The Cell

Question 1

What is a chromosome?

Answer 1

An organized structure composed of a very long DNA molecule and associated proteins (histone proteins). It carries part or all of the hereditary information of an organism and is especially evident in plant and animal cells undergoing mitosis or meiosis.

Question 2

What is the main function of chromosomes in a cell?

Answer 2

Chromosomes carry most of the genetic material and, therefore, they carry inherited traits and the organization of the cell’s life.

Question 3

What is the significance of homologous chromosomes in an organism?

Answer 3

Homologous chromosomes consist of one paternal and one maternal chromosome, and they are hereditary. The intact set of chromosomes is passed to each daughter cell during each mitosis.

Question 4

How much must DNA be compacted to fit inside a cell, and what is the primary component of chromatin?

Answer 4

DNA needs to be compacted approximately 10,000 times to fit inside a cell. Chromatin, the primary component of DNA packaging, is composed of 30% DNA, 60% histone protein, and 10% RNA chains.

Question 5

What are nucleosomes, and how are they structured in eukaryotes?

Answer 5

Nucleosomes are the fundamental units of chromatin and the basic units of DNA packaging in eukaryotes. Each nucleosome is made up of DNA coiling twice around a core of 8 histone proteins, including two of each H2A, H2B, H3, and H4.

Question 6

Why do histone proteins bind tightly to DNA, and what types of enzymatic modifications can histones undergo?

Answer 6

Histone proteins bind tightly to DNA because DNA is negatively charged due to the phosphate groups in its backbone, while histones are positively charged. This electrostatic attraction results in tight binding. Histones can undergo enzymatic modifications, including acetylation, phosphorylation, and methylation, primarily at the N-terminal tails of the core histones protruding from nucleosomes. Adjacent nucleosomes are connected by a length of linker DNA (8-114bp) giving it a ‘string of beads’ appearance. Packaging of DNA into nucleosomes shortens the fibre length about 7X (a 1-meter-long strand will become a “string-of-beads” chromatin fibre of just 14 cm in length), however further compaction is still required.
When cell is preparing to divide the chromatin shorten and condense to form chromosomes.

Question 7

What is DNA replication, and when does it occur in the cell cycle?

Answer 7

DNA replication is the process of making a copy of a DNA molecule. It occurs during the Synthesis (S) phase of the cell cycle.

Question 8

What is the role of helicase in DNA replication, and what does it create in the DNA molecule?

Answer 8

Helicase unwinds the double-stranded DNA helix by breaking the hydrogen bonds between the two strands, creating a replication bubble.

Question 9

What is the function of single-stranded DNA binding proteins in DNA replication?

Answer 9

Single-stranded DNA binding proteins bind to single-stranded DNA, preventing the unwound strands from rejoining and maintaining them in a single-stranded state.

Question 10

What is the role of topoisomerase in DNA replication, and why is it important?

Answer 10

Topoisomerase prevents the supercoiling of DNA as strands unwind, relieving pressure and ensuring that DNA replication proceeds smoothly.

Question 11

What is the function of primase in DNA replication, and why is it necessary?

Answer 11

Primase synthesizes a short RNA primer that is required for DNA polymerization to begin. It provides the starting point for DNA synthesis.

Question 12

How does DNA polymerase function during DNA replication, and in which direction does it synthesize new DNA strands?

Answer 12

DNA polymerase positions complementary nucleotides along the template strand and synthesizes daughter strands from parental strands. It can only function in the 5’ to 3’ direction, which means it synthesizes new DNA in the direction of the replication fork.

Question 13

Describe the difference between continuous replication and discontinuous replication during DNA synthesis.

Answer 13

Continuous replication occurs on the leading strand, where DNA synthesis proceeds continuously from the 5’ to 3’ direction starting at the 3’ end of the parent strand. Discontinuous replication occurs on the lagging strand, where DNA polymerase has to jump back during coding, resulting in Okazaki fragments with gaps in between them.

