Untitled Flashcards Set
DNA & DNA replication->
### DNA & DNA Replication
#### Key Figures in DNA Discovery:
1. Rosalind Franklin:
- Rosalind Franklin was a British biophysicist whose X-ray crystallography images of DNA provided critical insights into its structure. Franklin's famous Photograph 51 revealed the helical nature of DNA, which was pivotal in deciphering the DNA structure. Although her work was used by Watson and Crick, Franklin did not receive the recognition she deserved during her lifetime. Her X-ray diffraction images showed that DNA had a helical shape with repeating units.
2. James Watson & Francis Crick:
- Watson and Crick were the scientists who, using Franklin's data, proposed the double helix structure of DNA in 1953. They were awarded the Nobel Prize in 1962 for their discovery, though much of their success was due to Franklin's contributions. Watson and Crick's model showed that DNA consists of two strands that coil around each other to form a double helix, with bases in the center connecting the two strands.
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#### Structure of DNA:
- DNA (Deoxyribonucleic Acid) is a double-stranded helix composed of nucleotides.
- Nucleotide = Sugar (deoxyribose) + Phosphate group + Nitrogenous base.
- The two strands of DNA run in opposite directions (called anti-parallel). One strand runs from 5’ to 3’, and the other runs from 3’ to 5’.
- Base pairs: The nitrogenous bases pair in a specific way—**Adenine (A)** pairs with Thymine (T) (two hydrogen bonds), and Cytosine (C) pairs with Guanine (G) (three hydrogen bonds).
- The sugar-phosphate backbone of DNA is on the outside, while the nitrogenous bases are on the inside, forming the rungs of the helix.
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#### Origins of Replication:
- Origins of replication are specific locations on the DNA molecule where replication begins.
- In prokaryotes, there is typically a single origin of replication on their circular chromosome.
- In eukaryotes, there are multiple origins of replication on each linear chromosome.
- The importance of origins of replication:
- These sites are essential for DNA duplication. Replication proceeds bidirectionally from the origin, allowing for the fast replication of long DNA molecules.
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#### DNA Replication Process & Enzymes Involved:
DNA replication is a semi-conservative process, meaning each new DNA molecule consists of one old (parental) strand and one newly synthesized strand.
Key Enzymes in DNA Replication:
1. Helicase:
- Function: Unwinds the DNA double helix by breaking the hydrogen bonds between the base pairs, creating the replication fork.
- Direction: Helicase moves in the 5' to 3' direction on the lagging strand.
2. Single-Strand Binding Proteins (SSBs):
- Function: Bind to single-stranded DNA to prevent the strands from reannealing during replication.
3. Primase:
- Function: Synthesizes a short RNA primer that provides a starting point for DNA polymerase to begin replication.
- Direction: Works in the 5' to 3' direction.
4. DNA Polymerase III:
- Function: Adds new nucleotides to the growing DNA strand in the 5' to 3' direction. It is the primary enzyme for DNA replication.
- Leading Strand: Works continuously on the leading strand (the strand that is synthesized in the 5’ to 3’ direction).
- Lagging Strand: Works in discontinuous fragments on the lagging strand (which is synthesized in the 3’ to 5’ direction) as it moves backward.
5. DNA Polymerase I:
- Function: Removes RNA primers and replaces them with DNA.
6. Ligase:
- Function: Seals the nicks between Okazaki fragments on the lagging strand, ensuring the two newly synthesized DNA strands are joined together.
7. Topoisomerase (DNA Gyrase):
- Function: Relieves the supercoiling tension that builds up ahead of the replication fork as the DNA is unwound by helicase.
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#### Direction of DNA Replication:
- Leading Strand: The leading strand is synthesized continuously in the 5' to 3' direction as the replication fork opens.
- Lagging Strand: The lagging strand is synthesized discontinuously in the opposite direction (3' to 5') as the replication fork opens. This results in the formation of short fragments called Okazaki fragments, which are later joined together by ligase.
