Biology Unit 1

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  • Created by: danielle
  • Created on: 08-04-19 16:42
What is a Proteome?
The Proteome is the entire set of proteins expressed by a genome.
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Why is the Proteome larger than the number of genes (genome)?
This is due to Alternative RNA Splicing and Post Translational Modification
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Describe the Structure of Proteins
Folded Nature, Bind tightly to Molecules, Must be Folded in a Specific Manner to allow them to function properley
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What do Amino Acid Sequences do?
Determine Protein Structure
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Name the 4 Different Types of Amino Acids
Acidic (-), Basic (+), Polar (Hydrophilic) & Non-Polar (Hypodrophobic)
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Describe the Primary Structure of Proteins
The order in which the amino acids are synthesised into thhe polypeptidechain
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Describe the Secondary Structure of Proteins and the 2 Types of Structures
Some amino acids form hydrogen bonds whihc result in the Seconday Structures (Beta Pleated Sheet & Alpha Helix). The Beta Sheet can be either Antiparallel or Parallel
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What is the Tertiary Structure?
Refers to the OVERALL folding of the polypeptide and its FINAL shape.
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Whart causes the conformation of the Tertiary Structure to take place?
This conformation is caused by bonding such as interactions of the R Groups in hydrophobic regions, ionic bonds, hydrogen bonding, Van der Waals Interactions and Disulphide bridges
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What is a Prosthetic Group?
It is a non-protein unit tightly bound to a protein necessary for its function.
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What is the Quarternary Structure?
Quarternary Strucutre exists in proteins with several conneted polypeptide subunits.
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Interactions between R Groups can be affected by what?
HIGHT TEMP- tertiary structure is destabalised= DENATURED & Changes in pH = No longer bond correctly and POLYPEPTIDE CHAIN UNFOLDS
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Describe both Hydrophilic R-Groups and Hydrophobic R-Groups.
Hydrophillic R Groups will predominate at the surface of a solubl protein found in the cytoplasm and Hydrophobic R Groups may cluster at the centre to form a globular strucure.
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What holds integral proteins within the fluid mosaic model of membrane structure?
Strong hydrophobic interactions.
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Describe both Integral and Peripheral proteins with Examples.
Some Integral proteins are transmembrane, for example channels, transporters and many receptors. Peripheral proteins have fewer hydrophobic R groups interacting with the phospholipid bilayer.
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What types of small non-polar molecules does the hydrophobic centre allow in?
Oxygen and Carbon Dioxide
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What polar Molecules and Charged Ions does the hydrophobic centre act as a barrier to?
(Hydrogen, Sodium,)= Charged Ions, (Water, Glucose)=Polar Molecules
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What is a Ligand?
A ligand is a substance that can bind to a protein.
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Describe the shape of a ligand in reference to a protein.
The binding sites will have complementary shape and chemistry to ligand.
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Describe DNA as a Ligand.
DNA binds to several proteins. Positively charged Histones bind to the negatively charged sugar-phosphate backbone of DNA in eukaryoes; the DNA wraps around histones to form NUCLEOSOMES packaging the DNA in chromoomes.
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How does DNA control Transciption?
Some prote ins are transcription factors that bind to DNA to INNATE or INHIIBIT transcription.
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Describe induced fit. (Ligand Binding & Conformational Change)
As a ligand/substrate binds to an enzyme's active site, the conformation of the protein changes. Induced fit occus when the correct substrate stars to bind resulting in a temporary change in shape of active site= increases binding & interaction with
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What is an Allosteric Enzyme? (''Allo''=''Other'')
is an enzyme (& LIGAND) that can have its activity altered by a ligand called a modulator; they bind at secondary bining sites away from the active site.
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Describe the Two Types of (Allosteric) Modulators.
Negative Modulators REDUCE the enzyme's AFFINITY for the substrate & Positive Modulators INCREASE the enzyme's AFFINITY for the substrate.
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What is Cooperativity within Quarternary Structure?
Some proteins with Quarternary structrure show COOPERATIVITY in which changes in binding at one subunit alter the affinity of the remaining subunits.
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Describe how Haemoglobin shows Cooperativity.