Question 14

What is the role of DNA ligase in DNA replication?

Answer 14

DNA ligase removes the RNA primers between the Okazaki fragments on the lagging strand and fills in the gaps to create a continuous DNA strand.

Question 15

What is meant by “semi-conservative replication” in DNA replication?

Answer 15

Semi-conservative replication means that each newly formed DNA molecule consists of one new DNA strand and one old DNA strand, preserving some of the original genetic information.

Question 16

mRNA (Messenger RNA)

Answer 16

Carries instructions from genes to ribosomes for protein synthesis.

Question 17

rRNA (Ribosomal RNA):

Answer 17

Part of ribosomes, essential for protein synthesis.

Question 18

tRNA (Transfer RNA):

Answer 18

Adaptors between mRNA and amino acids during protein synthesis.

Question 19

snRNA (Small Nuclear RNA):

Answer 19

Involved in nuclear processes, including splicing pre-mRNA.

Question 20

snoRNA (Small Nucleolar RNA):

Answer 20

Assist in processing and modifying rRNAs.

Question 21

miRNA (MicroRNA):

Answer 21

Regulates gene expression by blocking translation of specific mRNAs.

Question 22

siRNA (Small Interfering RNA):

Answer 22

Turns off gene expression by directing mRNA degradation.

Question 23

piRNA (Piwi-interacting RNA):

Answer 23

Binds to piwi proteins and protects germ line from transposable elements.

Question 24

ncRNA (Long Noncoding RNA):

Answer 24

Regulates various cell processes, including X-chromosome inactivation.

Question 25

What is transcription, and how does it differ from DNA replication?

Answer 25

Transcription is the process of copying one strand of DNA into a complementary RNA sequence using the enzyme RNA polymerase. Unlike DNA replication, transcription does not require a primer, transcribes only a portion of the genome, and lacks proofreading.

Question 26

What are the components required for transcription, and what are the two DNA strands involved in transcription?

Answer 26

Transcription requires a DNA template, ribonucleotides (ATP, CTP, GTP, UTP), RNA polymerases, and Mg2+ ions. The two DNA strands involved are the coding/sense strand (almost a perfect match to transcribed pre-mRNA) and the DNA template/antisense strand (complementary to the coding strand and pre-mRNA).

Question 27

Describe the three steps involved in the transcription process.

Answer 27

The transcription process involves three steps: Initiation, Elongation, and Termination.

Question 28

Initiation of transcription

Answer 28

Transcription factors (RNA polymerase) bind to the promoter, separating the two DNA strands and initiating mRNA synthesis at the start point on the template strand. Helicase unwinds the DNA, and topoisomerase prevents supercoiling.

Question 29

Elongation of transcription

Answer 29

RNA polymerase moves along the template strand, synthesizing the mRNA transcript. The DNA double helix unwinds and rewinds, and ribonucleic acid polymerization proceeds in the 5’ to 3’ direction.

Question 30

Termination of transcription

Answer 30

mRNA synthesis stops when a termination signal is reached, leading to the release of the mRNA transcript and RNA polymerase. The termination codon is typically located 10-35 base pairs downstream of the polyadenylation signal.

Question 31

How do antibiotics inhibit transcription, and what are some examples of antibiotics that do so?

Answer 31

Antibiotics can inhibit transcription through various mechanisms:

Quinolones inhibit topoisomerase, preventing access to DNA.
Rifampicin reacts with the subunit of RNA polymerase, blocking the formation of the first phosphodiester bond between nucleotides.
Actinomycin D prevents RNA polymerase from accessing DNA.

Question 32

How is transcription regulated, and what are some factors involved in transcriptional regulation?

Answer 32

Transcription can be regulated through several mechanisms:

Chromatin structure modifications (e.g., acetylation of histones, methylation of CpG islands).
Signal transduction pathways that activate transcription factors.
Transcription factors binding to control elements in the promoter, such as TATA and CAAT boxes.
Enhancer and silencer control regions with associated activator and repressor transcription factors.

