Cels191 Progress Test

Scale of Life

Eukaryote cells: 10-100um

Prokaryote cells: >5um

Organelles:

-mitochondria: 1-10um

-chloroplasts: 2-5um

Natural Selection

Variation, Inheritance, Selection, Time

Three Domains of Life

Bacteria, Archaea, Eukarya

Building Blocks

Amino acids, nucleobases, simple carbohydrates, lipids

Macromolecules

Proteins, Nucleic acids (DNA and RNA), complex carbohydrates, lipids

Supramolecular asssemblies

Membranes, ribosomes, chromatin

Organelles

Nucleus, mitochondria, Golgi and Endoplasmic reticulum

Levels of Carbohydrates

Monosaccharides, disaccharides, oligosaccharides, polysaccharides

Functions of Carbohydrates

1. Recognition 2. Energy 3. Structure

Lipids

Not polymers, large, bulky and very different

Functions of Lipids

1. Structural 2. Regulatory 3. Energy

Function of Organelles

Provide conditions for specific processes, keep incompatible processes apart, allow formation of concentration gradient, package substances for transport

What stabilises membrane fluidity

Cholesterol

Passive Transport

Diffusion, facilitated diffusion

Diffusion

Membranes permeable to lipid soluble, membrane restricts water molecules and charged molecules (glucose and ions)

Facilitated diffusion

Movement of hydrophilic molecules require membrane proteins, channels and carriers, aid the movement of specific substances

Active transport (energy)

Active transport, co-transport

Active transport

Requires transport proteins

Co-transport

Indirect active transport, The concentration gradient used to power the movement of a second substance against its concentration gradient

Roles of Membrane Proteins

Transporters

Membrane proteins are involved in

Signal transduction, cell recognition, intercellular joining, linking cytoskeleton and extra cellular matrix

Signal transduction

Relays messages from the body into the cell (e.g. Grow, divide etc.)

Cell recognition

Involves glycoproteins

Intercellular joining

Formation of long-lasting connections between cells

Linking cytoskeleton and extracellular matrix

Allows a cell to physically connect with protein structures outside the cell (in the extracellular matrix)

Endomembrane system includes

Nuclear envelope, endoplasmic reticulum, Golgi apparatus, vesicles, lysosomes, vacuoles, plasma membrane

Endomembrane system

A membrane system interconnected by direct physical contact or transfer by vesicles.

Functions of the smooth endoplasmic reticulum

Metabolism of Carbohydrates, lipids synthesis for membranes (make phosphate lipids), detoxification of drugs and poisons, storage of calcium ions, extensive sER in cells active, sER can be increased and decreased to meet demands

`Functions of the rough endoplasmic reticulum

Protein synthesis (ribosomes), secreted and membrane-bound proteins enter the lumen (interior) of the rER, processed by rER and the endomembrane system for release from the cell or retention on cell membrane.

Function of the Golgi complex

Receives, modifies, sorts and ships proteins arriving from the rE, has polarity (cis and trans), vesicles arrive at the cis face leave at the trans face, Glycosylation, sorting proteins, directing vesicle trafficking

Glycosylaction

Additions/ modification of carbohydrates to proteins (important for secreted or cell surface proteins), Golgi produce many polysaccharides that may need to be secreted from the cell

Sorting proteins

Adds molecular makers to direct proteins to the correct vesicles

Directing vesicle trafficking

Adds molecular 'tags' to vesicles leaving the Golgi to direct them to the correct targets, short proteins exposed on the vesicle surface, acts as docking site, vesicles travel to lysosomes as well we secretory pathways, important for release and surface expression.

Bulk transport across the plasma membrane

Moving things out of the cell: Exocytosis, constitutive exoocytosis, regulated exocytosis

Moving things into the cell: Endocytosis, Phagocytosis, Pinocytosis, Receptor-medicated endocytosis

Exocytosis

Transports material (glycoproteins) out of the cell or delivers it the the cell surface

Constitutive exocytosis

Release extracellular matrix proteins

Regulated exocytosis

Releases hormones and eurotransmitters

Endocytosis

The cell takes in molecules and particulate matter at the plasma membrane

Phagocytosis

Cell 'eating', uptake of 'food' particles, forms a phagocytic vacuole which is 'digested' by the lysosomes

Pinocytosis

Cell 'drinking', up-take of extracellular fluid containing various solutes such as protein and sugars, up-take vesicle is formed with the aid of a coat protein, up-take is non-selective

Receptor-medicated endocytosis

Specialised form of Pinocytosis (looks for specific molecules that a receptor is attached to), allows the cell to take up bulk quantities of specific substances which may be present at only low concentrations in the extracellular fluid, receptor proteins are used to selectively capture the required solute

Lysosomes

Degrade proteins, lipids, carbohydrates and nucleic acids and release breakdown products into the cell, digest and recycle unwanted cellular material called autophagy, interior acidic for enzymes to be activated, phagocytic vacuoles fuse with lysosomes containing hydrolysis enzymes.

