Molecular Biology of DNA Structure

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Questions and Answers

What type of bond is responsible for linking the 3'-hydroxyl group of one sugar to the 5'-phosphate group of the next in a DNA strand?

  • Hydrogen bond
  • Phosphodiester bond (correct)
  • Ionic bond
  • Van der Waals interaction

Which of the following statements accurately describes the orientation of the two DNA strands in a double helix?

  • They are twisted around each other in a random orientation.
  • They are antiparallel and run in opposite directions. (correct)
  • They are parallel and run in the same direction.
  • They are perpendicular to each other.

What is the primary force that holds the two strands of a DNA double helix together?

  • Hydrogen bonds between complementary bases (correct)
  • Hydrophobic interactions between the sugar-phosphate backbones
  • Covalent bonds between the nucleotides
  • Electrostatic interactions between the phosphate groups

The polarity of a DNA strand is determined by the orientation of its __________.

<p>sugar-phosphate backbone (B)</p> Signup and view all the answers

Which of the following base pairs is NOT found in DNA?

<p>G-U (B)</p> Signup and view all the answers

Which of the following statements accurately describes the relationship between gene number, chromosome number, and total genome size?

<p>There is no simple relationship between gene number, chromosome number, and total genome size. (A)</p> Signup and view all the answers

What is the approximate percentage of the human genome that consists of protein-coding exons?

<p>Less than 1% (C)</p> Signup and view all the answers

Which of the following is NOT a type of repetitive nucleotide sequence found in the human genome?

<p>Telomeres (D)</p> Signup and view all the answers

What percentage of the human genome consists of unique sequences that are not part of introns or exons?

<p>Around 50% (D)</p> Signup and view all the answers

What is the primary function of regulatory DNA sequences?

<p>Controlling gene expression (A)</p> Signup and view all the answers

What is the best explanation for the observation that closely related species can have vastly different chromosome numbers?

<p>Chromosomal rearrangements over evolutionary time (D)</p> Signup and view all the answers

Which of the following is NOT a component of heterochromatin?

<p>Protein-coding genes (D)</p> Signup and view all the answers

The human genome was first completely sequenced In:

<p>2021 (C)</p> Signup and view all the answers

What is the primary reason why some individuals can digest milk into adulthood, while others cannot?

<p>Mutations in the gene responsible for lactase production. (A)</p> Signup and view all the answers

Domestication of cattle has had a significant impact on human evolution. What is the most direct connection between cattle domestication and the ability to digest lactose in adulthood?

<p>Cattle domestication led to increased consumption of milk, creating a selective pressure for lactase persistence. (B)</p> Signup and view all the answers

What is the relationship between the human genome and the ability to digest lactose into adulthood?

<p>The human genome contains a gene that regulates the expression of lactase, and mutations in this regulatory gene can influence lactose tolerance. (A)</p> Signup and view all the answers

What is the significance of the fact that the genetic variation for lactase persistence is found in populations that historically had access to domesticated cattle?

<p>It suggests that the human genome is constantly evolving in response to changing environmental conditions. (D)</p> Signup and view all the answers

The example of lactase persistence illustrates a concept that is central to human evolution. What is this concept?

<p>Humans are constantly evolving to adapt to new environments and dietary changes. (B)</p> Signup and view all the answers

How are human chromosomes distinguished from one another?

<p>They come in different sizes and have unique molecular markers. (D)</p> Signup and view all the answers

What is the primary function of a chromosome?

<p>To carry genes. (D)</p> Signup and view all the answers

What is a gene?

<p>A segment of DNA that codes for a specific protein. (D)</p> Signup and view all the answers

What is the difference between a genome and a gene?

<p>A genome is the total genetic information in an organism, while a gene is a segment of DNA that codes for a protein. (C)</p> Signup and view all the answers

What is the main reason for the difference in genome size between bacteria and humans?

<p>Humans have more noncoding DNA than bacteria. (B)</p> Signup and view all the answers

How is the human genome different from the genome of Saccharomyces cerevisiae?

<p>All of the above. (D)</p> Signup and view all the answers

What are the three techniques mentioned for distinguishing human chromosomes?

<p>Karyotyping, SKY, and FISH. (C)</p> Signup and view all the answers

Why is it important to study the organization and function of chromosomes?

<p>All of the above. (D)</p> Signup and view all the answers

What does the abbreviation 'ORF' stand for in the context of identifying protein-coding genes?

<p>Open Reading Frame (A)</p> Signup and view all the answers

What is the significance of a sequence exceeding 10,000 codons without encountering a stop codon for an ORF?

<p>It suggests the sequence is highly likely to encode a protein. (C)</p> Signup and view all the answers

What is the approximate percentage of the population that needs to have a single-nucleotide change for it to be considered a 'single-nucleotide polymorphism' (SNP)?