Haemoglobin is mad eup of 4 polupeptide subunits. Each contain a haem group capable of binding to a molecule of oxygen. When 1 of the subunitsbinds to O, the second binds easier & so on; the binding has INCRESEASED the AFFINITY for the next subunit.
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How does Temperature and pH influence Cooperativity?
As TEMP INCREASES, AFFINITY FOR OXYGEN DECREASES & As pH DECREASES, AFFINITY FOR OXYGEN DECREASES
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Describe the process of the reversal conformational change in proteins.
Desphorylation/Phosphorylation from particular R groups. This is a common form of Post-translational Modification. In this way, proteins such as enzymes & receptors can be regulated.
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What is responsible for phorylation and dephosphorylation?
KINASE ENZYMES are responsible for phorphorylation & PHOSPHATE Enzymes catalyse dephosphorylation.
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What do some proteins (ATPases) use for their phosphorylation?
ATP
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Decribe Muscle Contraction and ATP.
Sacromeres contain proteins called Actin & Myosin. Myosin has heads that act as cross bridges as they bind to actin. When ATP binds to Myosin, the myosin head detaches from actin, swings forward &rebinds. This releases the ADP & a Phosphate= shortens
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Decribe Muscle Contraction and ATP. p2
the sacromere and brings about muscle contraction
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**Describe the role of Specific Transmembrane Proteins
They act as channels or transporters, control ion concentrations and concentration gradients.
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Describe Channel Proteins, with an example.
Passage of molecules through channel proteins is PASSIVE, e.g. AQUAPORIN.
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What are the 2 Types of Channel Proteins?
Ligand-gated channels are controlled by SIGNAL MOLECULES & Voltage-gated chanells are controlled by the changes in ion concentration.
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Describe Transporter Proteins, with example/s.
They change CONFORMATION to transport molecules accorss a membrane e.g. NA/KATPase, Glucose Symport.
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What are the two mechanisms in which the tansorter proteins work?
Facilitated Transport' a PASSIVE process where facilitated transport involves a conformational change in a protein e.g. Glucose Transport. Active Transport is used in the Sodium-Pottassium Pump.
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What is a Signal Transduction?
Some cell surface receptor proteins convert extracellular chemical signals to a specific intracellular responce through a signal transduction pathway.
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What may Signal Transduction pathway result in? (4)
The activation of an enzyme or G protein, a change in the uptake or secretion of molecules (upon the binding of insulin, glucose uptake increases), rearrangement of the cytoskeleton or activation of proteins that regulalate gene transcription.
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Describe the role of G-proteins.
G proteins are involved in trasmitting signals from outide the cell inside. They can be ''Switched on''/activated by binding GTP and deactivated by binding GDP.
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Describe the Sodium-Potassium Pump in great detail.
LOOK AT BLUE SHEET FOR ANSWER IN GREAT DEPTH
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What are the functions for Na/KATPase? (4)
LOOK AT BLUE SHEET FOR ANSWERS
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What is Nerve Transmission?
It is a wave of depolarisation of the resting potential of a neuron. This can be stimulated when an appropriate signal molecule triggers the opening of ligand-gated ion chanels at a synapse.
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Describe the changes involved in Nerve Transmission.
LOOK AT BLUE SHEET FOR ANSWER IN GREAT DEPTH
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** What are the 3 Domains of Life?
Archea, Bacteria & Eukaryota
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What is the photoreceptor protein used by archea and where is it found?
Bacteriorhodopsin (found in Halobacteria)
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What do bacteriorhodopsin molecules do?
They generate potential potential differences by absorbing light to pump protons accross the membrane.
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Using the Blue Sheet, describe what happens when Bacteriorhodopsin generates ATP.
Archea converts light energy= chemical energy (ATP). When a photon of light is absorbed, the retinal undergoes a conformational change (STRAIGHT-> BENT); allowing protons to be pumped accross membrane and return through ATP Synthase= ATP
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How do plants convert light energy to chemical energy?
Plants use a photosynthetic pigment called Chlorophyll. (found in Chloroplasts)
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What membrane is found within the membrane-bound compartments (Grana) in Chloroplasts?
