BIOL1020 - UQ

triacylglycerol

Lipid composed of a glycerol molecule and 3 fatty acids. Joined with an ester linkage.

Amphipathic molecules

have both hydrophilic and hydrophobic properties

phospholipid bilayer

Plasma membrane layers composed of phospholipid molecules arranged with polar heads facing the outside and nonpolar tails facing the inside.

passive transport

Requires NO energy, Movement of molecules from high to low concentration, Moves with the concentration gradient

Active Transport

Energy-requiring process that moves material across a cell membrane against a concentration difference

prokaryotic cell

1. No true nucleus

2. No membrane bound organelles

3. Ribosomes and DNA free floating

4. Unicellular

Eukaryotic cell

1. True nucleus

2. Membrane bound organelles

3. Ribosomes on Rough ER and DNA in nucleus

4. Multicellular

Endosymbiosis

The original internalisation of prokaryotes by an ancestral eukaryotic cell resulting in the formation of mitochondria and chloroplasts.

Organelles (ALL)

1. Nucleus-command centre

2. Nucleolus-Ribosomes produced

3. Nuclear envelope-membrane between cytoplasm/nucleus

4.Nuclear pore-opening that regulates passage

5. Rough ER-Contains ribosomes (Synthesise proteins)

6. Mitochondria-converts glucose into ATP

7. Lysosome-contains hydrolytic enzymes which breaks down macro molecules

8. Smooth ER-Manufacture lipids and metabolise carbohydrates and detoxify the cell

9. Golgi Complex-Collects, packages and modifies macromolecules and exports them

10. Peroxisome contain digestive enzymes

11. Centrioles-organise microtubules for structure

12. Vacuole hold material/waste

Organelles (PLANTS)

1. Large central Vacuole-hold material/waste

2. Chloroplasts-site of photosynthesis

3. Cell wall-gives structural support to plants

saturated vs unsaturated fats

saturated have NO double bonds

unsaturated have double bonds

cis vs trans fatty acids

Cis-have hydrogen on the same side of the C chain

Trans-have hydrogen bonds on different sides of the C chain

Macromolecules

A very large organic molecule (Polymer) composed of many smaller monomers

Carbohydrates

Macromolecules that provide structure

Dehydration (Condensation) Reaction

a reaction in which two molecules are covalently bonded to each other through loss of a water molecule

hydrolosis reaction

Water is added to molecule to separate polymers (many pieces) into monomers (one piece)

Starch

-Multiple Alpha glucose molecules undergo condensation reactions

-Amylose (1,4 bonds)

-Amylopectin (1,6 bonds and 1,4 bonds) branched

Glycogen

An extensively branched glucose storage polysaccharide ( Alpha 1, 6 bonds and 1, 4 bonds (LIKE amylopectin)

cellulose

Beta 1,4 bonds, BUT every second glucose molecule is flipped

glycemic index

- A measure of how quickly your blood glucose level rises after eating.

Glycoproteins

Membrane carbohydrates that are covalently bonded to proteins. (RESPONSABLE for cell-cell recognition)

amino acids

Monomers of proteins (N terminus=Amino Group) (C terminus=Carboxyl group)

Primary structure

The first level of protein structure, sequence of amino acids

Secondary Structure

The second level of protein structure; the regular local patterns of coils (ALPHA HELIX) or folds (BETA PLEATED SHEETS) of a polypeptide chain.

tertiary structure

The third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain. (Disulphide bonds, ionic bonds, hydrogen bonds and dispersion forces)

quaternary structure

The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits.

