Biology SL UNIT A

aqueous solution

aqueous solution

water with substances dissolve in

Metabolism

Reactants/products of most chemical reactions in living organisms dissolved in water

Reproduction

sperm swim to egg through water; mammalian foetuses are supported by water in uterus

Growth

cytoplasms is aqueous solution, so cell must absorb through osmosis to increase in size

Response to stimuli

nerve impulses are movements of dissolved Na+ and K+ ions; hormones transport is in blood

Excretion

Urine is aqueous solution of waste product; excretion of gas (CO2) requires moisture surface

Homeostasis

blood plasma + tissue fluid are aqueous solutions that are regulated to form stable and ideal internal environment for cells

Movement

aquatic organisms swim/drift through water current; pumping of blood and sap transports substances dissolved in water

molecule

2 or more atoms joined together by 1 or more covalent bonds

covalent bond

when 2 atoms share a pair of electron

Why is electrons not share equally

sometimes the nucleus of one is attractive to electrons than others ⇒ covalent bond is polar. One have slight positive charge and other have slight negative charge.

polarity

Molecules with polar covalent bond have polarity

Structure of water molecules

• water molecules are polar. Hydrogen have slight positive charge. Oxygen have slight negative charge.

• Intramolecular bond form between oxygen and hydrogen atoms in water molecule

• intermolecular bond form between positive pole of 1 water molecule and negative pole of another molecule is called hydrogen bond.

Hydrogen bonds are…

Individual hydrogen bond are weak, but water molecules are small so relatively large numbers of bonds form in volume of water. These bonds influence properties of water.

Cohesion

water molecule stick to each other (cohere) because of hydrogen bonds that form between them

Cohesion in water

• strong pulling forces (tension) are exerted to suck water up to the top in tubular xylem vessels. The columns of water molecules in the vessels rarely break despite the strong suction forces

• surface of water on pond is use as a habitat by some animal, even though they’re dense than water.

Surface tension

To break through water surface, hydrogen bond need to be broken. This requires more energy than available. The cohesive structure on the surface that resist breakage is called surface tension.

Adhesion

water stick to another substance. It occurs if other substance is hydrophilic.

Hydrophilic substance

Hydrophilic substances are attractive to water because they can make intermolecular bond with water molecule

Polar and charged materials are hydrophilic:

• polar substances e.g. cellulose. Cell walls remain saturated with water and draw the water from nearest supply if they have become unsaturated due to evaporation

• Capillary action: water drawn through narrow spaces due to adhesion with surfaces. Water moves through pores in dry soils because solids in soil (humus and particles of silt and clay) are hydrophilic. The water can move upwards.

Solvent properties of water linked to its role as a medium for metabolism and for transport in plants and animals

wide variety of hydrophilic molecules dissolve in water and that most enzymes catalyse reactions in aqueous solution. the functions of some molecules in cells depend on them being hydrophobic and insoluble.

Buoyancy

• Buoyancy is the upward force applied to an object in a medium and is determined by the density of the medium

• As water is more dense than air, it applies a greater upward force which allows objects to float in water

• The capacity of an object to float in water will be determined by its relative weight (heavier objects will sink)

Viscosity

• Viscosity is a measure of a fluid’s tendency to flow (more viscous fluids are more resistant to flow)

• Water is more viscous than air as it can form hydrogen bonds which increase the friction of flowing molecules

• Additionally, water can dissolve many solutes and these solutes can increase the viscosity of the solution

Thermal Conductivity

• Thermal conductivity is a measure of a medium’s ability to move heat across a temperature gradient

• Water absorbs and transfers heat more readily than air because water particles are packed more tightly together

specific heat capacity

the quantity of heat needed to raise the temperature of 1g of a material by 1ºC

Black-Throated Loon

• The loon has lighter (less dense) bones, allowing it to float on water (due to buoyancy) – however, the bones are not hollow like in many other birds of flight (allowing it to dive under water)

• Loons have difficulty walking on land because their legs are located at the rear to better propel them through water (higher viscosity)

• The loon’s feathers form an interlocking structure that functions as a barrier to water, preventing heat loss (water has higher thermal conductivity)

Ringed Seal

• The seal has denser bones than the loon, allowing it to stay submerged upon diving (less buoyant)

• The seal possesses a streamlined body to better propel them through water (higher viscosity than air)

• Ringed seals have an outer coat of fur that traps air for waterproofing and also has a thick layer of blubber to prevent heat loss while in water

• Ringed seals do not have many effective cooling mechanisms because water temperatures are generally stable (due to specific heat capacity) – this makes the seal particularly vulnerable to climate change

Water as medium of life

the first cells originated in water and that water remains the medium in which most processes of life occur.

DNA

the genetic material of all living organisms. Some viruses use RNA as their genetic material but viruses are not considered to be living.

