Midterm Study Guide PDF

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CHAPTER 1

Cells: The Fundamental Units of

Life UNITY AND DIVERSITY OF CELLS 1.1.a

Compare, with examples, some ways in which cells may vary in appearance and

function. 1.1.b

Outline, with examples, ways in which cells share a basic fundamental chemistry.

1.1.c

Explain how the relationship between DNA, RNA, and protein—as laid out in the central dogma—makes the self-replication of living cells possible.

1.1.d

Summarize how the processes of mutation and selection promote the gradual

evolution of individuals best suited for survival in a wide range of habitats. 1.1.e

Explain how differentiated cell types can vary widely in form and function despite

having the same genome sequence.

CELLS UNDER THE MICROSCOPE 1.2.a

List the three tenets of cell theory and explain their ramifications for the study of cell

biology. 1.2.b

Contrast light microscopy, super-resolution fluorescence light microscopy, and

electron microscopy in terms of the cell components that can generally be distinguished using each. 1.2.c

Compare how samples are prepared for light versus electron microscopy and explain how these preparations affect whether the technique can be used for viewing living cells or tissues.

THE PROKARYOTIC CELL 1.3.a

Describe the structural differences between prokaryotes and eukaryotes.

1.3.b

Analyze how eukaryotic cells and organisms rely on the function of prokaryotic cells

and their descendants. 1.3.c

Compare prokaryotes and eukaryotes in terms of their relative preponderance on Earth, their range of habitat, and their tendency toward multicellularity.

1.3.d

Justify the division of prokaryotes into bacteria and archaea.

THE EUKARYOTIC CELL 1.4.a

State the function of the nucleus and describe its structural features.

1.4.b

Explain how the structure of the mitochondrion supports its function.

1.4.c

Outline the evolution of mitochondria and chloroplasts and cite the evidence for these origins.

1.4.d

Explain how chloroplasts and mitochondria cooperate as plant cells convert light

energy into chemical energy. 1.4.e

Compare the function of lysosomes and peroxisomes.

1.4.f Compare the structure, location, and function of the endoplasmic reticulum and Golgi apparatus. 1.4.g

Outline the role that transport vesicles play in endocytosis, exocytosis, and the

movement of materials between one membrane-enclosed organelle and another. 1.4.h

Relate the location of the cytosol with respect to the cell’s membrane-enclosed

organelles. 1.4.i List the three major filaments of the cytoskeleton and contrast the roles they have in animal cells. 1.4.j Outline the role the cytoskeleton has in plant cells. 1.4.k

Describe the ancestral cell that likely engulfed the aerobic bacteria that gave rise to mitochondria and explain why this event is thought to have preceded the acquisition of chloroplasts.

MODEL ORGANISMS 1.5.a

Review why scientists study model organisms.

1.5.b

Compare E. coli, S. cerevisiae, and A. thaliana and list the types of discoveries made

by studying each. 1.5.c

Compare flies, worms, fish, and mice as model organisms and name a benefit of studying each.

1.5.d

Review the benefits of studying cultured human cells.

1.5.e

Assess the relationship between genome size and gene number.

1.5.f Explain the significance of homologous genes and proteins. 1.5.g

Summarize the roles played by the nucleotide sequences contained in an organism’s

genome. 1.5.h

Outline an experiment that would allow investigators to determine whether proteins

from different eukaryotes are functionally interchangeable.

CHAPTER 4

Protein Structure and Function THE SHAPE AND STRUCTURE OF PROTEINS

4.1.a

Explain how noncovalent interactions—including electrostatic attractions, hydrogen

bonds, van der Waals attractions, and hydrophobic forces—influence the shape of a folded protein and how the polypeptide backbone and amino acid side chains participate in these interactions. 4.1.b

Describe the relationship between free energy and protein conformation.

4.1.c

Explain how chaperone proteins guide the folding of a polypeptide chain—and why some proteins can fold without chaperone assistance.

4.1.d

Contrast the hydrogen bonding patterns that give rise to alpha helices with those

that produce beta sheets. 4.1.e

Explain how amyloid structures form and discuss some of the consequences of their

formation. 4.1.f Describe the role that protein domains play within a protein’s three-dimensional structure. 4.1.g

Define a protein’s primary, secondary, tertiary, and quaternary structures.

