1. Introduction to Biology

2. Chemistry

3. Water

4. Biomolecules

5. Cell Components

6. The Membrane

7. Energy and Metabolism

8. Respiration

9. Photosynthesis

10. Cell Signaling

11. Cell Division

12. Meiosis

13. Mendelian Genetics

14. DNA Synthesis

15. Gene Expression

16. Regulation of Expression

17. Viruses

18. Biotechnology

19. Genomics

20. Development

21. Evolution by Natural Selection

22. Evolution of Populations

23. Speciation

24. History of Life on Earth

25. Phylogeny

26. Prokaryotes

27. Protists

28. Plants

29. Fungi

30. Overview of Animals

31. Invertebrates

32. Vertebrates

33. Plant Anatomy

34. Vascular Plant Transport

35. Soil

36. Plant Reproduction

37. Plant Sensation and Response

38. Animal Form and Function

39. Digestive System

40. Circulatory System

41. Immune System

42. Osmoregulation and Excretion

43. Endocrine System

44. Animal Reproduction

45. Nervous System

46. Sensory Systems

47. Muscle Systems

48. Ecology

49. Animal Behavior

50. Population Ecology

51. Community Ecology

52. Ecosystems

53. Conservation Biology

[BOOK BIO] CLUTCH

Use a highlighter to color any amino acid that varies among the species. (Color that amino acid in all sequences.)
e. Primates and rodents diverged between 60 and 100 million years ago, and chimpanzees and humans about 6 million years ago. Compare the amino acid differences between the mouse and the C, G, R species with those between the human and the C, G, R species. What can you conclude?<img src="https://lightcat-files.s3.amazonaws.com/problem_images/4250a88936da9ca7-MCQ%20Bio.jpg" alt="" />

No. Alu elements are found in other primate genomes.

No. Alu elements do not contain a protein-coding gene.

No. They account for about 10% of the human genome&#151;a substantial fraction, but not close to half.

are derived from or related to transposable elements

What kind of DNA sequence is an Alu element?

Alu elements __________.

A homeotic gene does which of the following?
a. It serves as the ultimate control for prokaryotic operons.
b. It regulates the expression of groups of other genes during development.
c. It represses the histone proteins in eukaryotic chromosomes.
d. It helps splice mRNA after transcription.

determining what gene mutation causes insulin resistance

No. That is not a systems biology experiment.

determining the normal biochemical function of the gene involved in insulin resistance

comparing the insulin resistance gene in human, mouse, and chimpanzee genomes

No. Only one of the above answers is correct.

determining how insulin resistance affects transcription of thousands of other genes in the genome

Systems biology takes an integrative approach.

An example of a systems biology experiment might be __________.

Coding DNA | Non Coding DNA | Coding Vs Non Coding DNA | Coding Vs Non Coding Strand |

Explain how RNA-seq can be used to analyze patterns of gene expression.

Non-coding regions in the genome - Robert Tjian (Berkeley/HHMI)

The Evolution of Hox Genes

To reconstruct chimpanzees if they become extinct

No. Sequencing the genome is a poor substitute for conservation.

To be able to study human diseases in chimpanzees

No. Chimpanzees are not a good model system for human disease because they are too difficult to obtain and expensive to maintain.

To determine whether another human pathogen such as HIV could originate from viruses that infect chimpanzees

No. The genome sequence would not be especially helpful with this question.

To determine whether any chimpanzee genes could be used to genetically engineer superior humans, or vice versa

No. Such experiments would be highly unethical.

To determine what genetic changes determine uniquely human features such as large brains and language ability

Chimpanzees are the closest relative of humans.

What is a valid rationale for sequencing the chimpanzee genome?

No. Alleles are alternate versions of a gene.

No. Plasmids are circular pieces of DNA apart from the main bacterial chromosome.

No. Transposons move by means of a DNA intermediate.

No. Introns are unexpressed regions of eukaryotic DNA.

What kinds of genes did McClintock discover?

Segments of eukaryotic DNA that can move from one site to another in the genome by means of an RNA intermediate are called __________.

attempt to determine a gene's exact locus in the genome

No. This is determined by cytogenetic mapping procedures.

determine the frequencies of specific genes throughout the genome

No. Gene annotation is identifying protein-coding genes among existing genetic elements within a genome.

use fluorescent RNA probes to determine the presence and location of a gene

simultaneously sequence the genomes of multiple species in an environmental sample

No. This describes a metagenomic technique; gene annotation is identifying protein-coding genes among existing genetic elements within a genome.

identify which genes are protein-coding within a genome

This is reverse genetics.

Studies that determine gene annotation __________.

Replacing the FOXP2 gene in mice with the human form of the gene had a neutral effect on development of vocalization in mice.