Question 33

Define a “gene” and briefly explain its role.

Answer 33

A gene is the basic, physical unit of heredity, consisting of a region of DNA that carries information for a discrete hereditary characteristic. Genes typically correspond to either a single protein or a single RNA molecule and are responsible for encoding traits or functions in an organism.

Question 34

How does the sequence of nucleotide bases in a gene translate into instructions for amino acid sequences in polypeptides during translation?

Answer 34

The sequence of nucleotide bases in a gene serves as a template for the synthesis of messenger RNA (mRNA) during transcription. This mRNA, with its complementary base pairs, carries the genetic information from the gene to the ribosome. During translation, ribosomes read the codons (three-base sequences) on the mRNA and match them with the corresponding amino acids carried by transfer RNA (tRNA) molecules. This process ultimately results in the assembly of amino acids into polypeptides and proteins.

Question 35

Explain the difference between exons and introns.

Answer 35

Exons are segments of a eukaryotic gene that encode amino acids, specifying informational sequences. They are represented in mRNA or other mature RNA molecules and are typically adjacent to noncoding DNA segments called introns. In contrast, introns are noncoding regions of a eukaryotic gene that are transcribed into an RNA molecule but are excised by RNA splicing during the production of mature mRNA or functional RNA. Exons are usually smaller in size (~100-200 base pairs), while introns can be larger (~3000 base pairs) and vary in length.

Question 36

In prokaryotes, how are genes primarily regulated at the transcriptional level, and what are the key regulatory elements involved?

Answer 36

Prokaryotic genes are primarily regulated at the transcriptional level by DNA binding proteins that influence the rate of transcription. Key regulatory elements include enhancers, promoters, and DNA binding proteins.

Question 37

What is the function of enhancers in eukaryotic gene regulation, and where can they be found in relation to genes?

Answer 37

Enhancers activate the utilization of a promoter and control the efficiency and rate of transcription in eukaryotic cells. They can be found at various locations relative to genes, including at the 5’ end, 3’ end, or internally, either proximal or thousands of nucleotides away from the gene. Enhancers can work in either direction and may also act as silencers.

Question 38

Describe the role of promoters in gene regulation, and mention any conserved sequences often found in promoters.

Answer 38

Promoters serve as controllers of gene activity by determining when and where a gene must be active. Promoters are responsible for binding RNA polymerase and initiating transcription. Common conserved sequences found in promoters include TATA boxes and CAAT boxes. The TATA box is typically located 27 base pairs upstream from the 5’ end of the gene.

Question 39

What is DNA methylation, and how does it relate to gene regulation?

Answer 39

DNA methylation is a process in which promoter sequences remain inactive and unable to transcribe RNA. It is a method of silencing genes and plays a vital role in ensuring that important inherited features within gametes are preserved. DNA methylation is an epigenetic modification that can control gene expression by preventing transcription factors from binding to the promoter region.

Question 40

Explain the concept of gene amplification and provide an example of its significance.

Answer 40

Gene amplification involves copying genes, chromosome fragments, or entire chromosomes numerous times to increase the quantity of RNA produced. For example, genes in ova are copied many times to ensure sufficient ribosomes are available for protein synthesis. In the context of cancer, gene amplification can result in the overproduction of a protein product that resists chemotherapeutic drugs, making cancer cells highly resistant to treatment.

Question 41

What is the main application of the Polymerase Chain Reaction (PCR), and how does it work?

Answer 41

The main application of PCR is to amplify specific DNA sequences for various purposes. It works by using sequence-specific primers and multiple cycles of DNA synthesis, each followed by a brief heat treatment to separate complementary strands. This process results in the exponential amplification of the target DNA region.

Question 42

How does PCR contribute to the diagnosis and monitoring of certain blood cancers?