The Thylakoid Membrane
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Describe ATP Synthesis is Plants. 1
When a molecule of chlorophyll absorbs light, one of its electrons is boosted up a higher energy level. The electron passes a no. of protein systems & as this happens, H ions are pumped accross the thylakoid membrane.
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Describe ATP Synthesis is Plants. 2
The H ions are pumped accross the membrane and DIFFUSE the ATP Synthase= ATP
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What forms the photoreceptors of the eye in Animals?
Retinal and Opsin and a CASCADE of proteins amplifies the signal.
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Animals have what two types of photoreptor cells within the Retina of the eye?
Cone Cells (Wave-lengths) and Rod Cells (Low light)
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Describe Rod Cells and Nerve Impulse.
In rod cells, the retinal-opsin complex is called Rhodopsin. When stimulated by a photon, a rhodopsin molecule activates G-protein molecules, actibating molecules of an ezyme. if the enzyme triggers sufficient product, a neve impulse might generate.
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What are the 5 steps that converty light energy to a nerve impulse? 1
1. a photon of light excites rhodopsin 2. excited rhodopsin activated G-proteins 3. G-proteins excie enzyme molecules
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What are the 5 steps that converty light energy to a nerve impulse? 2
4. The enzyme removes the Ligand from Na channels 5. The Na channels close so membrane potential increases, this hyperpolarisation stimulates a nerve impulse
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What happens within Rod cells in low light intensities?
A very high degree of amplication from a single photon
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What happens in cone cells when different forms of opsin combine with retinal to give phoreceptor proteins?
There is maximal sensitivity to specific wavelengths (green, blue, red & UV)
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**What is Coordination?
Multicellular organisms achieve coordination of communication by means of EXTRACELLULAR signalling molecules, receptors and responces. In animals, communication is mediated by nervous transmission and hormonal secretion.
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What are receptor molecules of target cells? (Coordination)
Are proteins with a binding site for a specific signal molecule.
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Explain what happens during singnal reception. (Coordination)
Binding changes the conformation of the receptor and this can alter the responce of the cell.
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What does specificity of signals mean? (Coordination)
Different cell types produce specific signals which can only be detected and responded to by cells with a specific receptor.
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What happens in multicelular organisms? (Coordination)
Different cell types may show a tissue specific responce to the same signal.
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Describe Hydrophobic Signals.
Hydophobic signals can pass through the membrane so their receptor molecules can be within the nucleus.
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What can hydrophobic signals control?
Transcription
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Give 2 examples of hydrophobic signals.
The thyroid hormone;Thyroxine and The steroid hormone
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What happens in the absense of thryroxine?
Thyroxine receptor protein binds to DNA; Transcription of Na/KATPase gene is INHIBITED; less Na/KATPase is transcribed; Metabolic Rate REDUCES
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What happens in the presence of thryroxine?
Thyroxine binds to thyroxine receotor protein; Receptor Protein undergoes a conformational change & can no longer bind to DNA; gene or Na/KATPase is transcribed; Metabolic Rate INCREASES
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Describe steroid hormones acting as a transcription factor.
Steroid hormone passes membrane;Hormone binds toreceptor protein;The activated receptor protein acts as a transcription factor & binds to DNA; The activated receptor protein (transcription factor) brings about transcription of specific genes
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Describe Hydrophillic Signals.
They require receptor molecules to be at the surfaace of the cell because they are not capable of passing the hydrophobic membrane.
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What do Hydrophillic signals control?
Transduction
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Give 2 examples of hydrophilic signals.
Peptide Hormones & Neurotransmitters
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What do Transmembrane receptors do when a ligand binds to the cell?
Change conformation; the signal molecule does not enter the cell but the signal is TRANSDUCED accross the membrane of the cell.
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What do transduced hydrophilic signals often involve?
Cascades of G-proteins or phosphorylationby Kinase Enzymes.
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How does Glucose travel into the plasma membrane?
Transporter Proteins
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Describe the process of The Hydrophillic Signalling Molecule; Insulin.
The binding of insulin to its receptor triggers recruitment of GLUT4 glucose transporter to the cell membrane of fat and muscle cells.
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Explain the causes of both Type 1 & 2 Diabetes.
