Emergence of Life & Biomolecul

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### Emergence of Life: Overview #### What is Life? Living organisms have the ability to: - Replicate - Reproduce The origin of life deals with: - How life originated on Earth - How different kinds of organisms are found all over the Earth #### Was Life Supposed to Evolve? - **Carbon-based life:** Life as we know it is based on chains of carbon atoms with other primary atoms like oxygen, hydrogen, nitrogen, phosphorus, and sulfur. - **Silicon-based life:** While possible, carbon-based chemistry is considered more favorable due to its richer chemistry. - **Anthropic Principle:** For a given universe, the values of physical constants may allow the existence of objects like carbon atoms that can act as the building blocks of living systems. #### Understanding the Origin of Life: Challenges The origin of life is a **very hard** problem because: - Organisms are **very complex**. - We have data from **one origin**. - It happened a **very long time ago** (4.6-4.8 billion years ago). Humans appeared much later (~300,000 years ago). - We don't have much data from that period. - Earth's conditions were **predominantly different** from what they are now (e.g., no free oxygen). ### Timeline of Early Earth Events - **Hadean Eon:** Formation of Earth, Jack Hills Zircon (4.4 billion years ago), Core Formation, Moon Formation. - **Archean Eon:** Isua: Sediment Isotopic Evidence for Life, Acasta Gneiss. - **Proterozoic Eon:** Cells with Nucleus, Apex Chert Fossils, Rise in Atmospheric Oxygen, Hard-shelled Animals. - **Phanerozoic Eon:** Dinosaurs, Humans. **Key Evolutionary Milestones:** - Origin of Earth - Radioactive Dating - Earliest Fossil records - Prokaryotes - Atmospheric oxygen - Single-celled eukaryotes - Multicellular eukaryotes - Animals - Colonization of land - Humans ### Development of Life 1. **Chemical Evolution:** Geological molecules forming complex organic polymers. 2. **Acquisition of Replicative Ability:** Transition from lifeless, chemically interacting entities to self-replicating systems. 3. **Biological Evolution:** Eukaryotes, multi-cellularity, plants and animals, metabolic evolution. ### Hypotheses and Theories for Life's Origin - **Elemental Composition:** 96% of mass of most cells consists of Carbon, Hydrogen, Oxygen, and Nitrogen (CHON), or CHNOPS if Phosphorous and Sulfur are included. - **Chemical Properties of Carbon:** Carbon's versatility is key. - **Primordial Earth's Atmosphere:** Was reducing (N$_2$, CO$_2$, CH$_4$, NH$_3$, SO$_2$, H$_2$O, H$_2$, CO) unlike the present oxidizing atmosphere. #### Hypothesis 1: Abiotic Synthesis of Small Molecules (Oparin & Haldane, 1929) - **Concept:** Any initial biological molecules (e.g., proteins, sugar) would have been made by abiotic interactions between small molecules. - **Mechanism:** High energy discharges (UV/lightning) in the reducing environment of primordial Earth would have favored spontaneous synthesis of simple organic molecules from existing geological molecules on Earth's surface. #### Urey-Miller Experiment (1953) - **Simulated:** Pre-life atmosphere (water vapor, methane, hydrogen, ammonia) subjected to electric arc (lightning). - **Result:** Produced amino acids, sugars, lipids, nucleic acids, and organic monomers. - **Conclusion:** Living organisms are more than just monomers; this experiment showed the *building blocks* could form. #### Hypothesis 2: Abiotic Polymerization of Small Molecules (Sydney Fox) - **Concept:** Monomers can polymerize into polymers without enzymes under certain conditions. - **Mechanism:** Dripping organic monomers on hot clay (iron pyrite) or charged sites led to polymerization. - **Observation:** Polymerization rate was greater than hydrolysis rate; no enzymes were needed. #### Hypothesis 3: Abiotic Replication - **Earliest Genetic Material:** RNA is considered the earliest genetic material. - **RNA as Enzyme:** Sydney Altman and Tom Cech (1980 Nobel Prize) demonstrated RNA can act as an enzyme (ribozyme). - **RNA Capabilities:** Can cleave and polymerize itself, acts