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Questions and Answers
What is the direction in which nucleic acid sequences are written?
Which type of bond connects nucleotides within an individual DNA strand?
In the DNA structure, guanine pairs with which nucleotide?
Why is DNA referred to as anti-parallel?
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How many nucleotide pairs are approximately in chromosome 22?
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What is the primary role of histone proteins in chromosome structure?
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Which statement accurately describes the composition of a chromosome?
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What is an octamer in the context of nucleosome structure?
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How do histone modifications impact gene expression?
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What mechanism allows DNA strands to separate during replication?
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What is the primary reason that RNA can form multiple distinct shapes?
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Which type of RNA is most directly involved in the synthesis of proteins?
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What is the role of RNA polymerase in transcription?
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What distinguishes the RNA strand from the DNA template during transcription?
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What is a consequence of RNA misfolding?
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Study Notes
DNA Structure and Asymmetry
- DNA is a nucleic acid chain which is read in a consistent order.
- DNA has directionality, with one end having a phosphoryl group attached to the 5' carbon of the sugar, and the other end having a free hydroxyl attached to the 3' carbon of the sugar.
- Nucleic acid sequences are written in the 5' to 3' direction.
- Guamine pairs with cytosine, and Adenine pairs with Thymine.
- Nucleotides within a strand are bonded by strong covalent bonds, called phosphodiester bonds.
- Nucleotides between strands are held together by weaker hydrogen bonds.
- DNA is double-stranded, forming the familiar ‘double helix’ structure.
- DNA is called anti-parallel because the strands run in opposite directions.
DNA Packaging and Chromosomes
- Human DNA is stored in condensed form in chromosomes.
- Chromosomes contain long lists of genes, each containing millions of nucleotide pairs.
- The condensed form of DNA is incredibly efficient, considering a chromosome like #22 would stretch to 1.5cm if laid out in a single double helix, yet the nucleus that holds it is only 6μm in diameter.
- Specialised proteins bind to and fold DNA, creating levels of organisation such as coils and loops.
Chromosome Proteins
- DNA-binding proteins that form chromosomes are divided into two classes: histone proteins and non-histone chromosomal proteins.
- Histone proteins are responsible for the basic level of chromosome packaging called the nucleosome, which has a “bead-like” structure.
- Non-histone chromosomal proteins also play a role in chromosome structure.
- Chromatin refers to the mixture of DNA and proteins that form chromosomes.
- Chromosomes are made up of 1/3 DNA and 2/3 protein.
Nucleosome Structure
- Each nucleosome (each “bead”) is an octamer (eight subunits), composed of two of each of the following histone proteins: H2A, H2B, H3, and H4.
- The double-stranded DNA winds around the octamer.
- Histones can be modified through mechanisms like acetylation and phosphorylation, which can alter DNA accessibility and influence gene expression.
DNA Replication: Templated Polymerisation
- DNA replication is essential for life, as it ensures the information in DNA can be accurately copied and replicated.
- Replication relies on base complementarity.
- The bonds between bases between strands are weaker, making it possible to “pull apart” DNA without damaging the integrity of individual strands.
- New strands are synthesised against a template (old strand) in a semi-conservative manner.
Key Underpinnings of DNA Replication
- Replication relies on base complementarity and enzymes like DNA polymerase.
RNA Structure and Folding
- Like DNA, RNA has nucleotide subunits linked together by phosphodiester bonds.
- Being single-stranded gives RNA a flexible backbone, allowing the polymer chain to bend back on itself and self-bond.
- This flexibility can lead to multiple distinct shapes of RNA, which are guided by the RNA’s sequence.
- RNA folding is crucial to health, but misfolding can lead to disease.
RNA in Gene Expression
- There are several types of RNA, each with their own function.
- The most abundant classes of RNA are rRNA, mRNA, and tRNA.
- Cells produce varying amounts of different proteins, which is regulated through the efficiency of transcription and translation.
Transcription: DNA to RNA
- Transcription produces single-stranded RNA that is complementary to a DNA strand.
- The sequence of bases in the RNA molecule is the same as the sequence of bases in the non-template DNA strand, with T substituted for U.
- Transcription requires RNA polymerase (instead of DNA polymerase used for replication).
- Transcription uses ribonucleoside triphosphates (NTPs) instead of dNTPs.
Key Facts about Transcription
- Transcription begins with the unwinding of a small portion of the DNA double helix.
- One strand serves as a template for RNA synthesis, relying on base complementarity.
- The RNA chain is displaced, and the DNA helix re-forms.
- RNA transcripts are copied from limited regions of the DNA strand and are generally much smaller than DNA molecules.
Transcription in Eukaryotes
- Eukaryotes have three types of RNA polymerase (I, II, and III) each responsible for transcribing specific types of RNA.
- RNA polymerase II transcribes all protein-coding genes.
- Transcription factors can bind to promoter or enhancer elements in DNA, modulating gene expression.
- Eukaryotic transcription initiation must take place on DNA packed into nucleosomes.
Promoter Structure
- Promoters are specific DNA sequences that direct RNA polymerase to the proper initiation site.
- The average sequence of promoters for different genes is called the consensus sequence.
Transcription: Initiation, Elongation, and Termination
- RNA polymerase II requires a set of general transcription factors (e.g., TFIID) for initiation.
- Transcription factors help in the recognition and unwinding of DNA.
- The process of transcription involves initiation, elongation, and termination steps.
Colinearity of DNA, RNA, and Amino Acid Sequences
- The sequence of DNA dictates the sequence of RNA, which in turn dictates the sequence of amino acids in a protein.
- This is called the central dogma of molecular biology.
Messenger RNA (mRNA): Start and Stop Signals
- mRNA contains start and stop signals for protein production.
- The start codon is almost always AUG, which codes for methionine.
- In eukaryotes, the AUG nearest the 5' end of mRNA is the initiator codon.
Transfer RNA (tRNA): The Adaptor Molecule
- tRNA molecules function as adaptor molecules between a codon and an amino acid.
- A portion of tRNA called the anticodon base pairs with the codon on mRNA, ensuring the correct amino acid is brought into the ribosome.
- There is at least one tRNA molecule for each amino acid.
- The third base in the codon is sometimes less discriminating, allowing for “wobble” in the base pairing.
Ribosomes and Protein Synthesis
- Ribosomes are protein-RNA complexes, with about 1/3 protein and 2/3 RNA content.
- Ribosomes have three tRNA binding sites:
- A (aminoacyl) site: binds the incoming tRNA.
- P (peptidyl) site: binds the tRNA with the growing peptide chain.
- E (exit) site: binds the uncharged tRNA before it leaves the ribosome.
- The ribosome moves along the mRNA, reading codons and adding amino acids to the growing polypeptide chain.
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Description
Test your knowledge on the structure and asymmetry of DNA. This quiz covers key concepts such as directionality, base pairing, nucleotide bonding, and the packaging of DNA into chromosomes. Enhance your understanding of why DNA's structure is essential for its function.