No. Results suggest that the human version of FOXP2 has evolved since the divergence of humans and mice: the mice were healthy for the most part but demonstrated slightly different vocalizations and had modified brain cells in the same neural circuits responsible for speech development in humans.

Knocking out one of the two FOXP2 genes in mice and humans had no effect on the development of vocalization in either species.

No. Only one faulty gene was required to cause significant problems with vocalization in mice; no such experiments were conducted with human subjects because it would be unethical to do so.

Replacing the mouse FOXP2 gene with songbird versions of the gene caused the transgenic mice to vocalize like songbirds.

No. No such experiment was conducted; furthermore, FOXP2 is a gene for a transcription factor that regulates genes related to vocalization and by itself wouldn't cause mice to vocalize like songbirds in such a gene transplant.

When scientists knocked out the FOXP2 gene in human subjects, they observed the development of severe speech and language impairment.

No. It is both unethical and impractical to perform such experiments on human subjects.

Replacing the FOXP2 gene in mice with a humanized version of the gene had no negative effects on the mice but did lead to the development of brain cells in neural circuits that are associated with speech development in humans.

Consider the scientific value of nonhuman model systems.

Which of the following best describes the experimental evidence that the FOXP2 gene is vital to the normal development of vocalization in vertebrates and yet has evolved among different vertebrate lineages?

Use a highlighter to color any amino acid that varies among the species. (Color that amino acid in all sequences.)
c. The O sequence differs from the C, G, R sequences at one amino acid (having V instead of A) and from the H sequence at three amino acids. Identify the O sequence.<img src="https://lightcat-files.s3.amazonaws.com/problem_images/f80876450529463c-MCQ%20Bio.jpg" alt="" />

Pseudogenes | What Are Pseudogenes | Junk DNA |

Two eukaryotic proteins have one domain in common but are otherwise very different. Which of the following processes is most likely to have contributed to this similarity?
a. gene duplication
b. alternative splicing
c. exon shuffling
d. random point mutations

What does it mean to say that experimental conditions are controlled? Select True or False for each statement.
T/F The test groups consist of the same individuals.
T/F The null hypothesis is correct.
T/F There is no difference in outcome between the control and experimental treatment.
T/F All physical conditions except for one are identical for all groups tested.

Hybridize the DNA with probes specific for known genes from other organisms.

No. This wouldn't be terribly efficient and in any case would miss all genes with no known counterpart in another species.

Use DNA microarrays to examine the expression of huge numbers of sequences from the genome under different conditions.

No. DNA microarrays are extremely useful for examining gene expression patterns (among other things), but they are not the most efficient way of identifying genes within genomes.

Individually mutate all of the nucleotides within the genome, and determine which mutations cause a detectable phenotype.

No. Although this would likely tell you where many of the genes are, it would not be very efficient and would miss all the genes that do not cause a detectable phenotype.

No. One of the other responses is correct.

Analyze the sequence using software that scans the sequence for telltale sequence elements such as promoters, transcription start and stop sites, and so on.

This is generally carried out by scientists called "bioinformaticians."

Once an organism's genome sequence has been determined, how do scientists generally start identifying all the genes within the genome?

Genomes

What is a genome?

Gene Families

WACE Biology: Coding and Non-Coding DNA

Organisms do not wish to evolve new genes.

No. Such a hypothesis is outside the realm of scientific reasoning.

Multiple copies of a transposon suppress each other.

No. A transposase or a reverse transcriptase can facilitate transposition of any member of the same family.

The immune system attacks active transposons as foreign invaders.

No. Because transposons are present in the host genome, they are not recognized as foreign.

Transposons have a dramatically higher rate of mutation than other genes.

No. Though reverse transcriptase is more error-prone, the chromosomal DNA copies appear to experience the same rate of mutation as most other noncoding DNA.

Individuals with active transposons are usually eliminated by natural selection because transposition events usually produce harmful mutations.

What effect might active transposons have on an organism?

Why might active transposons be rare in natural populations?

Part 1: How Does New Genetic Information Evolve? Point Mutations

A tool-kit gene is                .

Transposable Elements and Pseudogenes

Types of Gene- Structural, Constitutive, Regulatory, Jumping, Overlapping, Split gene#Bio knowledge

Animation: Alterations of Chromosome Structure

What is a homeotic mutant?
a. an individual with a structure located in the wrong place
b. an individual with an abnormal head-to-tail axis
c. an individual that is missing segments
d. an individual with double the normal number of structures

What would researchers have to demonstrate to convince you that they had discovered life on another planet?

alternative splicing can increase the number of polypeptides made from a single pre-mRNA

No. This statement is true, but it is not the best response.

post-translational modifications can increase the types of proteins produced by a single gene

individual polypeptides can interact to form multiple types of protein complexes

individual genes can be expressed in more or less complex ways in different organisms

How would the different possible answers affect the varieties of proteins produced from a single gene?