4.1.h

Explain the role that unstructured sequences play in protein function and how amino

acid changes in these regions may affect these functions. 4.1.i Explain how binding sites allow the assembly of multisubunit proteins and multiprotein complexes. 4.1.j Compare how covalent crosslinks and noncovalent bonds help to establish protein structure.

HOW PROTEINS WORK 4.2.a

Summarize the roles that noncovalent interactions and exact protein conformation play

in allowing proteins to recognize and bind specifically to their ligands. 4.2.b

Explain how antibodies, which share the same basic structure, can recognize a

limitless diversity of antigens. 4.2.c

State the significance of an enzyme’s Michaelis constant, KM, and explain how this value influences which biochemical pathway a substrate might follow.

4.2.d

Describe how enzymes can reduce the activation energy needed to catalyze chemical

reactions.

HOW PROTEINS ARE CONTROLLED 4.3.a

Explain how and why different forms of feedback control might be used to regulate

enzyme activity. 4.3.b

Explain how the binding of a ligand at a regulatory site can alter the activity of a

protein or enzyme. 4.3.c

Explain how chemical modification such as phosphorylation can influence a protein’s location and interactions.

4.3.d

Contrast how protein activity is regulated by phosphorylation or by the binding of

nucleotides such as GTP or ATP. 4.3.e

Explain how the hydrolysis of ATP or GTP can produce the directional movement of

motor proteins or coordinate the activity of large protein machines. 4.3.f Describe how scaffold proteins aid in the assembly of protein complexes. 4.3.g

Explain how intracellular condensates can form biochemical subcompartments in a

cell.

HOW PROTEINS ARE STUDIED 4.4.a

Contrast chromatography and electrophoresis as methods for protein separation.

4.4.b

Explain how mass spectrometry allows the identification of proteins.

4.4.c

Compare X-ray crystallography, NMR spectrometry, and cryoelectron microscopy as methods for determining the three-dimensional structure of proteins.

4.4.d

Describe how the existence of protein families affects the determination of protein

structure.

CHAPTER 5

DNA and Chromosomes THE STRUCTURE OF DNA

5.1.a

Contrast the functions of the DNA and protein components of chromosomes.

5.1.b

Explain why biologists initially thought that proteins were the most likely carriers of

genetic information. 5.1.c

Describe how, experimentally, researchers demonstrated that DNA carries genetic information.

5.1.d

Distinguish between the bonds that link together the subunits in a single strand of

DNA and those that hold together the two strands in a DNA double helix, and summarize how these bonds affect the behavior of the DNA molecule. 5.1.e

Describe complementary base-pairing and explain how this arrangement gives rise to

the twisting, consistently proportioned, double helical structure of DNA. 5.1.f Describe the chemical differences that dictate the polarity of a DNA strand. 5.1.g

Explain how the structure of DNA carries information for producing proteins.

5.1.h

Explain how the structure of DNA suggests a mechanism by which genetic

information can be copied.

THE STRUCTURE OF EUKARYOTIC CHROMOSOMES 5.2.a

Contrast prokaryotic and eukaryotic chromosomes in terms of structure and

specialized sequence elements. 5.2.b Describe how human chromosomes can be distinguished from one another and how such information can be of value. 5.2.c Recall how many molecules of DNA are in each eukaryotic chromosome. 5.2.d Describe a full complement of human chromosomes in a diploid somatic cell, including sex chromosomes. 5.2.e Define the terms “gene” and “genome.” 5.2.f Describe the relationship among gene number, genome size, and organismal complexity. 5.2.g Explain why much “junk DNA” is thought to serve a biological function.

5.2.h Compare the roles played by centromeres, telomeres, and replication origins. 5.2.i Explain the organization and attachments that keep interphase chromosomes from becoming extensively entangled. 5.2.j Describe the structure and function of the nucleolus. 5.2.k Contrast the extents of compression in interphase and mitotic chromosomes. 5.2.l Compare the roles played by non-histone proteins and histone proteins (including histone H1) in the packaging of chromatin. 5.2.m Distinguish between a nucleosome and a nucleosome core particle. 5.2.n Explain how histone proteins are able to bind tightly to DNA.

