2), as well as small polar molecules like water (H2O)

Question 81

9.5: which molecules can't move across a cell membrane without assistance?

Answer 81

larger molecules, charged ions, and most polar molecules

Question 82

9.2: Concentration gradient

Answer 82

a difference in a substance’s concentration in space—usually across a cell membrane

Question 83

9.2: Facilitated diffusion

Answer 83

(passive) diffusion of substances across cell membranes through integral membrane proteins

Question 84

10.1: Define passive and active transport and explain the role of channels, carriers, and pumps in transport.

Answer 84

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Question 85

10.1: Passive transport

Answer 85

any movement of ions or molecules that does not require an input of energy

Question 86

10.1: Active Transport

Answer 86

any movement of ions or molecules that requires an input of energy.

Question 87

10.1: Membrane channels have three key points:

Answer 87

- Have a distinctive structure -Channels are extremely specific -regulation: few, if any, channels, are open at all times -They have open and closed configurations that are highly regulated

Question 88

10.1: Membrane carriers

Answer 88

Are similar to membrane channels but do not open a channel. They change its shape.

Question 89

10.1: Pumps

Answer 89

The unique aspect of pumps is that they transport substances against—or up—a concentration gradient (and/or electrical gradient—but more on that later).

Question 90

10.2: Describe the role of electrochemical gradients in primary and secondary active transport.

Question 91

10.3: Describe the processes of endocytosis and exocytosis.

Question 92

10.4: Predict what will happen to a cell when it is placed in a hypertonic, hypotonic, or isotonic solution.

Question 93

11.3: Explain how and why ions and molecules move in response to concentration gradients.

Answer 93

When a concentration gradient exists, ions and molecules will move from regions of high concentration to regions of low concentration by diffusion.

Question 94

11.2: Explain how ions move in response to electrical potential gradients, and why.

Answer 94

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Question 95

11.2: Membrane voltage

Answer 95

In cells, an electrical potential created by a separation of charge across a membrane. Also called a transmembrane potential or a membrane potential.

Question 96

11.2: electrical current

Answer 96

In cells, a flow of charge in the form of ions.

Question 97

11.1: Based on the information you are given about a specific cell, predict how it will be affected by ion movements that occur in response to a change in electrical potential gradients.

Answer 97

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Question 98

11.1: Electrochemical gradient

Answer 98

The overall gradient across a cell membrane or organelle membrane, produced by differences in concentration of substances combined with differences in the distribution of charge.

Question 99

12.1: Explain why viruses are considered obligate intracellular parasites, and why viral diseases are difficult to treat with drugs.

Answer 99

Viruses can only reproduce by entering a host cell and using the host cell's molecular machinery, ATP, and other resources to make copies of themselves. Because there are so few virus-specific proteins, it is difficult for researchers to design drugs that damage a virus without damaging the host.

Question 100

12.3: State the arguments for why viruses could be considered alive or not alive, then state and defend your opinion on this question.

Answer 100

Alive: -they evolve -they replicate Dead: -they can't perform metabolism -they don't have cell membranes

Question 101

12.2: Using a diagram, explain how the following events in a virus' life cycle occur: enter a host cell, produce viral proteins, replicate viral genome, assemble new virions, exit host cell, transmission to a new host.

Answer 101

A virus begins its life cycle by entering a host cell, typically binding to specific receptors on the cell surface and gaining entry through membrane fusion, endocytosis, or direct injection of its genetic material. Once inside, the virus produces viral proteins by using the host's machinery to transcribe and translate its genome. Simultaneously, it replicates its genome using either host or viral enzymes, depending on whether it is a DNA or RNA virus. Newly synthesized viral components then assemble into new virions, often through self-assembly. The virus exits the host cell either by lysis, which destroys the cell, or by budding, which allows the virus to acquire a membrane envelope. Finally, transmission to a new host occurs through various means, such as direct contact, airborne droplets, or vectors, ensuring the continuation of the viral infection cycle.

Question 102

12.2: Enveloped vs non enveloped viruses exit of cell

Answer 102

Enveloped viruses insert their surface proteins into a lipid bilayer present in the host. Non-enveloped viruses have a mechanism for disrupting the host cell's membrane as well as its cell wall, if one is present.

Question 103

12.2: Protease

Answer 103

An enzyme that catalyzes breaking peptide bonds in a long string of amino acids. Some proteases function as digestive enzymes; other break long amino-acid chains at specific points to create several to many independent proteins.

Question 104

13.1: Compare key elements of prokaryotic versus eukaryotic cell structure.

Answer 104

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Question 105

13.1: What are the common elements found in every cell?

Answer 105

cell membrane, genetic material, ribosomes, cytoskeletal elements, organelles, cell wall, flagella

Question 106

13.1: Archaean Cells

Answer 106

-live in extreme habitats -not known to cause disease or are important to humans -have unique hydrocarbon chains in their membrane lipids -unique types of carbohydrates in their cell walls

Question 107

13.1: Bacterial Cells

Answer 107

Although a few species have linear chromosomes, most bacteria have a single, circular chromosome — a circular double helix that associates with DNA-binding proteins and coils and folds on itself into a compact structure.

Question 108

13.1: Eukaryotic Cells

Answer 108

- have a double membrane nucleus (nuclear envelope) studded with pores

Question 109

13.2: Compare key elements of plant versus animal cell structure.