as an enzyme, and is not dependent on proteins. - **Role in Protein Synthesis:** RNA is used in multiple steps of protein synthesis; ribosomes are 2/3rd RNA. - **Central Dogma:** DNA → RNA → Protein (with RNA serving as a key intermediate and catalyst). #### Hypothesis 4: Protobionts - **Definition:** First formed cells, considered aggregates of abiotically produced organic molecules surrounded by membranes. - **Evolution:** Through gradual improvements in growth, reproduction, and metabolism, protobionts transformed into the first prokaryotic organisms. - **Endo-symbiont Theory:** Prokaryotes evolved into eukaryotes, and further into multi-cellularity. ### Metabolic Evolution - **Early Earth:** Limited resources, sufficient energy from the environment. - **Transition:** Chemosynthesis and Photosynthesis emerged. - **Oxygen Revolution:** Significant increase in atmospheric O$_2$ around 2.5-2 billion years ago, leading to oxidative metabolism. ### Role of Environment in Sustaining Life - **Hydrothermal Vents:** Support unique ecosystems independent of sunlight. - **Thermophiles:** Organisms thriving in extreme heat (e.g., Yellowstone national park). - **Cyanobacterium at very low pH:** Life can adapt to extreme acidic environments. - **Rio Tinto (Spain):** Extremely acidic river (pH 1.7-2.5) supporting diverse microbial life. #### MCQ for Lecture 2: Emergence of Life 1. Which of the following is NOT considered a fundamental ability of living organisms? a) Replicate b) Reproduce c) Metabolize d) Photosynthesize **Answer:** d) Photosynthesize (While many organisms photosynthesize, it's not a universal fundamental ability defining all life, unlike replication and reproduction). 2. The Anthropic Principle suggests that: a) Life can only evolve on Earth. b) The universe's physical constants are fine-tuned for carbon-based life. c) Silicon-based life is more common than carbon-based life. d) All life forms are ultimately derived from a single common ancestor. **Answer:** b) The universe's physical constants are fine-tuned for carbon-based life. 3. The Urey-Miller experiment demonstrated the abiotic synthesis of: a) Whole cells b) Organic monomers like amino acids c) Complex proteins d) Self-replicating RNA **Answer:** b) Organic monomers like amino acids 4. Which of the following is considered the earliest genetic material due to its catalytic and self-replicating properties? a) DNA b) Protein c) RNA d) Lipids **Answer:** c) RNA 5. The "Oxygen Revolution" was primarily driven by the emergence of: a) Abiotic polymerization b) Chemosynthesis and photosynthesis c) Protobionts d) Eukaryotic cells **Answer:** b) Chemosynthesis and photosynthesis ### Evolution: Overview #### What is Evolution? - **Definition:** Evolution explains how life has diversified into multiple forms. It is the change in the inherited traits of a population through successive generations. - **Mechanism:** When living organisms reproduce, they pass on a collection of traits to their progeny. - **Common Ancestry:** Present-day organisms are *descendants of a common ancestor* due to multiple heritable modifications. - **Genetic Change:** Involves genetic changes in a population over time. - **Unity and Diversity:** Accounts for both the unity (e.g., skeletal architecture of limbs, DNA, metabolic processes) and the diversity of life. #### Evidence for Evolution - **Skeletal architecture of limbs:** Homologous structures (same origin, different function) across species (e.g., whale, human, lizard, bird). - **Genetic similarity:** Comparison of human and chimpanzee chromosomes shows striking similarities, implying common ancestry. - **Common Ancestor:** Evolutionary trees illustrate how traits are passed from ancestor to descendant, leading to the diversification of species (e.g., humans, chimps, gorillas, orangutans from a common ancestor). ### Lamarckian Evolution (Jean-Baptiste de Lamarck, 1744-1829) - **Hypotheses (1809):** 1. Organisms develop traits by the *use and disuse* of body parts. 