Biology Summaries PDF

Preview

Summary

Brief summaries of Biology modules and each lecture...

Description

Biology Summaries Module 1 What is life? L1 What is Life? Defining life -

Characteristics of living things: Composed of a common set of elements Grow and change Respond to stimulus (environment) Are comprised of cells Use molecules and make new molecules Extract energy and use it Contain genetic information Exist in populations and can evolve

-

Viruses? Alive: contains nucleic acids (genetic info); can replicate; evolve and adapt to the environment Not alive: not capable of independent replication; do not contain required metabolic processes to be considered ‘alive’

The origins of life -

Early conditions of Earth could result in the production of: Bases present in DNA and RNA (A,C,G,T,U) All 20 amino acids found in proteins A range of 3- and 6- carbon sugars Fatty acids Vitamin B6, NAD and organic acids

-

Forces creating life on earth? 1/ life formed spontaneously on early Earth (a reducing environment facilitated organic molecule formation, such as DNA bases) 2/ Extra-terrestrial origin – life from another planet or comet (panspermia)

The fossil record as evidence of early life on earth -

Stromatolites – ‘living fossils’ thrive in hyper saline solutions exist there with no competition due to the high salinity on the surface of cyanobacteria were discovered, basic lifeforms that were fixing carbon (photosynthesising) Found to originate 3.5 billion years ago and still present today (evidence of early types of life)

L2 Molecules of Life: Part 1 The elements of nature (C, H, N, O) -

Major elements Hydrogen, Carbon, Oxygen, Nitrogen (>99%) Carbon most adaptable element, can enable four different bonds to occur

-

Smaller amounts: P, S, Ca, Na, Mg, Cl, K

-

Trace elements: F, Si, V, Cr, Mn, Fe, Ni, Co, Cu, Zn, Se, Mo, I

Water is the matrix of life -

Partial negative charge of oxygen end of molecule (pull e- away from H), Hydrogen: partial positive charge); Polarity of water allows bonding between other H 2O molecules with opposite charges attracting (why water sticks together)

-

Water molecules surround ions and molecules through ionic interactions and can maintain them in solution

Water + biomolecules (the big five) -

Major biomolecules: Nucleic acids, Proteins, Carbohydrates, Lipids

Nucleic Acids (DNA, RNA) -

DNA: Deoxyribonucleic acid Nucleotides: Adenine (A) Cytosine (C) Guanine (G) Thymine (T) Deoxyribose sugar

-

RNA: Ribonucleic acid In RNA, Thymine is replaced with the related nucleotide Uracil (U) Ribose sugar

-

Both form long, linear chains (polynucleotides) that never branch

-

Nucleotides (building blocks of nucleic acid) Pyrimidines (C, U, T) Purines (A, G)

-

Formation: Base + sugar (ribose or deoxyribose) = Nucleoside + Phosphate = nucleotide

-

Nucleotides are linked together by phosphodiester bonds to form nucleic acids (dehydration reaction). Phosphate – sugar backbone, Hydrogen bonds between Nitrogenous bases

-

Stronger bonds between CG than T=A due to 3 hydrogen bonds

-

DNA consists of 2 strands (double stranded), strands are complementary of one another

-

Genes: genes are found along DNA, DNA encodes information. Coding strand/sense (more important) and non-coding/template/antisense strand

-

RNA is single stranded, no complementary strand. Bases can also bond, sometimes folded up (5’ -> 3’) Types of RNA: mRNA, tRNA, rRNA. RNA is produced via transcription

Protein (amino acids, enzymes) (Polypeptide) -

Proteins are the most functionally diverse of all biological molecules

-

Composed of amino acids (building blocks) all amino acids have a basic amino group and an acidic carboxyl group and a variety of different side-chain groups (R). Polypeptides may be 100s or 1000s of amino acids long

-

Peptide formation: joins amino acids together; dehydration reaction (H2O produced)

-

20 different amino acids: allows many combinations diverse functionality of proteins

-

3 groups of amino acids: Hydrophobic (non-polar, tend to aggregate together); Hydrophilic (happy to interact with water, polar, can be charged or uncharged)

Overview of transcription and translation -

Decoding mRNA into protein (translation), decodes the information from the coding strand into a protein