THE REGULATION OF CHROMOSOME STRUCTURE 5.3.a

Explain how chromatin-remodeling complexes and histone-modifying enzymes

regulate the accessibility of DNA. 5.3.b

Explain why a cell might decondense a particular segment of DNA.

5.3.c

Contrast euchromatin and heterochromatin in terms of structure, gene activity, and location along an interphase chromosome.

5.3.d

Explain how heterochromatin is established and spreads.

5.3.e

Explain how heterochromatin participates in gene silencing and provide an example.

CHAPTER 6

DNA Replication and Repair DNA REPLICATION

6.1.a

Explain how a DNA double helix provides a template for its own replication, and

describe the resulting daughter helices in terms of their sequence and the distribution of parental and newly synthesized DNA strands. 6.1.b

Describe the experiment that revealed the semiconservative nature of DNA

replication. 6.1.c

Recall where along a chromosome DNA synthesis begins, and explain what characterizes these nucleotide sequences in simple cells such as bacteria and yeast.

6.1.d

Compare the direction in which replication forks move with the direction in which the

new DNA strands are synthesized. 6.1.e

Compare the bonds that link together nucleotides in a DNA strand with the bonds

that hold together the two strands of DNA in a double helix. 6.1.f Explain how nucleoside triphosphates provide the energy for DNA synthesis. 6.1.g

Explain why an asymmetrical replication fork poses a challenge for DNA

polymerization and how DNA polymerase solves this problem to keep the replication fork moving forward. 6.1.h

Explain how DNA polymerase contributes to the accuracy of DNA replication.

6.1.i Describe the primers required for DNA replication and compare how they are used in synthesizing the leading and lagging strands. 6.1.j Explain how primers are removed and replaced to produce a continuous newly synthesized DNA strand. 6.1.k Name five proteins that form part of the replication machine and state the role each plays in DNA replication. 6.1.l Describe the problem created by a moving replication fork, and explain how DNA topoisomerases relieve this difficulty. 6.1.mDescribe the “end replication problem” and explain how telomerase solves this dilemma.

DNA REPAIR 6.2.a List some of the causes of DNA damage. 6.2.b Name some of the types of damage that can alter DNA. 6.2.c List the three main steps involved in repairing damage that affects only one strand of the DNA double helix. 6.2.d Explain how the mismatch repair system recognizes and corrects replication errors. 6.2.e Contrast nonhomologous end joining and homologous recombination as mechanisms for repairing double-stranded DNA breaks. 6.2.f Describe the consequences of a failure to repair damaged DNA.

CHAPTER 7

From DNA to Protein FROM DNA TO RNA

7.1.a

Recall the central dogma and explain how its steps relate to gene expression

depending on whether the final product of the gene is an RNA or a protein. 7.1.b

Explain how cells can produce large quantities of one protein and tiny quantities of

another. 7.1.c

Compare RNA and DNA in terms of chemical composition, base-pairing properties, and overall structure.

7.1.d

Compare the reactions catalyzed by RNA and DNA polymerases in terms of

templates, substrates, directionality, and sources of energy to drive the reactions. 7.1.e

Explain why RNA and DNA polymerases differ in their fidelity.

7.1.f Explain how the behavior of RNA polymerase allows multiple RNA transcripts to be made from a single gene at once. 7.1.g

List the most common types of RNA produced by transcription and identify those that

represent the final product of gene expression. 7.1.h

Explain how a bacterial RNA polymerase recognizes where transcription will begin,

which DNA strand to transcribe, and when to stop. 7.1.i Contrast transcription initiation in bacteria and eukaryotes. 7.1.j Explain how the eukaryotic general transcription factors assemble on a promoter, form a transcription initiation complex, and release RNA polymerase to begin transcription. 7.1.k Contrast the structures of bacterial and eukaryotic mRNAs and compare how these transcripts are handled as they are being synthesized. 7.1.l Describe how RNA splicing is carried out largely by RNA molecules. 7.1.m State the potential benefits of the presence of introns in eukaryotic genes. 7.1.nDescribe the assembly of the molecular aggregates that act as “factories” for the synthesis and processing of RNA. 7.1.oExplain how cells control the quality of the RNAs that are exported from the nucleus. 7.1.pDescribe how cells control the lifetime of an mRNA molecule.