2. *Acquired characteristics* are passed from parents to offspring (Inheritance of acquired characteristics). - **Example:** Giraffes originally had short necks and ate grass. When grass died, they stretched their necks to eat leaves from trees, causing their necks to grow. These acquired long necks were then passed to future generations. - **Vestigial Organs:** Structures like the large intestine, cecum, and appendix were considered evidence of disuse. #### Disproving Lamarck (August Weismann, 1834-1913) - **Experiment:** Weismann cut off the tails of mice for several generations. - **Observation:** The babies born from this line of tailless mice still grew tails as long as their ancestors. - **Conclusion:** Acquired characteristics (like losing a tail) are **not** inherited. - **Critique:** This was not a perfectly "fair test" as the mice hadn't stopped *using* their tails in an attempt to adapt. ### Darwin's Evolution (Charles Darwin) #### Voyage of the H.M.S. Beagle - Darwin's voyage (1831-1836) collected extensive observations, particularly from the Galapagos Islands. #### Darwin's Questions - Why are there so many species of living things? - How do new species arise? - Within a population, how does an organism evolve? - How do organisms adapt to their environment? - How is one species related to another? #### Darwin's Observations: Theory based on 4 main ideas: ##### 1. Inheritance of Traits - **Variations:** Differences in traits occur among members of the same species (e.g., different breeds of dogs, cats, finches). - **Mechanism:** Once adaptations are selected, these traits are inherited. ##### Darwin's Finches - **Observation:** Finches on the Galapagos Islands showed variations in beak size and shape. - **Adaptation:** - **Short, strong beaks:** For cracking nuts. - **Long, fine beaks:** For reaching insect larvae. - **Conclusion:** These finches adapted to their environment to survive (**natural selection**). ##### 2. Overproduction - **Concept:** Organisms produce more offspring than can survive and reproduce. - **Outcome:** Ensures some offspring will survive to reproduce. - **Driving Force:** Overproduction is a driving force in natural selection, leading to adaptation. - **Examples:** Fish, insects, frogs. ##### 3. Adaptation and Survival of the Fittest - **Adaptation:** Adjustments between organisms and the environment. - **Natural Selection:** Favors adapted characteristics that enhance survival and reproduction. - **Homologous Structures:** Origin same, functions different (e.g., human arm, cat leg, whale flipper, bat wing). - **Analogous Structures:** Origin different, functions same (e.g., bat wing, butterfly wing, bird wing). ##### 4. The Struggle for Existence & Natural Selection - **Struggle for Existence:** Members of each species compete for food, shelter, and other life necessities. - **Survival of the Fittest:** Individuals better suited for the environment survive. - **Natural Selection:** Environment determines which variations will be selected. - **Core Principle:** "Individuals with traits which allow them to best adapt to the environment will most likely survive and reproduce." #### Example of Natural Selection: Peppered Moth - **Pre-Industrial Revolution:** Light moths camouflaged on light-colored trees, dark moths were easily seen and eaten by birds. Light moths were more numerous. - **Industrial Revolution:** Soot darkened trees. Dark moths now camouflaged, light moths stood out and were eaten. Dark moths became more numerous. - **Conclusion:** If an organism cannot adapt to its environment, it will eventually become extinct. #### Three Types of Natural Selection 1. **Stabilizing Selection:** Favors intermediate variants, selecting against extreme phenotypes (e.g., average birth weight). 2. **Directional Selection:** Favors individuals at one end of the phenotypic range (e.g., larger body size in a cold climate). 