Component of nucleotide

subunits in DNA and RNA are nucleotide

Nucleotide contains:

• a pentose sugar with 5 carbon atoms and a five-atom ring

• a phosphate

• Nitrogenous base

Sugar phosphate “backbone” of DNA and RNA

Nucleotides are linked together by covalent bonds between pentose sugar of 1 nucleotide and phosphate of the next one
Sugar and phosphates alternate in RNA and DNA molecules, with an unbroken chain of covalently bonded atoms in the sequence (-O-P-O-C-C)n (n is number of nucleotides).

⇒ chain of atoms is covalently bonded so it gives strength to DNA and RNA molecules, helping them to store information reliably for long periods.

Nitrogenous bases

The bases arranged in random sequence along a strand of nucleotides. The sequence forms the basis of the genetic code that all organisms use to store information

Nitrogenous bases pattern

Thymine/uracil - Adenine

Cytosine - guanine

formation of RNA

• polymer formed by condensation of nucleotide monomers

• Messenger RNA (mRNA) is the transcript copy of the DNA instructions (it encodes the protein sequence)

• Transfer RNA (tRNA) carries the protein subunits (amino acids) to the mRNA transcript

• Ribosomal RNA (rRNA) provides the catalytic activity for combining the amino acids according to the mRNA sequence

DNA as a double helix

Complementary base pairs: each base form hydrogen bonds with one other base, A-T and C-G.

There are 2 strands of nucleotides in DNA, and linked by hydrogen bond between bases.

⇒ 2 strands are antiparallel - they run alongside each other but in opposite directions

⇒ the strands are wound together to form a double helix

comparing DNA and RNA

1. Pentose is ribose in RNA. Pentose is deoxyribose in DNA.

2. DNA has base thymine but RNA has uracil

3. RNA has 1 strand of nucleotides whereas DNA has 2

Complementary base pairing roles

1. DNA replication: sequences of bases in DNA can be copied accurately, so the genetic information of a cell can be passed on to daughter cells.

2. Transcription: RNA can be made with the same base sequence as 1 of the 2 strands of a DNA molecule. Messenger RNA (mRNA) carries the base sequence of a protein-coding gene to the ribosome.

3. Translation: base sequence use to determine the amino acid sequence in polypeptide. Messenger RNA carries a series of 3 base codons. Each transfer RNA molecule (tRNA) has one 3-base anticodon and it carries 1 amino acid. Ribosomes link codons to anticodons by complementary base pairing, allowing the base sequence of every codon to be translated into a specific amino acid in a polypeptide.

diversity of DNA base sequences

The genetic information stored by DNA is encoded in the base sequence of the nucleotide chain

• DNA is composed of four bases, a DNA strand of x length would result in 4x different sequences

• This means that even a sequence as short as 10 bases could give rise to over 1 million combinations

• As the median length of a gene sequence is roughly 24 kilobases, there is a huge diversity of possible base sequences for any given gene

DNA is a compact and stable molecule ⇒ a limitless capacity for storing information

Conservation of the genetic code

DNA stores the instructions for the production of proteins in triplets of bases called codons

• Each codon codes for a specific amino acid – the order of codons in a gene sequence determines the order of amino acids in a polypeptide chain

The totality of all codon combinations and the amino acids represented by each is known as the genetic code

• The genetic code is considered universal – all living organisms on Earth use the exact same code (with some minor exceptions)

• The conservation of the genetic code across all life forms is considered evidence that all living organisms evolved from a universal common ancestor

Cell

basic structural unit of all living organisms. Also the smallest unit of self sustaining life

Microscopy skills
Skill 1: making temporary mounts

put cell/tissue on microscopy slide in a drop of water. Lower the cover slip to the sample carefully to avoid air bubbles. Ensure there’s only a thin sample on slide by squeezing out excess fluid

Microscopy skills
Skill 2: staining

Colourless/white structures in cell are hard to see unless it’s stain. Stain = pigment that binds to specific chemical. e.g. methylene blue binds to DNA so useful for revealing nuclei in cells. Stains are usually added to cells or tissues on the microscope slide before adding cover slip.

Microscope skill
Skill 3: Measuring sizes using eyepiece graticule

Graticule is scale placed inside eyepiece of microscope. Use as ruler to measure length of structure

Microscope skill
Skill 4: focusing with coarse and fine adjustment

• start with specimen and lens as far as possible

• use the coarse focusing knob to move specimen and objective lens closer until specimen comes into focus

• fine focusing knob can be used to get the sharpest possible focus/focus on particular level in specimen

fluorescent stains

absorbance of light and re-emission at longer wavelength.

Immunofluorescence stains

development of fluorescent staining. Antibodies bind to specific chemical in cell

Electron microscopes

Magnification can be increase with a microscope. Electron microscope have better resolution than light microscopes, so they can give higher magnification and smaller structures can be seen. It allows examine detailed structure (ultrastructure) of cells

Freeze fracture electron microscopy

use to produce images of surfaces within cells. A sample is plunged into liquefied propane at -190C so it rapidly freeze. A steel blade use to fracture the frozen sample.