#### Anti-Parallel Configuration:
- The anti-parallel configuration of the two strands of DNA means that one strand is synthesized in the 5' to 3' direction (leading strand), while the other is synthesized in the opposite direction (lagging strand). This is due to the nature of DNA polymerase, which can only add nucleotides in the 5' to 3' direction.
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#### Proofreading and DNA Repair:
- DNA Polymerase Proofreading:
- DNA polymerase has proofreading ability. It checks each nucleotide added to the growing strand and removes incorrect nucleotides through its 3’ to 5’ exonuclease activity.
- DNA Repair Mechanisms:
- Mismatch Repair: Corrects errors that escape proofreading. Mismatch repair proteins detect mismatched bases, remove the incorrect one, and fill in the correct base.
- Base Excision Repair (BER): Removes damaged or abnormal bases (e.g., due to oxidation) and replaces them with correct ones.
- Nucleotide Excision Repair (NER): Repairs large-scale DNA damage, such as pyrimidine dimers caused by UV radiation.
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#### Causes of Mutations:
- Mutagens: Environmental factors that cause mutations, such as radiation (UV light, X-rays), chemicals (cigarette smoke, industrial chemicals), and viruses (e.g., HPV).
- Spontaneous Mutations: Mutations that occur without external influence, often due to errors during DNA replication or chemical changes in bases.
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#### Telomeres and Telomere Problem:
- Telomeres:
- Telomeres are repetitive nucleotide sequences at the ends of chromosomes. They protect the chromosome from degradation and prevent the loss of important genetic material during DNA replication.
- Telomere Problem:
- As cells divide, the telomeres shorten with each round of DNA replication (because DNA polymerase cannot fully replicate the very ends of chromosomes). Eventually, the telomeres become too short, leading to cellular senescence or apoptosis (programmed cell death).
- Telomerase:
- Telomerase is an enzyme that extends the telomeres by adding repetitive nucleotide sequences, restoring the telomere length.
- Telomerase activity is high in stem cells, germ cells, and some cancer cells, but it is absent or low in most somatic cells.
- Telomerase adds repetitive sequences to the 3' end of the telomere, which is extended before the DNA is replicated. This compensates for the loss of DNA at the telomere during cell division.
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In summary, DNA replication is a highly coordinated process involving multiple enzymes that ensure accurate copying of genetic material. The anti-parallel configuration of DNA results in different mechanisms for synthesizing the leading and lagging strands. Proofreading and DNA repair mechanisms correct errors, while telomerase helps maintain the stability of chromosomes in certain cells.
Gene expression ->
1. Gene → Polypeptide (A.A. sequence) Overview
The flow of genetic information from DNA to RNA to Protein is called the central dogma of molecular biology. It describes how a gene (a segment of DNA) gets transcribed into messenger RNA (mRNA), which is then translated into a polypeptide (protein) sequence. The genetic code links nucleic acids (DNA and RNA) to amino acids (which make up proteins). Here's a breakdown of the process:
- DNA contains the information for making proteins.
- RNA is the intermediary that carries the genetic instructions from DNA to the ribosomes for protein synthesis.
- Polypeptide (protein) is the final product, formed by linking amino acids according to the sequence encoded in the RNA.
### 2. Nucleic Acid "Language" vs Amino Acid "Language"
- DNA/RNA Language: Nucleic acids (DNA and RNA) are composed of nucleotides, which are sequences of 4 types of molecules: Adenine (A), Thymine (T) or Uracil (U) in RNA, Cytosine (C), and Guanine (G).
- Amino Acid "Language": Proteins are made up of 20 different amino acids, and the sequence of amino acids determines the structure and function of the protein.
### 3. Steps, Structures, Enzymes & Machinery in Transcription & Translation
#### Transcription: (DNA → RNA)
Transcription is the process by which an RNA molecule is synthesized from a DNA template. It occurs in the nucleus (in eukaryotes) or the cytoplasm (in prokaryotes).