-

A protein can be described at four levels: Primary structure (the amino acid sequence); Secondary structure (the conformation changes in primary structures due to the formation of electrostatic); Tertiary structure (The ultimate configuration that a polypeptide chain takes in reaching the configuration of minimal free energy); Quaternary structure (association of the polypeptide chains in proteins which have more than one polypeptide)

-

Proteins are the cellular workhorses – the ‘central dogma’ of molecular biology

L3 Molecules of Life: Part 2 Carbohydrates (sugars, starch, polysaccharides) -

Primary functions: Source of chemical energy, a way to store energy if enough influx is supplied; Forms structural components eg. exoskeleton of insects; cell wall of fungi; some of the most abundant organic compounds in nature

-

General formula (CH2O)n (n is the number of carbon atoms, generally between 3-8)

-

Basic subunit is a sugar molecule or saccharide (3 main groups of carbohydrates are: monosaccharides, disaccharides and polysaccharides)

-

Carbohydrate isomers, each have different functions within the cell

-

Monosaccharides (simple sugars): found throughout biology, building blocks for biological molecules (DNA and RNA); biochemical intermediates (carbon skeletons); source of energy (Glycolysis)

-

Formation of glyosidic (sugar) bond

-

A disaccharide is produced from the union of 2 monosaccharides – maltose (glucose + glucose), lactose (galactose + glucose), sucrose (glucose + glucose)

-

Complex polysaccharides: tend to be structural or storage biomolecules eg. glycogen, pectin Formed by an enzyme bringing sugars together

-

Starch: polysaccharides of glucose, primary energy storage compound in plants ( – 1,4 glyosidic linkage backbone with – 1,6 glyosidic linkage branch)

-

Chitin: A major component of fungal cell walls; exoskeleton of arthropods

-

Cellulose: Linear polysaccharide of glucose; major structure of plant cell walls -> 1-4 bonds between glucose subunits

-

Glycogen: multibranched polysaccharide of glucose that serves as a form of energy storage; the main form of glucose storage in animals, fungi and bacteria -> in animals, glycogen is produced and stored in liver.

Lipids (basic structure and function) Properties: Insoluble in water (hydrophobic); Dissolves readily in organic solvents eg. ethanol; Composed mainly of carbon, hydrogen and oxygen (Differ from carbohydrates due to a smaller proportion of oxygen) Lipids are not polymers -

Common Lipids:  Long chain fatty acids: basis of many oils and fatty acids compounds with no double or triple bonds are saturated, perfectly straight Compounds with double or triple bonds are unsaturated, points of double, triple bonds form kinks (they are rigid)  more likely to be liquid at room temperature  Wax: comprised of 2 fatty acid chains and an Ester linkage; very hydrophobic  Fat (triacylglycerol) composed of 3 fatty acids and a glycerol group. Due to long carbon chains, lipids contain a large amount of energy, eg. seeds underground must sprout. Blubber is important for insulating marine animals and it stores energy and increases buoyancy.

Biological membranes (phospholipid bilayers and osmosis) -

Phospholipids (membrane lipids):

 Amphipathic due to head being hydrophilic (water loving) and tails being hydrophobic. In water they go tail to tail forming bilayer – allows cells to exist in liquid/water environments. Flexible / fluid Transport across membranes -

Passive transport (no energy input) follows concentration gradient (high -> low). Proteins may be hydrophobic and form pores in the phospholipid bilayer (protein channel). Active transport (requires energy) Against concentration gradient (low -> high) Primary active transport eg. antiporter pumps (Na+ out K+ in); Secondary active transport eg. glucose pump (new Na+ gradient created helps glucose and Na+ into the cell) – sodium circulates around driving transport of glucose Facilitated diffusion eg. water sugar.

L4 The development of early life on Earth - Prokaryotes Classification of Prokaryotes -

Single cellular organisms, no nucleus, very small (1m, never larger than 10m) and much simpler cell structure, lack complex internal structures present in Eukaryotes. Highly evolved to exploit their environments: small genomes and rapid rates of cell division, more chance of evolution.

-

First inhabitants of Earth were prokaryotes (eg. stromatolites, cyanobacteria on the surface that can photosynthesise, and secreting a mineral which is what forms their dome like shape)

Structure and composition of Prokaryotes -

Plasma Membrane: phospholipid bylayer (semi permeable membrane), restricts and allows diffusion of substances into the cell.