Rough Endoplasmic Reticulum

System of internal membranes within the cytoplasm. Membranes are rough due to the presence of ribosomes. functions in transport of substances such as proteins within the cytoplasm to the GOLGI BODY

Microtubules (Cytoskeleton 1)

-25nm Diameter

-Made of Tublin polymers

-Key for eukaryotic flagella

-DYNAMIC=MICRO

Microfilaments (Cytoskeleton 2)

-7nm Diameter

-Made of Actin Monomers

-Key for Cell Division

-DYNAMIC=MICRO

Intermediatefilaments (Cytoskeleton 3)

-8-12nm Diameter

-Made of Fibrous subunits (Keratins collided together)

-Key for support/Structure

-STABLE

Metabolism

All of the chemical reactions that occur within an organism

Thermodynamics

1st Law- Energy can be transferred/transformed

2nd Law- Every energy transfer/transformation increases the entropy of the universe

Endergonic Reactions and Exergonic Reactions

ENDERGONIC-Energy absorbing reactions (+ DELTA G NON-Spontaneous)

EXERGONIC-Energy Releasing reaction (- DELTA G Spontaneous)

4 steps of cellular respiration

1. Glycolysis

2. Pyruvate Oxidation

3. Citric acid cycle

4. Oxidative Phosphorylation (Electron transport and chemiosmosis)

Glycolysis

the breakdown of glucose by enzymes, releasing energy and pyruvic acid.

INPUT: Glucose, 2ATP, NAD+ and 4H+

OUTPUT: 2NADH, 2H+ 2H2O and 2 pyruvate

Pyruvate oxidation

Conversion of pyruvate to acetyl CoA and CO2 that occurs in the mitochondrial matrix in the presence of O2.

INPUT: Pyruvate, NAD+ and Coenzyme A

OUTPUT: Acetyl-COA, NADH and CO2

Citric Acid Cycle

A chemical cycle involving eight steps that completes the metabolic breakdown of glucose molecules to carbon dioxide; occurs within the mitochondrion;.

INPUT: 2 Acetyl CoA, 6 NAD+, 2 FAD,

OUTPUT: 2 cycles so 2x (FADH2, 3NADH and 1ATP)

oxidative phosphorylation (ETP and Chemiosmosis)

Made of 2 parts, The Electron Transport Chain and Chemiosmosis (Proton Gradient that can be converted into energy to create ATP).

INPUT: 9NADH, 2FADH2 and O2

OUTPUT: 26-28 ATP per glucose molecule NAD+ and FADH

DNA strcuture

A 5 Carbon sugar (deoxyribsoe)

A phosphate group

A nitrogenous base (A-T G-C and U-A) Triphosphate when unbounded

Double Helix

RNA vs DNA structure

RNA has a single polynucleotide strand, DNA is double helix (two polynucleotides)

DNA Replication

the process of making a copy of DNA, replication begins at the 3' end to the 5' end. DNA is replicated from 5' to 3'.

Helicase

An enzyme that unzips the double helix of DNA at the replication fork by breaking hydrogen bonds

Topoisomerase

corrects "overwinding" ahead of replication forks by breaking, swiveling, and rejoining DNA strands

DNA polymerase 1 and 3

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule (DNA Polymerase 3)

RNA primers removed by exonuclease activity, DNA is synthesised in its place at the same time (DNA Polymerase 1)

DNA Primase

synthesizes a short RNA primer to provide a 3'-OH group for the attachment of DNA nucleotides

single strand binding proteins

bind to and stabilize single-stranded DNA

DNA Ligase

A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3' end of a new DNA fragment to the 5' end of a growing chain.

Cell Division

the process in reproduction and growth by which a cell duplicates its genetic information before dividing to form daughter cells.

Stages

Interphase

Prophase

Prometaphase

Metaphase

Anaphase

Telophase

Cytokinesis

Interphase

Cell grows, performs its normal functions, and prepares for division; consists of G1, S, and G2 phases.

G1 phase-the cell grows in size and synthesizes mRNA and protein.

S phase- DNA replication occurs

G2 phase- Cell grows and prepares for the mitotic division

M Phase -Mitosis

Prophase

First and longest phase of mitosis in which the genetic material inside the nucleus condenses from chromatin and become chromosomes.