- Initiation:
- The enzyme RNA polymerase binds to the promoter region of a gene on the DNA.
- The DNA unwinds and the enzyme begins synthesizing a strand of RNA in the 5' to 3' direction.
- Elongation:
- RNA polymerase moves along the DNA template strand, adding complementary RNA nucleotides (A, U, C, G) to form the growing mRNA strand.
- Termination:
- RNA polymerase reaches a terminator sequence, causing it to detach from the DNA and release the newly formed mRNA.
#### Editing (in Eukaryotes):
Before the mRNA is translated, it undergoes RNA processing in eukaryotic cells:
- Introns: Non-coding regions of the mRNA are spliced out.
- Exons: Coding regions are retained.
- Spliceosomes: These are molecular machines made of RNA and proteins that splice out introns.
- 5' Cap and Poly-A Tail: The mRNA gets a protective 5' cap and a poly-A tail added to the 3' end to protect it from degradation and aid in translation.
#### Translation: (RNA → Polypeptide)
Translation is the process by which the mRNA is used to assemble amino acids into a polypeptide (protein). It occurs in the cytoplasm at the ribosome.
- Initiation:
- The mRNA attaches to the small ribosomal subunit.
- The first tRNA (carrying methionine) binds to the start codon (AUG) on the mRNA.
- The large ribosomal subunit then joins, forming a functional ribosome.
- Elongation:
- The ribosome reads the mRNA codons in sets of three nucleotides.
- Each codon is matched with a complementary anticodon from a tRNA, bringing a specific amino acid.
- Amino acids are linked together in a growing polypeptide chain.
- Termination:
- When the ribosome reaches a stop codon, translation ends.
- The polypeptide chain is released and folds into its functional structure.
### 4. Different Types of RNA and Their Functions
- mRNA (messenger RNA): Carries the genetic code from the DNA to the ribosome for translation.
- tRNA (transfer RNA): Matches the mRNA codon to the correct amino acid during translation.
- rRNA (ribosomal RNA): Part of the ribosome, where protein synthesis occurs. It catalyzes the formation of peptide bonds.
- snRNA (small nuclear RNA): Involved in splicing out introns during RNA processing in eukaryotes.
- miRNA (micro RNA): Regulates gene expression by binding to mRNA and preventing its translation.
### 5. Anti-Codons
An anticodon is a sequence of three nucleotides on a tRNA molecule that is complementary to an mRNA codon. It ensures that the correct amino acid is added to the growing polypeptide chain.
### 6. tRNA Structure/Function
- Structure: tRNA molecules have a characteristic L-shape. The anticodon loop binds to the mRNA codon, while the acceptor stem carries the appropriate amino acid.
- Function: tRNA delivers specific amino acids to the ribosome, matching the mRNA codons through the anticodon.
### 7. Ribosomes and Their Role in Translation
Ribosomes are molecular machines made of rRNA and proteins. They have two subunits:
- Small subunit: Binds to the mRNA.
- Large subunit: Contains the catalytic site for peptide bond formation.
Ribosomes move along the mRNA, reading its codons, and facilitate the binding of tRNA molecules, thereby adding amino acids to the growing polypeptide chain.
### 8. Protein Folding: Chaperonins & Endomembrane System
- Chaperonins: Specialized proteins that help other proteins fold into their correct three-dimensional shape, preventing misfolding or aggregation.
- Endomembrane system: Includes structures like the rough ER (where protein synthesis occurs) and Golgi apparatus (where proteins are processed and modified) that aid in the proper folding and transport of proteins.
### 9. Polyribosomes
- Polyribosomes (Polysomes): Groups of ribosomes that work together to translate the same mRNA simultaneously. This allows for efficient, mass production of proteins.
### 10. Prokaryotic Protein Production
In prokaryotes (e.g., bacteria):
- Transcription and translation happen simultaneously in the cytoplasm because there is no nucleus.