-

Cytosol: liquid portion inside the cell

-

DNA: single loop of double stranded DNA, freely floats no nucleus. Resides inside a ‘space’ in the cell known as the nucleoid region (not actual organelles)

-

Ribosomes: area of protein synthesis (lots present if cell is undergoing lots of metabolic activity)

-

Cytoplasm: aqueous gel containing cytosol, DNA and ribosomes

-

Pili: attachment sites for other prokaryotic cells to exchange genetic material

-

Flagellum: (plural = flagella), composed of a protein called flagellan. Generates motion (not always present)

-

Outer Capsule: composed of sugars, can aid in survival during tough times. Eg. pathogenic bacteria can ‘camouflage’ by putting particular sugars on their surface.

-

Cell wall: (semi rigid) holds the prokaryotic cell together

Unique functions of Prokaryotes -

Prokaryotes utilized by humans for recycling; genetically modified bacteria in pharmaceuticals (e. coli produces insulin, growth hormone, interferon); GM crops (Agrobacterium) inserts genes into plants

-

Binary Fusion: spontaneous mutations occur at high frequencies in prokaryotes, generating enormous biochemical diversity

-

Replication: Prokaryotes have 0.001 times as much DNA as a Eukaryotic cell, and divide every 20 mins (early/young prokaryotes are generally more metabolically active and contain a larger number of ribosomes compared to older prokaryotic cells)

Abundance and diversity of Prokaryotes -

2 of the 3 domains of life are Prokaryotic: The Bacteria, The Archaea. Archaea are more closely related to the 3rd domain, Eukarya or Eukaryotes

-

How do archaea differ from bacteria: morphologically they don’t (under the microscope/how they appear); Biochemically archaea are nearly as different from bacteria as they are from Eukarya (hence the separation of domains); The 2 central biological processes in Archaea (genetic transcription and translation) are more similar of Eukaryotes than Bacteria. Features of the Archean lipids and their membranes are unusual (and lack a peptidoglycan wall) As of 2020, no clear examples of Archean pathogens are known

-

Prokaryotes are ubiquitous and diverse: Acidic – many archaea are thermophilic, acidophilic (acid loving) or both. Thermophiles can live in pH levels of 2 or 3 whilst maintaining an internal pH of 5.5-7; Heat – pyrolobus fumarii are found in deep sea hydrothermal vents, they grow at temperatures of 106C (become metabolically inactive below 90C.

L5 The rise of the eukaryotic cell: Part 1 Prokaryotes vs eukaryotes -

Eukaryotes are larger and have more complex structures with a nucleus.

-

Nucleus is the command centre of the cell: surrounded by a double membrane of nuclear envelope; presence of nuclear pores (annular), defined spaces made up of multi protein components, allows transfer of RNA out of the nucleus; Nucleolus = subregion of nucleus containing (transcribing) ribosomal genes (ribosomal biogenesis); DNA in long strands covered with histones (chromosomes) Different organisms have different numbers of chromosomes (humans = 23); RNA transcribed from DNA leaves nucleus via pores and is travelled in the cytoplasm

-

Histones, positively charged proteins aid in condensing DNA  negatively charged backbone in DNA wraps around histones

How the eukaryotic cell evolved -

Grypania spiralis fossils, a form of algae, around 1.3-1.8 billion years old

Mitochondria -

Mitochondria (Powerhouse of the cell): cells may contain several mitochondria or have a single large mitochondrion. Surrounded by 2 membranes: an outer membrane (linear), and a highly convoluted inner membrane whose inward projections are called cristae, to increase SA; Mitochondria carry out the aerobic respiration of all eukaryotic cells (production of ATP) TCA cycle, citric acid cycle (CAC), Krebs cycle occurs in matrix of mitochondria

-oxidation (breaking down of fatty acids *also in matrix*)

Chloroplasts -

Chloroplasts, energy catches of plant cells. Plant cells may contain one or many chloroplasts per cell. Chloroplasts are surrounded by 2 membranes (an outer membrane, plus an inner membrane that forms a complex internal network of lamellae or thylakoids); The photosynthetic pigments are located within the thylakoids. Chloroplasts are responsible for photosynthesis, of the conversion of light energy to chemical energy

-

Photosynthesis: 6CO2 + 12H2O  C6H12O6 + 6O2 Calvin-benson-Bassham (CBB) cycle

Accessory pigments: Chlorophyll B, enhances the ability to capture light Chlorophyll A is the basis of all photosynthetic organisms -

Marine algae have different pigments to capture different wavelengths of light (eg. algae growing in the ocean can vary in colours)

Origin of these organelles (nucleus, mitochondria, chloroplasts)

-

Nucleus: may have formed from invaginations of the plasma membrane around the nucleoid of an ancient prokaryote. Nuclear envelope began forming likely due to a selective advantage (mutation) protecting DNA then evolving through natural selection.

