Georgia White – BIOL1903

MODULE 1.1: The microscope

• Carry upright, both hands • Base 5cm from edge of bench • Determine if dirt on slide – move slide, dirt will move • Determine if dirt on eyepiece – rotate eyepiece, dirt will move • Determine if dirt on objective lens – change objective lens, dirt disappears Clean eyepiece and objective lens – lens cleaning tissues, 70% ethanol cleaning

solution Parts of a microscope

Setting up the microscope 1. Check lenses are clean and undamaged 2. Swing LP objective into line 3. Switch on light source 4. Adjust light intensity - 4-5 adequate for most specimens 5. Position slide on stage 6. Focus on specimen - course focus knob 7. Raise condenser and open iris diaphragm, move specimen aside 8. Lower condenser until paper on light source is in focus 9. Adjust iris diaphragm by removing eyepiece and closing diaphragm until ¾ of FOV is

illuminated 10. Replace specimen, focus with fine focus knob 11. Centre specimen 12. Positon HP objective 13. Adjust iris diaphragm 14. Fine focus

Georgia White – BIOL1903

• Magnification - the enlargement of an image • Minimum resolved distance - the minimum distance at which 2 objects can be

identified as distinct from each other • Maximum resolving power - obtained when the cone of light just fills the lens of the

objective • Lenses in condenser – control focus of light by moving up and down • Iris diaphragm – controls amount of light reaching the objective • Image seen through the eyepiece is inverted and magnified

Troubleshooting FOV too bright/dull → Check lamp intensity → Check opening of iris diaphragm Poor contrast → Close iris diaphragm Poor resolution → Move condenser up → Open iris diagram

Making a wet mount

1. Cell sample on slide 2. Drop of methylene blue stain structures containing nucleic acids 3. Add coverslip 4. Remove excess stain with blotting paper

Biological drawing

• Pencil • No shading/colour • Ruled label lines, parallel to bottom of page, no arrowheads • Title • Scale bar

o So drawing can be related to size of specimen o Horizontal o Units should be whole numbers, represent ¼-⅓ of the size of the drawn object

• Double lines to indicate hollow structures • 𝑎𝑝𝑝𝑟𝑜𝑥. 𝑠𝑖𝑧𝑒 𝑜𝑓 𝑎𝑛 𝑜𝑏𝑗𝑒𝑐𝑡 = 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑡𝑖𝑚𝑒𝑠 𝑜𝑏𝑗𝑒𝑐𝑡 𝑓𝑖𝑡𝑠 𝑎𝑐𝑟𝑜𝑠𝑠 𝑑𝑖𝑎𝑚𝑒𝑡𝑒𝑟 𝑜𝑓 𝐹𝑂𝑉

𝑠𝑖𝑧𝑒 𝑜𝑓 𝐹𝑂𝑉

Georgia White – BIOL1903

MODULE 1.2: Cell structure

Levels of organisation

• Atomic • Molecular • Cellular

Cell Theory ➢ A cell is the basic structural and functional unit of living organisms ➢ Composition of a cell defines its function within the body ➢ New cells arise from pre-existing cells

• Tissue o Connective o Muscle o Epithelial o Nerve – integrates into other layers

• Organ • Organ system • Organism

Organelles

➢ Compartmentalise biochemical reactions → efficient without negating each other ➢ Different shapes depending on function and location

Organelle Structure

Function Nucleus Contains DNA – 23 pairs of chromosomes in humans

Directs cell processes Nucleolus Contains protein and RNA

rRNA synthesized and combined with proteins Nuclear membrane Separates nucleus from cytoplasm

Nuclear pores Controls exchange between nucleus and cytoplasm

Cytoplasm Semi-fluid material in which organelles are found Site of metabolic processes

Ribosome May be attached to rough ER or free in cytoplasm Protein synthesis

Mitochondrion Double membrane, inner membrane highly folded SA:V for aerobic cellular respiration (ATP production) Theory: bacteria internalised by early cell, symbiotic relationship

Endoplasmic reticulum (ER)

• A network of membranes forming sacs and tubules • Extends from nuclear membrane to cytoplasm

Rough ER Many ribosomes attached Protein synthesis and transport

Georgia White – BIOL1903

Smooth ER Lipid synthesis Detoxification of chemicals Special type = sarcoplasmic reticulum

o Specialised o Produce Ca o Large conc. in skeletal system

Golgi body Closely packed stacks of curved, membrane-bound sacs Stores, modifies, packages and distributes proteins and lipids

made by ER in secretory vesicles that pinch off from margins of Golgi apparatus

Secretory vesicle Formed by golgi body Contains materials produced in cell Secreted by exocytosis

Lysosome Formed by golgi body Contains hydrolytic enzymes – digest material taken into a cell (cellular digestion) Exocytosis - fuse with membrane of a cell and release contents Endocytosis - cell membrane internalises contents of vesicle

Microtubule Hollow structures Support cytoplasm Assists in cell division Forms components of cilia and flagella

Centriole Facilitate movement of chromosomes during cell division Cilia Project from cell surface (many)

