BIOL1020 - University of Queensland

The hierarchy of biological classification

Domain

Kingdom

Phylum

Class

Order

Family

Genus

Species

• Macromolecules

Polymers that are made up of monomers (Carbohydrates, Proteins, Lipids, Nucleic Acids)

Dehydration Reaction

Add a monomer to a generic polymer - hydrogen and a hydroxide group join when water is released

Hydrolysis Reaction

supply water molecule and split the molecule into two original

Carbohydrates

Monosaccharides, Disaccharide's and Polysaccharides.

Disaccharides

Are glycosidic bonded or linkages between two saccharides or disaccharides e.g. maltose (alpha-configuration) or cellulose (beta-configuration)

Alpha-Configuration

joining of ring carbohydrates between

H-C-OH and H-C-HO (1-4 bonds), which release water when joined together

Beta-configuration

joining ring carbohydrates between

OH-C-H and H-C-HO (1-4 bonds), which release water when joined together

Polysaccharides

e.g. starch and glycogen

Starch

(polymer of glucose monomer) major storage of energy in plants, has 1-4 and 1-6 linkages

- humans can digest this as it's in alpha-configuration

Glycogen

(polymer of glucose monomer) major storage of energy in animals, has 1-4 and 1-6 linkages

- humans can digest this as it's in alpha-configuration

Cellulose

Major component in tough walls in plant cells,

- mammals can't digest this as it's in beta-configuration

Glycemic Index

Measuring how quickly your blood glucose level rises after eating carbohydrate-containing food

- quicker digestion the faster glucose level increases

- Low GI foods (brown rice & bread) - harder to break down because unrefined carbs

Glycoproteins

Combination of Carbohydrates and Proteins

- found on cell surface

- can be the unique identifier of different cell types (immune to non-self cells)

Chitin

exoskeleton of arthropods/ cell wall in fungi

- highly resistant to enzymatic activity

- used in surgical thread

Lipids

Constructed from two types of smaller molecules, a single glycerol and usually three fatty acids

- Found in cellular membrane structures, storage compounds

- Hydrophobic

- vary in length and number and locations f double bonds they contain

Saturated Fatty Acids

have the maximum number of hydrogen atoms possible

- no double bonds

- straight/ overlapping is easy

Unsaturated Fatty Acids

Have on or more double bonds

- changes structure to have bends

- harder to pack on top of each other

Trans Fats

A type of unsaturated fatty acid that doesn't bend at the double bond like normal

- easier to pack on each other

Phospholipid

- Have two fatty acids

- have a phosphocholine group instead of a third fatty acid

- quite charged and makes the head hydrophilic

- hydrophobic tails

- result in bilayer arrangement found in cell membranes to allow semi-permeability

Proteins

Consists of one or more polypeptides (polymer of amino acids)

Amino Acids

- Organic molecules possessing both carboxyl and amino groups - Differ in their properties due o differing side chains, called R groups

- Compare the chemical structure of amino acid - all have amino terminus and carboxyl terminus

- 20 amino acids that we know of

Four levels of Protein structure are:

Primary

Secondary

Tertiary

Quarternary

Primary structure of Protein is:

amino acid sequence / linear changes

Secondary structure of Protein is:

either forms alpha-helix (loops round and round) depending on the proteins or beta-sheet (ladder-like structure)

Tertiary structure of Protein is:

folding of the proteins (3D structure)

Quaternary structure of Protein is:

add on more then one structure forming one big complex structure

Enzymes:

Specific Type of Protein

Enzymes do:

- bind to catalyse a reaction

- highly specific for their substrates and reactions - determined by protein structure

- speed up metabolic reactions by lowering energy barriers

e.g. Alcohol Dehydrogenase (ADH)

- breaks down alcohol

- high amounts in stomach and liver

What does DNA stand for?

Deoxyribonucleic Acid

What does RNA stand for?

Ribonucleic Acid

What is the importance of DNA?

- Stores information for the synthesis of specific proteins

- Directs RNA synthesis

- Directs protein synthesis through RNA

What are the variable subunits of DNA?

Nitrogenous Bases: A (adenine), C (cytosine) , G (guanine) , T (thymine)

Meselson-Stahl Experiment

- Labeled the DNA so the new synthesis could be differentiated from the DNA present

- How did they tag the DNA - nitrogen (continually integrated into the DNA)

- Semi-conservative - evenly distributed

- Conservative replication - all of one and none of the other

- Dispersive replication - randomly distributed but not equal

- 15N (old DNA) 14N (newly synthesised DNA/lighter)

Bacterial Cell - Where does DNA begin?