3. **Diversifying (Disruptive) Selection:** Favors individuals at both extremes of the phenotypic range over intermediate phenotypes (e.g., oyster shell color: light and dark shells camouflaged, medium shells stand out). #### Divergent Evolution - **Definition:** Two or more related species become more and more dissimilar over time. - **Example:** Red fox (mixed farmlands, forests) and Kit fox (plains, deserts). - Both had a common ancestor but adapted to different environments, leading to distinct appearances (e.g., Kit fox's larger ears for desert heat). #### Convergent Evolution - **Definition:** Unrelated species become more and more similar in appearance as they adapt to the same kind of environment. - **Example:** Frogs and Chameleons both developed harpoon-like tongues to catch insects, despite being different amphibians. #### Co-evolution - **Definition:** Joint change of two or more species in close interaction. - **Examples:** - Predators and prey co-evolve. - Parasites and hosts co-evolve. - Plant-eating animals and the plants they feed on co-evolve. - Pollination of orchids by African moths (moths get nectar, orchids get pollen spread). #### Why is Evolution Important? - Divergent, convergent, and co-evolution are different ways organisms adapt to the environment. - These phenomena explain how the diversity of life on Earth is due to the ever-changing interaction between a species and its environment. #### What Darwin's Theory Fails to Answer - What is the **molecular mechanism** that causes variation and how are these variations passed on? - How do species become extinct? #### MCQ for Lecture 3: Evolution 1. Lamarck's theory of evolution included the idea that: a) Traits acquired during an organism's lifetime are inherited by its offspring. b) Natural selection acts on existing variations. c) All species share a common ancestor. d) Only the fittest individuals survive and reproduce. **Answer:** a) Traits acquired during an organism's lifetime are inherited by its offspring. 2. The Urey-Miller experiment is most relevant to which stage of life's emergence? a) Biological Evolution b) Acquisition of Replicative ability c) Chemical Evolution d) Development of Protobionts **Answer:** c) Chemical Evolution (It showed the formation of basic organic molecules). 3. Which type of natural selection favors individuals at both extremes of the phenotypic range? a) Stabilizing selection b) Directional selection c) Diversifying (Disruptive) selection d) Artificial selection **Answer:** c) Diversifying (Disruptive) selection 4. Two unrelated species developing similar traits because they adapt to similar environments is an example of: a) Divergent evolution b) Convergent evolution c) Co-evolution d) Stabilizing selection **Answer:** b) Convergent evolution 5. One limitation of Darwin's original theory of evolution was its inability to explain: a) The struggle for existence. b) Variation within a population. c) The molecular mechanism of inheritance. d) Adaptation to the environment. **Answer:** c) The molecular mechanism of inheritance. ### Biomolecules: Nucleic Acids #### What is a Biomolecule? - **Definition:** Organic molecules, especially macromolecules (like carbohydrates, proteins) found in living organisms. - **Composition:** All living forms of life are made of *similar macromolecules* and are composed of *biomolecules only*. - **Elements:** Consist mainly of carbon and hydrogen, with nitrogen, oxygen, sulfur, and phosphorus. - **Types:** Include macromolecules like proteins, carbohydrates, lipids, and nucleic acids. - **Structure:** Very large molecules of many atoms, covalently bound together. #### Composition of Biomolecules (Typical Cell) - Water: ~70% - Ions/Small Molecules: ~4% - Macromolecules: ~26% - Proteins: 55% - Nucleic Acids: 10% - Carbohydrates: 25% - Lipids: 5% #### Molecules of Life - **Genetic Information:** DNA/RNA - **Energy Production/Building Block:** Lipid, Carbohydrates - **Building Block/Enzyme/Metabolism:** Protein #### How Much DNA Do We Have? - **Chromosomes:** A human cell contains 46 chromosomes. - **Length:** Total DNA in a cell, end-to-end, is around 1.8m long. - **Diameter:** Cell nucleus is approximately 2µm. - **Ratio:** $\frac{\text{DNA length}}{\text{Nucleus Diameter}} \approx 900,000!