Actively move Move substances over cell surface e.g. mucus in respiratory tract

Flagella Sperm cell surface (one) Actively move Propel sperm cells

Intermediate filaments Mechanical support for cells Actin, myosin

Microfilaments Microvilli

Extensions of cell surface (many) Don’t actively move ↑SA of certain cells Abundant on surface of cells that line intestine, kidney (where

absorption is important) Cell membrane Phospholipid bilayer

• Centre – lipid tails = hydrophobic • Outside – phosphate heads = hydrophilic

Regulates movement of substances into and out of cells - ie. between intracellular and extracellular fluids

Protein channels Passive – allow movement across a gradient – high to low conc. Active – requires energy to move ions across membrane

Georgia White – BIOL1903

Georgia White – BIOL1903

Surface area to volume ratios

Cell ↑ size → ↓SA per unit of V across which to exchange substances → ↓ r of diffusion (nutrients, gases, wastes) → determines max. size a cell can grow to - must be sufficient enough to provide for cell Can ↑ max size with…

● Intracellular transport system e.g. ER ● Compartmentalise processes - organelles

→ determines r of heat loss - smaller cells/animals will lose heat at a faster rate Cell metabolism – all chemical reactions occurring in a cell

➢ Energy released from the breakdown of food molecules – used to produce ATP ➢ Aerobic respiration of 1 glucose 36-38 ATP ➢ Anaerobic respiration lactic acid (animals)

Genes in 1940-1950s

• Genes carried on chromosomes • Chromosomes consist of protein and DNA • Proteins – key component of organisms • DNA – consists of 4 nucleotides, structure unknown

Linus Pauling • Believed proteins were likely to be hereditary material • DNA contains only 4 nucleotides too simple • Proteins contain 20 aas able to make complex and diverse materials

Experimental evidence that DNA is hereditary material

1. 1928: Griffith’s work on streptococcus pneumoniae o S strain DNA survived heating o R strain takes in S strain DNA R strain can now kill mouse o S strain DNA has polysaccharide coating immune to host’s immune system

kill host o ⸫ by taking in S strain, R strain is immune able to kill host

Georgia White – BIOL1903

2. 1944: Avery

o Follows up from Griffith’s work o Proved DNA carries genetic info o Destroyed components of S strain 1 by 1 while keeping R strain intact o When DNA of S strain was destroyed the mouse lived DNA carries genetic

info Linus Pauling

• Began to accept DNA as hereditary material • Published ‘tripe helix’ model

Watson and Crick

• Used modelling, chemistry and physics • Structure of nucleotides and bases • Chargaff’s rules of base comp.

o A = T and C = G o A = G and T = C

• Franklin’s crystallography photos contained info about… o Double helix structure o How fast helix spins o Distance between molecules

DNA

Structure

• Long chain of nucleotides • Nucleotide – sugar, phosphate base, nitrogen base • Backbone – sugar, phosphate • Complementary base pairs – AT, GC

Georgia White – BIOL1903

• Twisted into a double helix • Anti-parallel strands – each strand runs in opposite direction

Replication

• Occurs during mitosis and meiosis • Semi-conservative – resultant DNA strand made up of new strand and original strand

1. DNA unwinds

o Enzyme = helicase – breaks hydrogen bonds between complementary bases 2 template strands

2. Free nucleotides from cell match with exposed bases o Cell manufacturers nucleotides from raw materials the organisms obtains from

environment o Enzyme = polymerase

▪ Can only add bases in 1 direction: 5’ 3’ i.e. can only add new bases to 3’

• New units can only be added to 3’ due to chemical comp. of nucleotides i.e. what the C atoms are bonded to

o 3’ hydroxyl group (–OH) o 5’ phosphate group

▪ Leading strand – bases added to 3’ ▪ Lagging strand – DNA synthesis is discontinuous short Okasaki

fragments 3. 2 identical strands produced

o Enzyme = ligase – seals up fragments in both strands All cells need a complete copy of DNA to be able to function properly – cell division

for growth and repair, reproduction Protein synthesis gene expression

• DNA directs production of proteins enables cell specialisation o Structural components of cells o Enzymes – regulate chemical reactions

• Transcription – making a copy of the info in a gene • Translation – converting copied info into a protein

Structure of RNA

• Single stranded • Ribose sugar

Georgia White – BIOL1903

3 types

• mRNA – messenger – carries genetic info from DNA in nucleus to ribosomes in cytoplasm

• tRNA – transfer – carries aas to ribosomes, 3 unpaired bases (anti-codon) on 1 end, other end is able to temporarily bind to aa (specificity)

• rRNA – ribosomal – form a structural part of ribosomes Transcription

• Occurs in nucleus • Info on template DNA strand copied to form mRNA molecule 1. DNA unzipped over a short length (the part that holds the gene to be used)

o Enzyme = helicase/RNA polymerase o Reads DNA from 3’ 5’ o Produces mRNA by adding nucleotides to 3’ end (A, U, C, G)

o 1 strand used as a template 2. RNA nucleotides assembled forming a single stranded mRNA molecule i.e. DNA is

transcribed into mRNA o Enzyme = polymerase – joins nucleotides

3. When mRNA polymerase reaches the termination site o Introns removed o Remaining exons connected mRNA o mRNA detaches and is transported out of nucleus and binds to ribosomal

subunit in cytoplasm o DNA zips back up

Translation

• Occurs at ribosomes

• Polypeptides are assembled using the info on the mRNA molecule 4. tRNA molecules carry appropriate aas from the cytoplasm to ribosome

o mRNA must be made because DNA can’t leave nucleus o mRNA leaves through nuclear pore o aas brought to ribosome in order directed by mRNA