- (schematic) Bacterial starts at the 'origin' - proceeds in both directions until the entire chromosome has been copied

Animal Cell - Where does DNA begin?

Unwinding the double helix without creating knots:

Helicase, topoisomerase, single-strand binding protein

Helicase

untwistis the DNA helix to give single stranded DNA, but increases coiling ahead of the replication fork

Topoisomerase

'Fixes' the increase coiling in the DNA template

- prevents supercoiling by transiently nicking both strands and allowing the two strands to rotate around each other

Single-strand binding protein

stabilises the single stranded template

How is new DNA synthesised?

- using nucleotide building blocks

- proceeds always in 5' to 3' direction

DNA polymerases

catalyse DNA synthesis

- have exonuclease activities that enables proofreading and editing (mismatch repair)

DNA primase

synthesises RNA primer

RNA Primer

(only begins at the first couple before letting DNA polymerase take over) and is removed by the action of the 5' exonuclease activity of DNA polymerase I

DNA polymerase III

extends on the RNA primer

Synthesis of the lagging strand

- new RNA primers have to be made frequently to keep DNA synthesis going

- creates lots of DNA fragments (OKAZAKI fragments)

- DNA ligase joins the OKAZAKI fragments to create a continuos strangs

Mutations:

caused if mismatched/damaged bases are not repaired.

- mutations are the basis of many disorders including cancer

Telomerase

is an enzyme that created an extension to the unreplicated end of DNA strand

DNA primase and DNA polymerase III can then synthesise the lacking piece of DNA

Plasma Membrane ( lipid membrane)

important for exchange of nutrients and other compounds with the environment

- Phospholipids

- Cholesterol control the fluidity

- Membrane proteins - cell recognition/transmitters/porters

- carbohydrates (attached to the outside and attachment sites for the cytoskeleton)

Three basic cells in life

Bacterial, Animal, Plant

Bacterial Cells:

extremely simple looking cells, extremely versatile regarding the environment in which they can occur

- can survive in inhospitable environments

- NOTE: bacteria Archea have visually similar cells but and Archea are more closely related to eukaryotic cells

- also supreme inhabitants of other organisms

What are the shapes of bacteria?

- Coccus

- Coccobacillus

- Bacillus

- Vibrio

- Spirilium

- Spirochete

Bacterial Cell is a single chamber:

All processes occur in the same space

- in the cytoplasm or in the cell membrane

i.e. energy generation, protein synthesis, DNA replication, Synthesis of cell components

Fimbriae

Help to attach to the surface (to help living)

Flagellum/pili

will allow them to move to another surface or are for nutrients and accessibility

- Nano machines (clutch protein) that puts the flagellum into gear or into neutral

Nucleoid

contains DNA, proteins and RNA and may also contain plasmids (cloning runs via plasmids_

Gram-Negative Bacterial Cell

PINK

in the periplasm - peptidoglycan is a polysaccharide a rigid polymer defines the cell shape - dye molecule will wash out because the wall is so thin

Gram-Positive Bacteria Cell

PURPLE

peptidoglycan defines cell shape (very thick cell wall) and will retain the layer of stain

Eukaryote - Nucleus

Dominant organelle in the cell

- Surrounded by a double nuclear membrane

- Pores (nuclear pores) highly structured assemblies of proteins - very selective in what they let through - an entry and exit point of the nucleus

- Contains DNA + Protein = chromatin

- Another structure inside - Nucleolus ("little nucleus" dense structure): ribosomes are assembled

Endoplasmic Reticulum

- Continuous with the membrane of nucleus

- ROUGH ER - proteins are synthesised - to be transported to certain places in the body

- Ribosomes: protein synthesis

- Found free in cytoplasm and attached to the RER in mitochondria and chloroplasts

Mitochondria

Energy Generator

- Double membrane (outer) which is smooth and the inner which is folded up to give more surface area (cristae)

- Site of respiration (process of harvesting of energy from food molecules) in BOTH animals and plant cells

- Semi-autonomous with their own DNA and ribosomes

- Can move around the cell with the help of the cytoskeleton - needed even distribution

Cytoskeleton

- Essential for cell shape and cell support and cell movement

- Three types of filaments

- Microtubules

- microfilaments

- intermediate filaments

Microtubules

largest 25 nm

- Diameter

- Dynamic

- Used in eukaryotic flagella

- Plus end and a minus end

- Assembles from various units that fall apart at the minus end and added to the positive end