- The mRNA produced is immediately translated by ribosomes.
- No RNA processing (like splicing) occurs in prokaryotes.
### 11. Types of Mutations and Their Effects
- Point Mutations: A change in a single nucleotide.
- Silent mutation: No change in the protein.
- Missense mutation: A single amino acid is changed, which may affect the protein function.
- Nonsense mutation: A codon is changed to a stop codon, resulting in a truncated (nonfunctional) protein.
- Frameshift Mutations: Insertion or deletion of nucleotides that shifts the reading frame, altering the entire amino acid sequence downstream.
- These mutations often have severe effects, as they change the whole sequence of amino acids in the polypeptide.
- Massive Missense: A large region of the protein is altered due to multiple mutations, severely affecting the protein's function.
### 12. Causes of Mutations
- Spontaneous mutations: Occur naturally due to errors during DNA replication or other cellular processes.
- Induced mutations: Caused by external factors, such as radiation, chemicals, or viruses.
### Natural Selection & Phylogeny: Key Discoveries & Scientists
Here’s an overview of the key scientists and their contributions to our understanding of natural selection and phylogeny:
#### 1. Carl Linnaeus (1707–1778)
- Contribution: Linnaeus is known for developing the system of binomial nomenclature, which is the method of naming species using two names (genus and species). This system is still in use today.
- Classification: He also established the hierarchical system of classification, which organizes species into groups based on shared characteristics: Kingdom, Phylum, Class, Order, Family, Genus, Species (the modern taxonomic ranks).
#### 2. Georges Cuvier (1769–1832)
- Contribution: Cuvier is considered the father of paleontology. He demonstrated that species could go extinct, a radical idea at the time. His work on fossil evidence showed that species in the past were different from those today, leading to the idea that life on Earth had changed over time.
- Catastrophism: He proposed the theory of catastrophism, which suggested that the Earth experienced sudden, short-lived, and violent events (e.g., floods, volcanic eruptions) that caused the extinction of species.
#### 3. Jean-Baptiste Lamarck (1744–1829)
- Contribution: Lamarck was an early proponent of the idea that species change over time, though his mechanism (known as Lamarckism) was incorrect.
- Lamarck's Theory: He proposed that organisms could pass on traits acquired during their lifetime to their offspring. For example, he suggested that giraffes' long necks developed because they stretched to reach higher leaves, and this acquired trait was inherited by their descendants.
- Impact: Lamarck’s ideas contributed to the understanding that species change, though modern biology uses Darwin’s theory of natural selection instead.
#### 4. James Hutton (1726–1797)
- Contribution: Hutton is known as the father of modern geology. He proposed the concept of uniformitarianism, which posits that the Earth’s geological processes (such as erosion and sedimentation) have remained constant over time and can explain the formation of geological features.
- Impact: Hutton’s ideas helped establish the Earth as ancient and continually changing, providing a long timeline for evolutionary processes.
#### 5. Charles Lyell (1797–1875)
- Contribution: Lyell expanded on Hutton’s ideas and further developed the theory of uniformitarianism in his influential work, Principles of Geology. He argued that the same geological processes observed in the present (e.g., earthquakes, volcanic activity) have been occurring in the same manner throughout Earth’s history.
- Impact: Lyell’s work helped establish the Earth’s great age, which was crucial for Darwin’s later theory of evolution by natural selection.
#### 6. Thomas Malthus (1766–1834)
- Contribution: Malthus was an economist who wrote An Essay on the Principle of Population, where he argued that populations tend to grow exponentially, but food and resources grow at a much slower rate, leading to competition for survival.
- Impact: Malthus’ work influenced Darwin by highlighting the idea of struggle for survival, which became a cornerstone of Darwin’s theory of natural selection.