Answer 42

PCR is used to detect specific DNA abnormalities or markers found in patients with certain blood cancers, such as acute promyelocytic leukemia and chronic myeloid leukemia. It allows for the sensitive detection of blood cancer cells not found by other methods and helps monitor a patient’s molecular response to treatment.

Question 43

What are some of the key applications of PCR beyond the diagnosis of blood cancers?

Answer 43

Some key applications of PCR include DNA cloning for sequencing, gene cloning and manipulation, gene mutagenesis, construction of DNA-based phylogenies, functional analysis of genes, diagnosis and monitoring of hereditary diseases, amplification of ancient DNA, genetic fingerprinting for DNA profiling (forensic science and parentage testing), and pathogen detection in nucleic acid tests for diagnosing infectious diseases.

Question 44

What is the primary purpose of a restriction digest, and what type of enzymes are used in this process?

Answer 44

To cleave DNA at specific sites. This process uses DNA-cleaving enzymes called restriction enzymes, which are isolated from bacteria.

Question 45

Describe the key role of restriction endonucleases in molecular biology, and what are the possible outcomes in terms of DNA ends after cleavage?

Answer 45

Restriction endonucleases are enzymes used extensively in recombinant DNA technology. They can cleave double-stranded DNA at specific sites, resulting in two possible outcomes: blunt ends or sticky ends.

Question 46

What is a karyotype, and how is it prepared? What information can be obtained from a karyotype analysis?

Answer 46

A karyotype is a display of the full set of chromosomes of a cell, arranged based on size, shape, and number. Karyotypes are prepared from mitotic cells arrested in metaphase. They provide information about the number of chromosomes and their physical characteristics, including length, centromere position, and banding patterns. Karyotype analysis can detect major genetic changes, such as aneuploidy.

Question 47

How is the sex of an unborn fetus determined using karyotype analysis, and where are sex chromosomes typically placed in a karyogram?

Answer 47

The sex of an unborn fetus can be determined by observing interphase cells in a karyotype analysis. Sex chromosomes are typically placed at the end of the karyogram, and their arrangement can reveal the sex of the individual.

Question 48

Briefly explain the principles of FISH (fluorescent in situ hybridization) and its applications in molecular cytogenetics.

Answer 48

FISH is a molecular cytogenetic technique that uses fluorescently labeled probes to detect specific DNA sequences. The probes are designed to hybridize with complementary sequences of interest. FISH can be used to identify the presence and location of nucleic acids within chromosomes, interphase nuclei, tissues, and cells in culture. It is applied in gene mapping, analysis of chromosome structural aberrations, toxicological studies, ploidy determination, cancer diagnostics, and more.

Question 49

What are the primary steps involved in performing FISH, and what types of samples can be used in this technique?

Answer 49

The primary steps in performing FISH include preparing probes against DNA sequences of interest, labeling the probes with fluorescent dyes or haptens, denaturing the DNA and hybridizing the probes to the sample, and imaging the results under a fluorescent microscope. Samples can include formalin-fixed paraffin-embedded tissues and fixed cell suspensions.

Question 50

What information can be obtained from FISH experiments, and how is the technique useful in identifying genetic abnormalities and gene localization?

Answer 50

FISH experiments can provide information about numerical chromosome aberrations, chromosomal translocations, gene amplification, and gene localization within chromosomes. FISH is useful in identifying genetic abnormalities, understanding gene mapping, and detecting specific gene rearrangements that may be targeted by specific treatments in cancer diagnostics and other genetic studies.

Question 51

Summarize the key steps in FISH and its applications in genetics and diagnostics.

Answer 51

The key steps in FISH include designing probes, labeling probes, denaturing DNA, hybridizing probes to the target DNA, and imaging the results under a fluorescent microscope. FISH is used for identifying chromosomal abnormalities, detecting translocations, studying gene amplification, and localizing genes within chromosomes for genetic diagnostics and research.