⇒ This creates replica of fracture surface. replica is removed from frozen sample and examined using electron microscope

⇒ the sample thickness is thin → give impression of a 3D image without shadowing it

cryogenic electron microscopy

Cryo-EM use for research structure of protein. It analyses protein at instant in time when water around froze. Allowing researches of protein change from 1 form to another as they carried out function.

Frozen protein solutions with liquid ethane at -183C to create smooth vitreous ice and prevent formation of water crystal. Then computer algorithms produce a DE image of protein molecules.

DNA as genetic material:

needed for producing mRNA so protein can be synthesize

plasma membrane composed of lipids

controls movement of substances in and out of cell and allows different chemical conditions to be maintain (e.g pH).

cytoplasm composed mainly of water:

contains enzyme which catalyze for chemical reaction

Structure of procaryote cell

70s means they’re small in size

Cell wall made from peptidoglycan

Structure of eukaryote cells

Number of membrane
0	ribosomes, microtubules, microfilaments
1	rough ER, smooth ER, golgi apparatus
2	nucleus, mitochondria, chloroplasts

animal cell structure

plant cell structure

eukaryotic cells key cellular components

• The genetic material is found within a double-membrane structure called the nucleus 

• The ribosomes within the cell that are responsible for protein synthesis are comparatively larger in size (80S)

• Eukaryotes all share a number of membrane-bound organelles – including mitochondria, endoplasmic reticulum, golgi apparatus and vesicles

• Plant cells possess chloroplasts (for photosynthesis) and have a large, fluid-filled vacuole surrounded by a tonoplast membrane

• Multicellular fungi form filamentous hyphae that are typically separated by internal walls called septa

All prokaryotic key cellular components:

• The genetic material is found within a region of the cytosol called the nucleoid (the single DNA strand is called the genophore)

• Prokaryotes may contain additional DNA molecules (plasmids) that can be exchanged via bacterial conjugation (horizontal gene transfer)

• The ribosomes within the cell that are responsible for protein synthesis are characteristically small in size (70S)

• Prokaryotic cells all possess a cell wall and may possess an additional outer covering (a slime capsule called a glycocalyx)

• They may possess hair-like extensions called pili, that aid in adhesion (attachment pili) or plasmid exchange (sex pili)

• Additionally, many prokaryotes may possess several whip-like projections called flagella, which facilitate movement

Nucleus:

• double membrane structure with pores that stores genetic material

• a specific region, nucleolus is responsible for ribosome assembly

Mitochondria:

• responsible for ATP production via process of aerobic cell respiration

• have inner membranes that’s highly folded

Endoplasmic reticulum:

• ER membranous network that synthesize and transport materials via vesicles

• Smooth ER synthesize lipids, rough ER synthesis proteins (via ribosomes)

Golgi complex:

• assembly of folded membranes responsible for material excretion

• material is sorted, stored, modified, exported from the cell within vesicles

Vesicles:

• vesicles are membranous containers involved in transport and storage of materials

• lysosomes responsible for breakdown of cellular wastes and pathogen debris

• vacuoles are larger containers that store excess fluid and regulate pH

Chloroplast:

• responsible for photosynthesis (light energy → chemical energy)

• chloroplast use photosynthetic pigment chlorophyll to absorb and utilize light energy

Centrosome:

• function of microtubule organizing centres composed of paired centrioles

• contribute cell division

Metabolism:

produces enzymes to catalyse chemical reaction in cytoplasm

Reproduction:

reproduces asexually using mitosis or sexually using meiosis and gametes

Growth

increases in size and dry mass by assimilating digested foods

Excretion:

metabolic waste products diffuse out of the cell

Nutrition:

feeds on smaller organisms which are engulfed by endocytosis and digested in vesicle

Movement:

draws cytoplasm from 1 side of the cell and uses it to extend the cell from the other side (ameboid movement)

Response to stimuli

e.g. moving towards higher concentrations of peptides released by bacteria

Homeostasis

regulate internal conditions, expelling excess water using contractile vacuoles

Cell walls in plant and fungi

Plant: cellulose
Fungi: Chitin

Vacuole in plant and fungi and animal

Large permanent vacuole in cells of fungi and plants. use for storage substances and pressurizing the cell.

small temporary vacuole occur in animal cell, where it have contractile vacuoles that expel excess water by exocytosis and food vacuoles that digest food or pathogens taken in by endocytosis

Plastids in plant

Plant cells have varied types such as chloroplasts (photosynthesis) and amyloplasts (to store starch).

centrioles in animal

Use in animal cells to organize assembly of spindle of microtubules during mitosis and meiosis

cillia and flagella in animal

generate movement by beating action. Animal cell have many cilia, which are small and move fluids adjacent to cell. e.g Male gametes have single flagellum → sperm to move

Anucleate

don’t have nucleus so can’t transcribe DNA to make mRNA and can’t synthesize protein