$ #### The Molecules of Life: Central Dogma - **Overview:** Functions of nucleic acid macromolecules in storing genetic information and transferring that codes for proteins. - **"THE CENTRAL DOGMA":** Information from nucleic acid to protein. - **DNA:** - **Self-Replication:** DNA polymerase, Mitosis and Meiosis. - **Transcription:** DNA to mRNA (DNA-dependent RNA polymerase). - **mRNA:** - **Translation:** mRNA to protein (Ribosome, tRNA, amino acids). - **Reverse Transcription:** RNA back to DNA (Reverse transcriptase). ### Nucleic Acid - **Genetic Material:** Most organisms have DNA as genetic material; some viruses have RNA. - **Biopolymer:** DNA or RNA are biopolymers and are **acidic** in nature. - **Location:** In eukaryotic cells, nucleic acid is present in the nucleus; in prokaryotic cells, it is present as free form in the cell. #### Nucleotides - **Components:** Nucleic acids are composed of 3 components: 1. Phosphate 2. Nucleobases 3. Sugar (2-Deoxyribose for DNA, Ribose for RNA) - **Structure:** Phosphate group linked to 5' carbon of sugar, nucleobase linked to 1' carbon of sugar. - **Nucleoside:** Sugar + Nucleobase - **Nucleotide:** Sugar + Nucleobase + Phosphate #### Nucleobases - **Purines:** Adenine (A), Guanine (G) - **Pyrimidines:** Cytosine (C), Uracil (U) (in RNA), Thymine (T) (in DNA) #### Nucleotides as Energy Source - **ATP (Adenosine Triphosphate):** Most common energy source inside a cell. - **GTP (Guanosine Triphosphate):** Another common energy source inside a cell. - **Dual Role:** Besides being building blocks for information storage, these components also combine to be the primary source of energy. ### Covalent Structure of DNA and RNA - **Phosphodiester Bond:** Forms between the phosphate group of one nucleotide and the sugar of another, creating the sugar-phosphate backbone. - **Directionality:** DNA and RNA strands grow from 5' to 3'. ### dsDNA Structure - **Chargaff's Data (1950-51):** Erwin Chargaff predicted that in all living organisms, the ratio of purines to pyrimidines is 1:1 (A=T, G=C). This is known as Chargaff's Rule. - **Rosalind Franklin (1920-1958):** "Photograph 51" (X-Ray diffraction image) provided critical dimensions for DNA structure. - **Watson and Crick (1953):** Used Franklin's data and Chargaff's rules to build the DNA model. - **Model Building:** Physically built models of wire, sheet metal, nuts, and bolts. - **Quote:** "Sometimes the fingers can grasp what the mind cannot." #### Watson and Crick Model - **Ladder Structure:** Sides made of alternating phosphate and deoxyribose. - **Rungs:** Bases form the rungs, attracted by weak chemical bonds (hydrogen bonds). - **Antiparallel:** The DNA double helix is anti-parallel (one strand 5' to 3', the other 3' to 5'). - **Base Pairing:** - Two hydrogen bonds connect T to A. - Three hydrogen bonds connect G to C. #### dsDNA Structure is Antiparallel - Studies show that parallel orientation is very unstable. #### B-form of DNA (Most Common) - **Helix:** Right-handed sense. - **Grooves:** Wide major groove (easily accessible to proteins) and narrow minor groove. - **Base Pairs:** Nearly perpendicular to the helix axis. - **Pitch:** One spiral is 3.4nm or 34Å. - **Distance between H-bonds:** 0.34nm or 3.4Å. ### Different Forms of DNA - **Factors involved in DNA conformations:** 1. Ionic or hydration environment 2. DNA sequences 3. Presence of specific proteins - In living cells, DNA can be A-DNA or B-DNA, with some regions forming Z-DNA. #### B-DNA (Most common in vivo) - **Conformation:** Favored at high water concentrations. - **Watson & Crick Model:** Also known as the Watson & Crick model. - **Identification:** First identified in fiber at 92% relative humidity. #### A-DNA - **Similarity:** Fairly similar to B-DNA. - **Helix:** Right-handed sense, shorter, more compact. - **Bp/Rotation:** Slight increase in bp/rotation (tighter rotation angle, smaller rise/turn). - **Grooves:** Deep major groove and shallow minor groove. - **Conformation:** Favored at low water concentrations or with high salt/alcohol. - **Pitch:** Every 2.3 nm makes a turn, with 11 base pairs per turn. - **Occurrence:** Occurs in dehydrated samples, used in crystallographic experiments. #### Z-DNA - **Nature:** Transient form of DNA. - **Helix:** Left-handed sense. - **Dimensions:** Narrower, more elongated helix than A or B. - **Pitch:** One turn spans 4.6 nm, comprising 12 base pairs. - **Occurrence:** Forms with alternating G-C sequences in alcohol or high salt solution. #### Franklin's Work: A vs B Form - X-ray diffraction images distinguished between A-Dry Form and B-Wet Form. ### DNA Origami - **Definition:** An emerging technology for designing and constructing defined multidimensional nanostructures. - **Process:** Template single-stranded DNA and staple DNA strands self-assemble to form complex shapes. #### MCQ for Lecture 4: Biomolecules - Nucleic Acids 1. Which of the following is NOT a component of a nucleotide? a) Phosphate group b) Amino acid c) Pentose sugar d) Nitrogenous base **Answer:** b) Amino acid (Amino acids are building blocks of proteins, not nucleic acids). 2. Chargaff's rules state that in a DNA molecule: a) The amount of A equals the amount of G. b) The amount of C equals the amount of T. c) The amount of A equals the amount of T, and the amount of G equals the amount of C. d) The amount of A+T equals the amount of G+C. **Answer:** c) The amount of A equals the amount of T, and the amount of G equals the amount of C. 3. The DNA double helix is described as "antiparallel" because: a) Its two strands run in opposite 5' to 3' directions. b) It contains both DNA and RNA. c) It has a left-handed twist. d) It is composed of two identical strands. **Answer:** a) Its two strands run in opposite 5' to 3' directions. 4. Which form of DNA is considered the most common in living cells and has a right-handed helix? a) A-DNA b) B-DNA c) Z-DNA d) C-DNA **Answer:** b) B-DNA 5. DNA origami is a technique used for: a) Sequencing DNA rapidly. b) Constructing complex nanostructures from DNA. c) Repairing damaged DNA in cells. d) Amplifying DNA segments. **Answer:** b) Constructing complex nanostructures from DNA. ### Biomolecules: Proteins #### The Composition of Biomolecules (Revisited) - Proteins account for **more than 50%** of the dry mass of most cells. - **Protein Functions:** Include structural support, storage, transport, cellular communications, movement, and defense against foreign substances. - **Examples:** Actin & Myosin (contractile), Immunoglobulin (protection), Insulin (hormonal), Hemoglobin (transport), Rhodopsin (receptor), Ferritin (storage), RUBISCO (enzyme), Spider silk (structural). #### Structure of Amino Acids - **Basic Unit:** Each amino acid has 4 different groups attached to a central alpha-carbon (Cα): - Amino group ($NH_3^+$) - Carboxyl group (COOH or $COO^-$) - Hydrogen atom (H) - Side chain (R group) - **Diversity:** Amino acids differ in their properties due to differing side chains (R groups). #### Amino Acids, Peptides, and Proteins - **R Group:** The physical and chemical properties of the side chain (R group) determine the unique characteristics of a particular amino acid. - **Primary Structure:** Amino acids assemble into a unique sequence of linear polymer to form the primary structure. - **Fold:** The primary sequence determines the 3D fold of the protein. - **Stability:** Thermodynamically most stable structure exists. - **Function:** The fold determines the function of proteins. ### Peptide Bond Formation - **Peptide Bond:** Amino acids are linked by peptide bonds. - **Polypeptide:** A polymer of amino acids. - **Length:** Polypeptides range in length from a few to more than a thousand monomers. - **Linear Sequence:** Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus). - **Mechanism:** - The alpha-carboxyl group of one amino acid (with side chain R1) forms a covalent peptide bond with the alpha-amino group of another amino acid (with side chain R2). - This is a **condensation reaction** (removal of a water molecule). - **Dipeptide:** Formation of a dipeptide results in the release of a water molecule. - **Polypeptide Chain:** Repetition of this process leads to the formation of a polypeptide chain. - **Peptides vs. Proteins:** AA chains less than 40 do not form a well-defined structure and are usually called peptides. - **Backbone:** The polypeptide backbone is the repeating sequence of the N-C-C-N-C-C... in the peptide bond. - **Side Chain:** The side chain or R group is NOT part of the backbone or the peptide bond. ### Protein Structure Protein structure or fold is described as: 1. **Primary sequence:** Based on covalent bonds. 