Type 1; caused by FAILURE TO PRODUCE INSULIN & Type 2; caused by loss of insulin receptor function (mainl caused by OBESITY)
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How is both Type 1 & 2 Diabetes Treated?
Type 1; Regular Insulin injections & Type 2; Exercise and a goof healthy, balanced diet.
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Describe the process of The Hydrophillic Signalling Molecule; Antidiruetic Hormone (ADH)
The binding of ADH to its receptor triggers recruitment of Aquaporin 2 (AQP2).
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What does AQP2 provide?
A Highly Efficient Route for water to move accross membranes.
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What does recruitment of AQP2 control?
Allows control of water balance in terrestrial vertebrates.
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What is Diabetes Insipidus?
Failure to produce ADH or insensitvity of its receptor.
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What does Inulin and ADH control?
Insulin; Involved in maintaining a constant blood glucose level & ADH; control the rate of water reabsorption in the nephron
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**What is the importance of the cytoskeleton?
gives mechanical support & shape to cells.
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What three types of proteins make up the cytoskeleton?
Intermediate Filaments, Microfilaments & MICROTUBULES
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What are microtubules composed of?
They are composed of hollow straight rods made of globular proyeins called tubulins.
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What do tubulins govern?
They govern the location and movement of membrane-bound organelles and other cell compartments.
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Where are microtuules found and what do they form?
They are found in all eukaryotic cells and radiate from the centrosome & they form spindle fibres.
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What does the cell cycle consist of?
Interphase and Mitotic Phase
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What occurs during Interphase? (General)
During interphase, protein synthesis takes place, cystoplasmic organelles are synthesised, the cell grows and replicates its chromosome.
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Describe each stage of Interphase.
G1; the initial growth period where proteins and organelles are synthesised, SPhase; cell continues to grow & copies its chromosomes in prep for mitosis &G2; anothher growth period where proteins and organelles are synthesised &then the Mitotic Phase
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What 2 stages does the Mitotic Phase consit of?
Mitosis (when the nucleus and contents divide) and Cytokinesis (seperation of the cytoplasm into 2 daughter cells)
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Describe the stages of Mitosis.
I Put My Arm There; Interphase, Prophase, Metaphase, Anaphase & Telophase; USE BLUE SHEET FOR DETAIL
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What does an uncontrollable REDUCTION in the rate of the cell cycle result in?
Degenerative Disease (Alzheimer's & Parkinson's Disease)
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What does an uncontrollable INCREASE in the rate of the cell cycle result in?
Tumour Formation
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Where are checkpoints?
They are critical control points where stop and go ahead signals regulate the cell cycle
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Where are the checkpoints within a cell cycle?
G1, G2 & Metaphase
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When is the G0 Phase of use?
This when a go ahead signal at the G1 checkpoint is not reached, the cell may switch to a non-dividing state called the GO phase
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Describe the 3 checkpoints of the cell cycle.
G1; (END) DNA replication must be completed & cell size, G2; (END) same thhing & M; (DURING METAPHSE) checks chromosomes are aligned on the metaphase plate properely
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As the cell increases during G1, what happens?
Cyclin proteins accumulate and combine with regulatory proteins called cyclin-dependent kinases (Cdks) and activate them. Active Cdks cause the phospholylation or proteins that stimulate the cell cycle.
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What happens if an insufficient threshold is reached? (Control of cell cycle)
The cell is held at checkpoint.
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Describe the function of G1 Cdk?
The G1 Cdk phosphorylates a transcription factor, retinoblastoma (Rb) protein, allowing DNA replication in S phase.
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What does DNA damage activation of? (3 things)
a protein called p53 which stimulate DNA repair, arrest the cell cycle or cause apoptosis (cell death).
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What is apoptosis?
Apoptosis is programmed cell death
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What is apoptosis triggered by?
Apoptosis is triggered by cell death signals which result in the activation of DNAases and proteinase (caspases) that destroy the cell.
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Describe both cell death signals that originate extracellularly and intracellularly.
BLUE SHEET
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Give 2 reasons as to why cell death must be controlled carefully in a multicellular organism
Denegerative disease; tumour growth
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