- Highways for transport

- Helps move the mitochondria

Microfilaments

Smallest 7nm

- Key for cell division

- Made of actin, monomers, dynamic

Intermediate filaments

Middle 8-12 nm

- Stable (support function)

- Can be made of different monomers

Golgi Apparatus

postage service/packaging and distributing of proteins

Lysosomes

membrane bound - digestive compartment

Peroxisomes

cells detoxification centres

Vacuoles

(mostly in plant cells)

- storage and detoxification

Cell wall

(plant and fungi Only)

- cell stability

Endosymbiont Hypothesis

- Mitochondria and chloroplasts came from prokaryotic cells that develops symbiotic relationship with another cell

- Mitochondria appear to have bee derived from aerobic respiring alpha proteobacteria

- Chloroplasts appear to have been derived from oxygen evolving photosynthetic cyanobacteria

Plant cell - Chloroplasts

Found in Plant cells

- Site where photosynthesis occurs

- Harvest sugars

- Contains 3 membrane systems

- Outer

- Inner - surrounds the stroma which contains soluble enzymes, ribosomes, DNA and thylakoids

- Thylakoid

• Contains chlorophyll - green colour

Energy

Capacity to do work

First law of thermodynamics

- Energy of universe is constant

- Energy can be transferred and transformed, but I cannot be created or destroyed

- Every organism or cell as a system - can convert energy from all surroundings but lose energy as well to the universe

Second law of thermodynamics

- Every energy transfer of transformation increases the entropy ('disorder') of the universe

Gibbs free energy

within a certain system (keeping everything else constant) can find the amount of free energy that occurs during the reaction

Catabolic reaction / exergonic

break down molecules and release energy

- neg delta G

- Release energy

- Has activation energy barrier

- Reactant energy level: HIGH

- Product energy: LOW

Anabolic reaction / endergonic

- pos delta G

- consume energy

- invest a lot of energy to reach activation energy

- still activation energy barrier

- save the molecule to save for later

- reactant energy level: LOW

ATP synthesis - hydrolysis

- Most common forms of stored cellular energy - ATP (adenosine triphosphate)

- Contains chemical energy in bonds between 3 phosphate groups

- After breaking down nutrients, the energy released is converted to ATP

- When ATP broken down to ADP (1P removed) this energy is released and can be used

Autotrophs

Producers

Heterotrophs

Consumers

Exergonic

spontaneous / still have activation barriers - the amount that put in is more that what is given back

- To do this cells break down glucose in multiple steps

- At each step electrons are moved between the reactants and products to enable breaking of chemical bonds

- These reactions are called REDOX reactions

- This allows the controlled release of energy that can then be transformed into ATP

Cellular respiration: Stage I: Glycolysis

- Produces two molecules of pyruvate from 1 molecule of glucose

- Produces two NADH and two ATP (net) by substrate-level phosphorylation (adding phosphate group to ADP/ really fast)

- Uses 10 individual enzymatic steps

Cellular respiration: Stage II: pyruvate decarboxylation & citric acid cycle

- Produces acetyl-Coa (after carboxyl group has been broken off) and carbon dioxide

- CoA = coenzyme A, it becomes linked to the acetate molecule during the reaction

- Catalysed by an enzyme complex called pyruvate dehydrogenase

- Produces 1 NADH/pyruvate and no ATP

- This process runs through twice for every single molecule of glucose

Cellular respiration: Stage IIb: Citric acid cycle

- Produces 2 Co2 from 1 Acetyl CoA (keep in mind that 1 glucose molecule generates 2 pyruvates which makes 2 Acetyl CoA)

- Produces 1 FADH2, 3NADH and 1 ATP (via GTP) by substrate phosphorylation per acetyl-CoA

- Uses 8 individual enzymatic steps

Cellular respiration: Stage III: oxidative phosphorylation

- Produces 30-32 ATP per glucose molecule

- Input NADH & FADH2

- Consists of two phases

- Electron transport chain (creates a proton gradient) - fuels chemiosmosis

- Moves across 4 complexes inside the mitochondrial matrix, whilst NADH binds to a bridge transport chain the transports the H+ across the membrane into the intermembrane space and turns into NAD

- FADH2 powers a second bridge

- This continues for the whole chain until the last complex when if oxygen is there to catch the H then the ATP can be produced if not all the energy is wasted

- Creates a proton gradient

- ATP synthase allows enough protons back into the cell to release the energy to make 1 ATP - if more than what needed there is still only enough to make 1 ATP and the rest of the energy is lost

- Chemiosmosis (forms ATP) transporting chemicals through membrane