2. **Secondary structure:** Based on non-covalent interactions. 3. **Tertiary structure:** Based on non-covalent interactions. 4. **Quaternary structure:** Based on non-covalent interactions. #### Interactions Stabilizing Tertiary Structure - Hydrophilic interaction (to water) - Disulfide bonds - Hydrophobic interactions - Hydrogen bonds - Ionic (salt bridge, electrostatic) interactions - van der Waals interactions #### Protein Assembly and Folding - **Primary:** Amino Acids → Assembly - **Secondary:** Pleated sheet, Alpha helix → Folding - **Tertiary:** Folded protein → Packing - **Quaternary:** Multiple protein subunits → Interaction ### Primary Structure - **Definition:** The sequence of amino acids present in the polypeptide chain. - **Bonding:** Amino acids are covalently linked by **peptide bonds** or **covalent bonds**. - **Convention:** Primary structure starts from the amino terminal (N) end and ends in the carbonyl terminal (C) end. ### Protein Folding - **Rotation:** The peptide bond allows for rotation around it, orienting R groups in favorable positions. - **Stability:** Weak non-covalent interactions hold the protein in its functional shape. Many weak interactions together create a strong, stable fold. ### Secondary Structure - **Definition:** Local, regularly occurring structure in proteins. - **Stabilization:** Mainly formed through **hydrogen bonds** between backbone atoms. - **Pauling & Corey:** Proposed two main conformations: - Alpha helix (α helix) - Beta sheets (β sheet) #### Alpha Helix - **Structure:** Right-handed spiral structure. - **Side Chains:** Extend outwards. - **Stability:** Stabilized by H bonding. - **Amino Acids per Turn:** 3.6 amino acids per turn. - **Segments:** Alpha helical segments are found in many globular proteins (e.g., myoglobin, troponin C). - **Length:** ~12 residues and ~3 helical turns. - **Common Amino Acids:** Ala, Leu, Met, Phe, Glu, Gln, His, Lys, Arg. #### Beta Sheet - **Structure:** Formed when 2 or more polypeptides line up side by side. - **Stability:** Stabilized by **hydrogen bond** between N-H and carbonyl groups of adjacent chains. - **Side Chains:** Lie above and below the sheet. - **Types:** - **All parallel:** All strands run in the same direction. - **Mixed parallel & anti-parallel:** Strands run in both directions. - **Common Amino Acids:** Tyr, Trp, Phe, Met, Ile, Val, Thr, Cys. ### Tertiary Structure of Proteins - **Definition:** Defines the specific overall 3-D shape of the protein. - **Interactions:** Based on various types of interactions between the side-chains of the peptide chain. #### MCQ for Lecture 5: Biomolecules - Proteins 1. What percentage of the dry mass of most cells do proteins account for? a) Less than 20% b) 20-30% c) More than 50% d) Approximately 10% **Answer:** c) More than 50% 2. Which part of an amino acid determines its unique characteristics? a) Amino group b) Carboxyl group c) Alpha-carbon d) R group (side chain) **Answer:** d) R group (side chain) 3. The primary structure of a protein refers to: a) Its overall 3D shape. b) The sequence of amino acids linked by peptide bonds. c) The formation of alpha helices and beta sheets. d) The interaction between multiple polypeptide chains. **Answer:** b) The sequence of amino acids linked by peptide bonds. 4. Which type of bond is primarily responsible for stabilizing the secondary structure (alpha helices and beta sheets) of a protein? a) Disulfide bonds b) Ionic bonds c) Hydrogen bonds between backbone atoms d) Hydrophobic interactions **Answer:** c) Hydrogen bonds between backbone atoms. 5. The overall 3D shape of a single polypeptide chain is described by its: a) Primary structure b) Secondary structure c) Tertiary structure d) Quaternary structure **Answer:** c) Tertiary structure.