FROM RNA TO PROTEIN 7.2.a Explain how the genetic code allows translation of the information contained in an mRNA into a protein sequence. 7.2.bExplain how a ribosome determines which reading frame in an mRNA specifies a protein, and describe the consequences of translating an incorrect reading frame. 7.2.c Explain how wobble base-pairing underlies the redundancy in the genetic code. 7.2.dExplain how each tRNA is charged with the correct amino acid, and describe the consequences of a tRNA carrying an incorrect amino acid. 7.2.e

Explain how investigators used synthetic polynucleotides and trinucleotides to

decipher the genetic code. 7.2.f Delineate the roles the small and large ribosomal subunits play in translation. 7.2.g

Contrast the roles that ribosomal proteins and ribosomal RNAs play in the structure

and activity of the ribosome. 7.2.h

Summarize the cycle by which amino acids are covalently linked to a growing

polypeptide chain. 7.2.i State the directionality of replication, of transcription, and of translation. 7.2.j Contrast translation initiation in eukaryotes and bacteria. 7.2.k

Describe how translation is terminated in eukaryotes and in bacteria.

7.2.l Explain the benefits of polyribosomes in protein translation. 7.2.m Explain why antibiotics that interfere with the synthesis of RNA or proteins eliminate bacterial infections without harming the patient. 7.2.n

Explain how and why proteins are targeted for degradation in proteasomes.

7.2.o

Describe the structure of proteasomes and summarize how these molecular

chambers destroy proteins marked for elimination. 7.2.p

Outline the steps at which the final concentrations of a functional protein can be

regulated by the cell.

RNA AND THE ORIGINS OF LIFE 7.3.a

Describe the properties of RNA that allow it to store genetic information and,

potentially, to catalyze its own synthesis.

7.3.b

Explain why RNA is thought to predate DNA in evolution.

7.3.c

Explain the features that make DNA a better molecule for the permanent storage of genetic information than RNA.

CHAPTER 8

Control of Gene Expression AN OVERVIEW OF GENE EXPRESSION

8.1.a

Review how nuclear transplantation experiments demonstrated that the different

specialized cell types in a multicellular organism contain the same genetic instructions. 8.1.b

Present and evaluate several methods for assessing the types of proteins produced

by different cell types. 8.1.c

Define and provide examples of housekeeping proteins.

8.1.d

Contrast how liver cells and fat cells alter their gene expression in response to the

hormone cortisol. 8.1.e

Articulate the steps at which gene expression can be regulated and identify the step

that, for most genes, is the main point of control.

HOW TRANSCRIPTION SWITCHES WORK 8.2.a

Distinguish between promoters and regulatory DNA sequences in terms of the roles

they play in gene expression and the proteins that bind to them. 8.2.b

Illustrate how transcription regulators recognize and bind to regulatory DNA

sequences in a DNA double helix. 8.2.c

Describe the structure of an operon and note the type of organism in which this arrangement is most common.

8.2.d

Review how, in bacteria, the amino acid tryptophan shuts down production of the

enzymes responsible for its biosynthesis. 8.2.e

Compare how the bacterial promoters that interact with transcriptional activators and

repressors differ in terms of how efficiently they bind and position RNA polymerase. 8.2.f Outline how the Lac operon allows bacteria to efficiently utilize the alternative carbon sources lactose and glucose. 8.2.g

Explain how eukaryotic activator proteins can enhance transcription even when bound to sequences hundreds or thousands of nucleotide pairs away from a gene’s promoter.

8.2.h

Summarize how eukaryotic repressor proteins decrease transcription.

8.2.i Compare how eukaryotic activator and repressor proteins exploit the mechanisms that regulate chromatin packaging to enhance or suppress transcription. 8.2.j Describe how enhancers are prevented from inappropriately activating the transcription of nearby genes.