5. tRNA molecules with anti-codons corresponding to mRNA codons temporarily attach – transcription begins when a start codon is read

6. Further tRNA molecules attach and a polypeptide chain is formed as aas join by peptide bonds – transcription stops when a stop codon is reached

7. Polypeptide chain released into cytoplasm 8. mRNA is broken down into nucleotides to be reused

mRNA reading frames

• Since each aa corresponds to 3 bases, there are 3 possible reading frames in the mRNA

Georgia White – BIOL1903

• Open reading frame (ORF) o Makes sensible transcript o Contains start codon, 100s of codons, stop codon

Amino acids

• Made up of 3 bases • AUG – start codon • Redundancy – several codons code for same aa

The central dogma of gene expression

𝐷𝑁𝐴𝑠𝑡𝑜𝑟𝑒𝑠 𝑔𝑒𝑛𝑒

𝑡𝑟𝑎𝑛𝑠𝑐𝑟𝑖𝑝𝑡𝑖𝑜𝑛→

𝑚𝑅𝑁𝐴𝑖𝑛𝑡𝑒𝑟𝑚𝑒𝑑𝑖𝑎𝑡𝑒 𝑐𝑎𝑟𝑟𝑖𝑒𝑟 𝑜𝑓 𝑖𝑛𝑓𝑜

𝑡𝑟𝑎𝑛𝑠𝑙𝑎𝑡𝑖𝑜𝑛→

𝑝𝑟𝑜𝑡𝑒𝑖𝑛𝑒𝑥𝑝𝑟𝑒𝑠𝑠𝑖𝑜𝑛 𝑜𝑓 𝑔𝑒𝑛𝑒

Cell cycle

• Mitosis – the division of the cell nucleus to produce 2 daughter nuclei identical to parent cell

• Cytokinesis – division of the cytoplasm to form separate daughter cells immediately after mitosis/meiosis

• Chromosome – a gene-carrying structure found in the nucleus, consists of a long DNA molecule

• Chromatid – one of the 2 identical strands that make up a chromosome after replication during interphase

• Centromere – the centralised region that joins 2 chromatids, spindle fibres attach here during mitosis/meiosis

• Nucleus – chromosome-containing organelle of a eukaryotic cell • Spindle – structure formed between 2 opposite poles of a cell during mitosis/meiosis,

formed by microtubules, guides movement of chromosomes • Centriole – produces spindle during mitosis/meiosis (animal)

Stages of the cell cycle

1. 1st growth stage 2. Synthesis stage ⇒ 1-3 = interphase 3. 2nd growth stage 4. Mitosis

Mitosis (IPMAT)

Georgia White – BIOL1903

1. Interphase ➢ Cell carrying out normal metabolic

functions ➢ Replication of DNA

2. Prophase ➢ Long thin chromatid pairs condense as the

chromatin becomes super coiled ➢ Nuclear envelope disappears ➢ Centrioles move to opposite ends of the cell

and for the spindle 3. Metaphase

➢ Chromatid pairs line up on spindle at midline of cell, attached at centromere

4. Anaphase ➢ Spindle fibres begin to shorten pulling

centromeres apart ➢ Chromatid pairs separated into single

chromosomes 5. Telophase

➢ Chromosomes reach poles of the cell ➢ Nuclear membrane reforms

6. (Cytokinesis) ➢ Division of cytoplasm ➢ Beginning of formation of a cleavage

furrow MODULE 1.3: Skeletal system

Anatomical position

• Standing erect • Eyes looking forward • Arms at sides • Palms and toes directed forward ➢ Position of body affects description of body parts relative to each other relational

descriptions always based on the anatomical position

Directional terms

Right Towards body’s right side Right ear Left Toward body’s left side Left ear Superior Above The mouth is superior to the chin Inferior Below The nose is inferior to the forehead Anterior Toward the front The teeth are anterior to the throat Posterior Toward the back The brain is posterior to the eyes

Georgia White – BIOL1903

Ventral Toward the belly (4 legged animals) The naval is ventral to the spine Dorsal Toward the back (4 legged animals) The spine is dorsal to the breast

bone Proximal Closer to a point of attachment The elbow is proximal to the wrist Distal Further from a point of attachment The knee is distal to the hip Medial Toward the midline The bridge of the nose is medial to

the eye Lateral Away from the midline The nipple is lateral to the breast

bone Superficial Toward the surface The skin is superficial to muscle Deep Away from the surface The lungs are deep to the ribs

Planes of section of the body

Sagittal Divides body into right and left parts Midsagittal Divides body into equal halves, passing through the midline Transverse Divides body into superior and inferior parts Coronal Divides body into anterior and posterior parts