Prometaphase

The second stage of mitosis, in which the nuclear envelope fragments and the spindle microtubules attach to the kinetochores of the chromosomes.

Metaphase

Third phase of mitosis, during which the chromosomes line up across the center of the cell

Anaphase

Phase of mitosis in which the chromosomes separate and sister chromatids move to opposite ends of the cell via spindle fibres.

Telophase

phase of mitosis in which the distinct individual chromosomes begin to spread out into a tangle of chromatin. Two nuclei have formed.

Cytokensis

-Actin filaments congregate near the metaphase plate to form a ring inside the cell.

-Pinching action separates cytoplasm into 2 separate cells.

binary fission prokaryotic cells

Prokaryotic cells reproduce through binary fission.

The bacterial cell copies its chromosome in preparation for division. Cell membrane pinches inward to divide the cell

2 new daughter cells are made

Cell Cycle Checkpoints (Interphase)

G1 checkpoint- cells decide whether or not to divide

G2 checkpoint- prevents cells from entering mitosis when DNA is damaged

M checkpoint- Ensures spindle fibres are correctly attached before continuing mitosis

Molecular control

-Passage of cells through checkpoints requires activation of a 2-subunit complex cyclin and CDK to form MPF complexes

Cyclin in the cell

-Cyclin concentration varies depending on the current phase of the cell cycle

-It accumulates in G2 and S phases

Entering M Phase Steps

1. Cyclin levels increase- Cyclin and CDK come in contact and become MPF

2. MPF use the kinase activity of the interaction to add phosphate groups

3. This allows cells to bypass the G2 checkpoint and enter M phase (Mitosis)

oncogenes and protooncogenes

If genes actively promote cell division (Protooncogenes) are not turned off at the right time they become oncogenes which leads to cancer.

Stops working due to

-Translocation

-Amplification of the gene

-Mutation (In promoter region)

Tumour Suppressor Genes (P53)

-Genes that normally inhibit cell division

Stops working due to

-Translocation (transfer of one part of a chromosome to another part, rearrangements of genes)

-Gene deletion

-Point Mutation

Metastasis

The spread of cancer cells to locations distant from their original site.

Malignant Tumours

Cancerous tumours

Will invade surrounding tumours

Benign Tumours

Non-cancerous tumours

Do not invade surrounding tumours

Leading vs Lagging strand

Leading: elongate continuously into the widening replication fork from parental 3' to 5' ends

Lagging: replicates away from the fork, must wait until it widens to polymerize and is discontinuous, leading to Okazaki fragments from parental 3' to 5' ends

membrane protein functions

1. Transport

2. Enzymatic activity

3. Signal transduction (Receptor+Messenger)

4. Cell-cell recognition (Glycoproteins=tags)

5. Intercellular joining (Adjacent cells hook together)

6. Attachment to the cytoskeleton and extracellular matrix

fluid mosaic model

model that describes the arrangement and movement of the molecules that make up a cell membrane

Cholesterol in membrane

Wedged into the bilayer, increases fluidity resistance to temperature change, important for the integrity and fluidity of the membrane.

hemiacetal group

carbon with an ether group and an alcohol group attached to it; R-O-C-OH

Gibs free energy

energy available to do work in a system.

Gene

-A segment of DNA on a chromosome that codes for a specific trait.

-Basic unit of inheritance

Trait

A characteristic that an organism can pass on to its offspring through its genes.

Exons and Introns

Exons code for amino acids,

Introns are noncoding segments that need to be spliced out by spliceosomes.

transcription factors

Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription.

Promoter region and Stop triplet

One is the a region of DNA where RNA polymerase begins to transcribe a gene and the other is a sequence of three nucleotides in DNA or messenger RNA that signals a halt to protein synthesis in the cell.

Histones

protein molecules around which DNA is tightly coiled in chromatin. Types include H1, H2A, H2B, H3 and H4. They are positively charged and associate with the negatively charged DNA.