<p>1% (C)</p> Signup and view all the answers

How many possible reading frames exist for a given DNA sequence?

<p>3 (B)</p> Signup and view all the answers

What is the specific start signal for translation in cells?

<p>AUG (A)</p> Signup and view all the answers

What is the primary purpose of using oligo(dT) primers in mRNA purification?

<p>To bind to the poly(A) tail of mRNA molecules (C)</p> Signup and view all the answers

What is the role of reverse transcriptase (RT) in the process of converting mRNA to cDNA?

<p>It synthesizes a complementary DNA strand from the mRNA template (A)</p> Signup and view all the answers

What makes identifying protein-coding genes in genomic sequence challenging for complex eukaryotes compared to bacteria and simple eukaryotes like yeast?

<p>Complex eukaryotes have more introns within their genes. (D)</p> Signup and view all the answers

In the Sanger method of DNA sequencing, what is the purpose of adding dideoxyribonucleotides (ddNTPs) to the reaction mix?

<p>ddNTPs terminate DNA synthesis by lacking a 3' hydroxyl group. (C)</p> Signup and view all the answers

What is the role of DNA polymerase in the Sanger method of DNA sequencing?

<p>DNA polymerase is responsible for synthesizing new DNA strands using a template and a primer. (A)</p> Signup and view all the answers

Which of the following is NOT a key difference between the Maxam-Gilbert and Sanger methods of DNA sequencing?

<p>The Maxam-Gilbert method is less accurate, while the Sanger method is more accurate. (A)</p> Signup and view all the answers

In modern automated DNA sequencing, what is the purpose of using fluorescently labeled ddNTPs?

<p>Fluorescent labels provide a visual marker for DNA fragments during electrophoresis. (D)</p> Signup and view all the answers

What is the significance of the "central dogma" of molecular biology?

<p>It outlines the flow of genetic information from DNA to mRNA to protein. (D)</p> Signup and view all the answers

Which of the following accurately describes the process of transcription?

<p>Transcription is the process of copying a DNA sequence into a complementary RNA sequence. (D)</p> Signup and view all the answers

What is the primary function of mRNA in the process of protein synthesis?

<p>mRNA acts as a template for the synthesis of a protein during translation. (A)</p> Signup and view all the answers

Which of the following describes the relationship between DNA, RNA, and protein in the central dogma of molecular biology?

<p>DNA is copied into RNA, which is then used to synthesize protein. (A)</p> Signup and view all the answers

Flashcards

Phosphodiester bond

A covalent bond linking nucleotides by connecting the 3’-OH of one sugar to the 5’ phosphate of another.

Polarity of DNA strand

The orientation of a DNA strand with a specific 5’ and 3’ end.

Antiparallel strands

Description of DNA strands that run in opposite directions.

Complementary base pairing

The specific pairing of bases A-T and C-G in DNA strands.

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DNA double helix

The twisted ladder shape formed by two strands of DNA held together by hydrogen bonds.

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Eukaryotic DNA

DNA organized into multiple chromosomes in eukaryotic cells.

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Chromosome types

Humans have 23 or 24 different types of chromosomes.

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FISH technique

Fluorescence In Situ Hybridization, used to identify chromosomes by color.

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Karyotype

A visual representation of an individual’s chromosomes.

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Gene

A segment of DNA that instructs making proteins or RNA.

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Genome

The complete set of genetic information in an organism's chromosomes.

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Compact genomes

Genomes tightly packed with genes, common in bacteria.

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Noncoding DNA

Segments of DNA that do not code for proteins, abundant in humans.

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Chromosomal variation

Varied chromosome number and size among species.

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Human chromosome count

Humans have 46 chromosomes from maternal and paternal sets.

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Species complexity and gene number

Gene number correlates roughly with species complexity.

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Bulk of human genome

Most of the human genome consists of repetitive sequences and non-coding DNA.

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LINEs

Long interspersed nuclear elements in the genome (e.g., L1).

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SINEs

Short interspersed nuclear elements, like Alu sequences.

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Unique sequences in the genome

Half of the human genome comprises unique sequences, not part of exons or introns.

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Protein-coding exons

Less than 1% of the human genome represents protein-coding exons.

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SNP (Single Nucleotide Polymorphism)

A genetic variation where a single nucleotide changes in the DNA sequence.

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Lactase enzyme

An enzyme that breaks down lactose, the sugar found in milk.

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Domestication of cattle

The process by which humans bred cattle, beginning around 10,000 years ago.

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Gene regulation in adults

Changes in gene expression that allow some adults to digest milk.

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Random mutations

Spontaneous genetic changes that can lead to new traits, such as adult lactose digestion.

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Maxam-Gilbert method

A DNA sequencing method using chemical cleavage at specific nucleotides.