-

Mitochondria: arose from primary endosymbiosis of a purple bacteria – this single event gave rise to the mitochondria in all eukaryotes. Outer membrane of bacteria disappears, genes transfer.

-

Chloroplasts: arose from primary endosymbiosis of a photogenic cyanobacteria – this single event gave rise to the chloroplasts in all algae and land plants. Outer membrane of bacteria disappears, genes transfer to nucleus.

Evidence for endosymbiosis (chloroplasts and mitochondria) -

Organelles appear morphologically similar to bacteria; surrounded by an outer membrane similar to a cell membrane while their inner membrane invaginates to form lamellae or cristae; mitochondria and chloroplasts are semi-autonomous, retaining their own genome (DNA, RNA); retain their own machinery for synthesising proteins; their metabolism is like existing prokaryotic organisms; the chloroplasts in some species still have the bacterial peptidoglycan wall between the inner and outer membranes.

Secondary endosymbiosis -

Secondary (or Eukaryotic) endosymbiosis *plastid with 3 or 4 membranes*: A chloroplast derived from an endosymbiotic, eukaryotic cell rather than a prokaryotic cell. Several protist groups such as; euglenoids, dinoflagellates and haptophytes obtained chloroplasts this way (Protistan pirates)

L6 The rise of the eukaryotic cell: Part 2 Partitioning and division of labour -

Distinct subcellular partitioning occurs within Eukaryotic cells (allows different processes to occur somewhat independently of each other, greater control and more complex patherways)

-

2 major eukaryotic cells: animal cells (nucleus, mitochondria *2 genomes*) and plant cells (nucleus, mitochondria, chloroplasts *3 genomes*)

The endomembrane and secretory system -

The endomembrane system: making, packaging and shipping proteins and molecules. A system of compartments that includes all of the membrane-bound components of the cell (including the nuclear envelope) except for the mitochondria, chloroplasts and microbodies

-

Major functions: provides a surface for biological reactions (for reach within cells allows movement of substances relatively easily); Establish a number of compartments to prevent mixing (division of reactions, staggers production of certain components – allows complex structures to be built in a stepwise manner); Provides transport of materials within the cell, from the cell to its exterior, or from the cell to an adjacent cell

-

Membranes: They always enclose a space: a cisterna or vesicle (no endpoint, completely enclosed); membranes are never open-ended, unless the cell is damaged; membranes have the consistency of olive oil in water, no stiff barriers as indicated in diagrams.

Structure and function of the Golgi apparatus, endoplasmic reticulum, vacuole, lysosomes -

Endoplasmic Reticulum (ER): considered the herat of the endomembrane system; consists of membrane cisternae that ramify through the cytoplasm. The result is internal compartments and channels; The ER is a dynamic structure, ever changing in structure and function; Rough ER has ribosomes attached; Smooth ER has no ribosomes; ER provides a surface for the synthesis of proteins, glycoproteins, carbohydrates and lipids – these biomolecules are then secreted throughout the endomembrane

-

Golgi Apparatus: consists of flattened stacks of membrane or cisternae, and are functional extensions of the ER and constantly receive vesicles from the ER. Golgi are polar structures.

-

Vesicles arrives at the cis face (receiving) and leave at the trans face (shipping); polysaccharides are also formed here. Many molecules such as hormones and digestive enzymes exit the Golgi in secretory vesicles and then exit the cell via exocytosis. Other molecules are packaged into vesicles such as lysosomes and remain within the cell.

-

Lysosomes: Recycle bins of the animal cell, surrounded by single membrane; breakdown material ingested by endocytosis or recycle old organelles (autophagy); Acidic interior and approximately 40 different hydrolytic enzymes derived from the rough ER and Golgi. Low pH (acidic) takes a large amount of energy to prevent it from exploding.

-

Plant vacuoles: The plant equivalent of lysosomes, surrounded by a single membrane called the tonoplast; Contain Hydrolytic enzymes and serve as degradative compartments; vacuoles also perform a diverse range of other functions: storage of nutrients, pigments and maintenance of cell turgor p...