#### 7. Alfred Russel Wallace (1823–1913)
- Contribution: Wallace independently developed the theory of natural selection around the same time as Darwin. He was a naturalist who conducted research in Southeast Asia, observing species variation.
- Impact: Wallace’s work prompted Darwin to publish his own ideas in On the Origin of Species. Though Wallace and Darwin are often credited together for the theory of natural selection, Darwin is more widely known due to his extensive research.
#### 8. Charles Darwin (1809–1882)
- Contribution: Darwin is best known for his theory of natural selection, outlined in On the Origin of Species (1859). He proposed that species evolve over time due to environmental pressures that favor certain traits, which are passed down to subsequent generations.
- Impact: Darwin’s work revolutionized biology, providing the mechanism by which evolution occurs and explaining the diversity of life on Earth.
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### Key Concepts in Phylogeny & Evolution
#### 1. What is a Cladogram?
- A cladogram is a diagram that shows the evolutionary relationships between species based on shared characteristics, called derived traits. It is a type of phylogenetic tree where the branches represent common ancestry and the nodes represent the most recent common ancestor of the groups connected by that node.
- How to read a Cladogram:
- The root of the tree represents the common ancestor.
- The branches represent the evolutionary pathways of different lineages.
- The tips represent individual species or groups.
- The closer two species are to each other on the tree, the more recently they share a common ancestor.
#### 2. Phylogeny
- Phylogeny refers to the evolutionary history and relationships among species or groups. It traces how different species or groups of organisms have diverged from common ancestors over time.
- Phylogenetic trees and cladograms are tools used to represent these evolutionary relationships.
- The goal of phylogenetics is to understand the pattern of evolutionary descent, which can be deduced through various data, such as morphology, DNA sequences, and fossils.
#### 3. What are Homologies?
- Homologies are traits that are shared by different species because they inherited them from a common ancestor. Homologies provide evidence for common ancestry and can be used to construct phylogenies.
- Types of Homology:
- Morphological Homology: Similar structures in different species that suggest a common ancestor. For example, the forelimbs of mammals (human arm, bat wing, whale flipper) show similar bone structures, indicating a common ancestor.
- Molecular Homology: Similarities in DNA sequences, proteins, or other molecular structures. For example, the similarity between the cytochrome c protein in humans and other organisms suggests common ancestry.
- Developmental Homology: Similarities in embryonic development across species. For example, vertebrate embryos (like fish, amphibians, reptiles, birds, and mammals) all exhibit similar stages in early development, which supports the idea of a common ancestor.
#### 4. Biogeography
- Biogeography is the study of the distribution of species and ecosystems across the planet. It examines how geological and environmental factors influence where species live and how they evolve.
- The patterns of species distribution provide evidence for evolutionary processes. For example, isolated island species often evolve to become unique species, supporting the idea of adaptive radiation.
#### 5. Convergent Evolution
- Convergent evolution occurs when unrelated species develop similar traits due to similar environmental pressures or ecological niches, rather than shared ancestry.
- Example: The wings of bats, birds, and insects all serve the same function (flight) but evolved independently from different ancestral structures. This is an example of convergent evolution.
#### 6. How Does the Fossil Record Affect Our Understanding of Phylogeny?
- The fossil record provides a historical record of life on Earth. It allows scientists to trace the evolutionary history of species and provides evidence of how organisms have changed over time.
- Fossils help to:
- Document extinct species and their characteristics.
- Reveal the timing of evolutionary events (e.g., when particular species or traits evolved).
- Show the transition between major groups, such as the transition from fish to amphibians or reptiles to birds.
- Fossils serve as important "missing links" in understanding phylogenetic relationships and the process of evolution over time.
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### Summary of Key Concepts:
- Cladograms and phylogenetic trees show evolutionary relationships, with homologies supporting common ancestry.
- Biogeography and fossil records provide critical evidence for how species evolved and adapted to different environments.
- Convergent evolution shows how similar traits can evolve in unrelated species due to similar selective pressures.