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Sanger method

A DNA sequencing method using enzymatic extension of DNA and chain-terminating nucleotides.

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dideoxyribonucleotide (ddNTP)

A modified nucleotide that terminates DNA strand extension due to lacking a 3' OH group.

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Sequencing primer

Short DNA strand that initiates DNA synthesis for sequencing.

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Fluorescently labeled ddNTPs

Chain-terminating nucleotides labeled with fluorescent dyes for detection in sequencing.

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Electrophoresis

A technique used to separate DNA fragments based on size during sequencing analysis.

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Central dogma of molecular biology

The process by which genetic information flows from DNA to mRNA to protein.

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Transcription

The process of synthesizing mRNA from a DNA template.

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Exon

A coding region of a gene that is expressed in the final mRNA.

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Start Codon

The specific signal marking the beginning of translation, typically AUG.

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Open Reading Frame (ORF)

A continuous sequence of codons without a stop codon, indicating a potential protein-coding gene.

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Single-Nucleotide Polymorphisms (SNPs)

Genetic variations involving a change in a single nucleotide, present in at least 1% of the population.

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Reading Frames

The ways to read the nucleotide sequence in groups of three, affecting how proteins are made.

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cDNA

Complementary DNA synthesized from mRNA template, often used in genetic research.

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Translation Initiation

The process where ribosomes begin to synthesize proteins using the mRNA sequence.

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Study Notes

Lecture Overview

  • Lecture 2 covers DNA, chromosomes, genes, genomes, DNA sequencing, and SNPs.

DNA Structure

  • DNA is a long polymer comprised of four nucleotide subunits.
  • Nucleotides consist of a phosphate, sugar, and a nitrogenous base.
  • Pyrimidines include Cytosine and Thymine.
  • Purines include Adenine and Guanine.
  • Nucleotides are linked together by phosphodiester bonds.
  • A DNA strand has a 5' end and a 3' end.
  • DNA strands are antiparallel.
  • DNA is a double helix.
  • Bases lie perpendicular to the axis of the helix.
  • Complementary base pairing: A=T and C=G.

Eukaryotic DNA Packaging

  • Nucleosomes are basic units of eukaryotic chromosome structure.
  • Nucleosomes are formed by DNA wrapped around histone proteins.
  • DNA+specialized proteins = histones.
  • Eukaryotic DNA is packed into chromatin, which further packs into chromosomes.
  • Interphase chromosomes are not uniformly packed with some regions more condensed (heterochromatin) than others (euchromatin).
  • The human cell contains about 2 meters of DNA, yet its nucleus is only (5-8 µm) in diameter.
  • Chromosomes can be distinguished by size and are identifiable by various techniques.
  • Including: karyotype, FISH, SKY.

Genes and Genomes

  • Genes are functional units of heredity.
  • A gene is a segment of DNA that codes for a particular protein or RNA molecule.
  • The total genetic information of a cell or organism is its genome.
  • Complete genome sequences exist for thousands of organisms, ranging from E. coli to humans.
  • Organisms vary significantly in their genome size, from the smallest to the largest.
  • In eukaryotes, genome size refers to the haploid genome (number of nucleotide pairs in a single set of chromosomes)
  • The human genome size is approximately 3.1 billion nucleotide pairs.

DNA Sequencing

  • Maxam-Gilbert method: chemical cleavage of DNA at specific nucleotides.
  • Sanger method: enzymatic extension of DNA strands to a defined terminating base.
  • Modern sequencing methods involve automated DNA sequencing, where labelled chain-terminating nucleotides are incorporated and subsequently identified by electrophoresis in capillary tubes.

Central Dogma of Molecular Biology

  • The flow of genetic information is from DNA to mRNA to protein.
  • Transcription is the process where cells synthesize mRNA using DNA as a template.
  • Translation is the process where cells use the information in mRNA to build proteins.

Human Genome

  • The first draft of the human genome was published in 1999, and the complete sequence was achieved in 2021.
  • Human genes are not uniformly distributed.
  • Most of the human genome consists of non-protein-coding DNA, including repetitive nucleotide sequences and introns.
  • Only a small portion of the genome (~1.5%) encodes for proteins.
  • Regions of the genome may be very conserved in closely related species or variable.

Single Nucleotide Polymorphisms (SNPs)

  • SNPs are single-base changes that are present in at least 1% of a population.
  • Two human genomes from anywhere in the world will differ by about 2.5 million SNPs scattered throughout the genome.
  • Examples of gene regulation differences.

Identifying Protein-coding Genes

  • Genes contain ORFs (open reading frames) sequences greater or equal to 100 codons that lack stop codons, which can suggest if a region encodes protein or not.
  • In bacteria and simple eukaryotes, the protein-coding region is usually a contiguous stretch of coding sequence.

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