The number of genes in an organism's genome is not a perfect indication of the organism's complexity because __________.

offspring who inherit two differently arranged sets of chromosomes instantly become a new species

No. Pairing of homologous chromosomes in meiotic prophase would be affected, and such offspring are most likely to be sterile.

chromosomal rearrangements caused the extinction of dinosaurs, thereby allowing mammals to become dominant

No. Although chromosome arrangements may have contributed to the evolutionary radiation of mammals, the available evidence indicates that the cause of dinosaur extinction was a large asteroid impact.

chromosome rearrangements cause new genes to evolve

No. This would be a rare event and not the most important way chromosome rearrangements contribute to speciation.

chromosome rearrangements may cause genetic diseases

No. Although this statement is true, it does not contribute to evolution of new species.

chromosome rearrangements lead to gene duplication, thus generating a "spare" copy of the gene that is free to evolve and acquire a new function

What factors contribute to evolution of new genes and new species?

Chromosomal rearrangements may be important in evolution because __________.

What are Genome Evolution, Mutations, Gene Duplications, Gene Losses, and Inversions?

provide reliable information about human genetic diversity

No. Both CNVs and SNPs provide reliable and valuable information regarding the genetic variation that exists among human populations.

occur only in noncoding DNA, which generally mutates at a constant rate and is more informative in measuring the genetic variation among human populations

No. CNVs are found in both coding and noncoding regions of the genome.

have revealed significant genetic diversity existing among different human populations at geographic locations both near and far apart

No. Studies using CNVs, SNPs, and other genetic markers have revealed a significant amount of genetic variation among different human populations.

are far greater in number but of equal size to SNPs

No. CNVs occupy much longer stretches of DNA and are fewer in number than SNPs.

occupy much longer stretches of DNA than SNPs and are likely to have greater phenotypic consequences

Consider how the size of genetic markers relates to their influence on phenotype.

The advantage of copy-number variants (CNVs) over SNPs in human genomic studies is that CNVs __________.

DRAW IT Below are the amino acid sequences (using the single-letter code; see Figure 5.14) of four short segments of the FOXP2 protein from six species: chimpanzee (C), orangutan (O), gorilla (G), rhesus macaque (R), mouse (M), and human (H). These segments contain all of the amino acid differences between the FOXP2 proteins of these species. <img src="https://lightcat-files.s3.amazonaws.com/problem_images/18c7898a72404b00-1664815694516.jpg" alt="" /> Use a highlighter to color any amino acid that varies among the species.

has two distinct evolutionary lineages, originating from an ancestral alpha-globin gene and an ancestral beta-globin gene

No. Alpha and beta globin are clearly related in sequence.

arose through convergent evolution, where genes of different ancestry become similar over time because they have the same function

evolved from a common ancestor of the alpha- and beta-globin genes but that myoglobin and leghemoglobin arose from a different ancestor

No. Myoglobin and leghemoglobin share clear sequence similarity with alpha and beta globins.

No. In this case, duplication involved entire genes, not individual exons.

evolved from a common globin gene ancestor that gave rise to both alpha- and beta-globin genes as well as myoglobin and plant leghemoglobin

How do multigene families arise?

The molecular data indicate that the globin gene family __________.

Homeotic genes
a. encode transcription factors that control the expression of genes responsible for specific anatomical structures.
b. are found only in Drosophila and other arthropods.
c. are the only genes that contain the homeobox domain.
d. encode proteins that form anatomical structures in the fly.

GENETIC EVIDENCE FOR EVOLUTION: GENE FAMILIES

Consider the validity of the following statements about genome editing. Select True or False for each statement.
T/F Cas proteins work as endonucleases.
T/F sgRNA is used by bacterial cells to detect which DNA to cut.
T/F Homologous recombination is always used to join pieces of broken DNA.
T/F It is possible to modify genes as well as disrupt them by genome editing.

No. This is the typical size of a prokaryotic gene.

No. Twenty thousand genes of this size would occupy 200 million base pairs, which is far less than 25% of a typical mammalian genome.

No. Twenty thousand genes of this size would occupy 400 million base pairs, which is approximately 1/8 of the typical mammalian genome.

No. Twenty thousand genes of this size would occupy 1.6 billion base pairs, which is approximately 1/2 of the typical mammalian genome.

Calculate the amount of DNA associated with genes, and divide by the number of genes.

Recall that the human genome contains roughly 3 billion base pairs per haploid genome and that about 25% of the human genome is associated with genes, including introns and regulatory sequence. What would be the approximate average length of DNA per human gene if the genome contained 20,000 genes?

Introduction to Transposons

How Much DNA Codes for Protein?

Part 2: How Does New Genetic Information Evolve? Gene Duplications

No. NCBI does have this, but there is a better answer.