Chromatin

Clusters of DNA, RNA, and proteins in the nucleus of a cell. Types include. Euchromatin - a lightly packed form of chromatin and Heterochromatin - a compact form of chromatin.

Karyotype

A display of the chromosome pairs of a cell arranged by size and shape.

The Central Dogma

Information is encoded in the DNA sequence of a gene - transcribed by mRNA - translated into amino acids

Transcription

Step 1 (Initiation): Transcription factors bind to the promoter region and RNA polymerase-unwinds DNA and breaks the H bonds

Step 2 (Elongation): RNA Polymerase (3'-5') builds a mRNA molecule in the 5' to 3' template strand direction.

Step 3 (Termination): RNA Polymerase reaches a stop codon which signals termination.

Splicing

the process of removing introns through spliceosomes and reconnecting exons in a pre-mRNA

Types of RNA polymerase

RNA polymerase I: Transcribes ribosomal RNA (rRNA)

RNA polymerase II: Transcribes mRNA, miRNA, snRNA

RNA polymerase III: Transcribes tRNA, 5S rRNA

Translation

A site: tRNA enters the ribosome and is tested for an anticodon match, mRNA attaches to the ribosomes (5') and moves along until a start codon is reached.

P site: Provided a correct match, tRNA shifts to the P site and deposits its amino acid to the chain.

E site: tRNA is ejected and the process continues until a stop codon is reached and the polypeptide detaches.

mRNA processing

- 5' guanine cap

- 3' poly-A tail

- RNA splicing of exons = remove introns + "splice" together exons

Operon Structure

Promoter: Site where RNA polymerase binds

Operator: The on/off switch positioned within the promoter

Repressor: Binds to the operator preventing RNA polymerase from binding

Tryptophan Absent Operon

Operon on-RNA polymerase attaches to the DNA at the operon's promoter and transcribes the operons genes (TRP repressor is inactive). Enzymes for tryptophan synthesis are made.

Tryptophan Present Operon

Operon off-As tryptophan accumulates it inhibits its own production by activating the repressor protein which binds to the operator blocking transcription. Enzymes for tryptophan synthesis are not made.

Tryptophan

A corepressor: a molecule/aminoacidic that cooperates with a repressor protein to switch an operon off

repressible operon

Transcription is usually on, but can be inhibited (repressed) when a molecule binds allosterically (TRP operon/ Tryptophan)

Repressor becomes active with binding of Corepressor

Inducible Operon

Transcription is usually off, but can be stimulated (induced) when a molecule interacts with a regulatory protein (lac operon/Allolactose)

Repressor is active without binding of inducer

lactose present operon

Operon on-Allolactose binds to the repressor inactivating it, so the inactive repressor cannot bind to the operator- genes of the lac operon are transcribed and enzyme for using lactose are transcribed.

lactose absent operon

The lac repressor is innately active, and in the absence of lactose it switches off the operon by binding to the operator. Enzymes for using lactose are not made.

positive gene regulation

The process by which gene expression is increased or enhanced in response to specific regulatory signals or factors

cyclic AMP (cAMP)

An allosteric regulatory protein which accumulates when glucose is scarce

cAMP receptor protein (CRP)

the activator protein that binds with cyclic AMP to increase the rate of lac operon transcription

lactose is present and glucose is absent

The high level of cAMP activates CRP which binds to the promoter and increases RNA polymerase binding there.

The lac operon produced large amounts of mRNA coding for the enzymes the cell needs to use lactose

Lactose present and glucose is present

Low cAMP levels and CRP is unable to stimulate transcription at a significant rate, even though no repressor is bound

7 step gene regulation in Eukaryotes

1. Regulation of chromatin structure

2. Transcription control

3. RNA processing

4. Mature RNA is localised

5. Degradation of mRNA

6. Translational control

7. Protein Folding + Post Translational Modification

Activator Protein

a regulatory protein that binds to specific sites on DNA and stimulates transcription; involved in positive control