Vacuoles

Large vesicles derived from the rER and Golgi, important in plants for storage of organic compounds, large central vacuoles absorb water for plant cells to grow without needing more cytoplasm

Th cytoskeleton

Maintains cell shape and position of organelles within cells, rapidly disassembles and reassembles which allows rapid change in cell shape, highly dynamic but still provides stability

Cytoskeleton made up of

Microtubules, microfilaments, intermediate filaments

Microtubules

Composed of tubular subunits (form larger hollow tube), radiate out from centrosome, help maintain cell shape, allow movement, atp-powered motor proteins walk organelles along microtubules, allows vesicles to be transport to specific targets within the cell

Microfilaments

Double chain of actin subunits, form linear strands and 3-dimensional networks (branching proteins), resist tension, cortical network under the plasma membrane makes the region less fluid and maintain cell shape, interactions between actin and motor proteins (myosin) support cell movement, actin-myosin interactions allow muscle contraction, amoeboid movement, cytoplasmic streaming

Intermediate filaments

Various proteins including keratins (hair), lamins (nucleus), supercoiled into cables, less dynamic, form relatively permanent cellular structures, help maintain shape, anchor organelles, remain after the cell has died.

Cell junctions

Tight junction, desmosomes, gap junction

Tight junction

Prevents movement of fluid across cell layers, hold neighbouring cells tightly pressed together

Desmosomes

Anchoring junction, attachments between sheets of cells (muscles)

Gap junction

Cytoplasmic contact between two cells, ions and small molecules can pass from cell to cell, allows rapid cell to cell communication (intercellular)

How are cells joined together?

Extracellular matrix

Extracellular matrix (ECM)

Composed of material secreted by cells, secretion occur by constitutive Exocytosis, proteins are glycoproteins most abundant collagen, collagen fibres have great tensile strength, embedded in a proteoglycan complex matrix, proteoglycans are proteins with extensive added sugar, they trap water in ECM, membrane proteins (integrins) connect the ECM to the cytoskeleton providing a communication link from ECM to the cell interior

Cellulose

Glucose polymer, forms microfibrils, highly organised structures that are strong and form a major component of both primary and secondary cell walls

Cell wall structure

Phase 1: crystalline microfibrillar phase (cellulose) phase 2: noncrystalline matrix, pectic polysaccharides, hemicellulose polysaccharides , plus a network of extension (protein)

No crystalline matrix (hemicellulose and pectin)

Hemicellulose: Long chain with short side chains

Pectin: branched, negatively charged

The Protein extensin

Cross-linking of pectin and cellulose dehydrates the cell wall, reduces extensibility and increased strength, extensibility controlled by cross-linking

Synthesis of the primary cell wall

1. Cellulose microfibrils at plasma membrane 2. Polysaccharides in the Golgi apparatus are transported to the cell wall in vesicles 3. Cell wall proteins from the rough er

The vesicles fuse with the plasma membrane, cellulose-producing rosettes move parallel to the cortical mircotubules

Cell wall functions

Influences cell morphology, provides structural support, prevents excessive water uptake

The secondary cell wall

Produced after cell growth stops, thicker and stronger than primary cell walls, provides more structural support

Secondary cell wall structure

Multiple layers, microfibrils in each layer have different orientations, chemical characteristics : more cellulose, less pectin, lignin

Lignin

Complex lignin, confers strength and rigidity, acts to exclude water

Secondary cell wall structural support

For specific cell types: water transporting cells and the whole plant

Plasmodesmata

Cell communication, intercellular connections, plasma membrane is continuous, prevent organelles movement, free exchange of small molecules

Major energy requirements of the cell

Mechanical work (motor proteins), formation of new material (growth and replacement), transport (molecules across membranes), maintain order

Mitochondria

Contains mitochondria, DNA and ribosomes ( produces some mitochondrial proteins), two membranes, mitochondrial matrix inside inner membrane, inner membrane (cristae), intermembrane space functionally important

Cellular respiration

Harvesting chemical energy from glucose

1. Glycolysis

2. Pyruvate oxidation and citric acid

3. Oxidative phosphorylation

Glycolysis

In the ctyosol, glucose is converted into pyruvate, generates 2 ATP, electrons are transferred to the high energy electron carrier NAD+ making NADH

Pyruvate oxidation and citric acid

In the mitochondrial matrix, pyruvate is converted into Acetyl CoA which enters the citric acid cycle, output of energy carrier ATP and high energy electron carriers NADH and FADH2

Oxidative phosphorylation

Inner membrane of the mitochondrion, electron transport ( electrons from NADH and FADH2 ), chemiosmosis -ATP production

Electron transport chain: electrons move through protein complexes embedded in the inner membrane, protons pumped across the membrane accumulate in the intermembrane space, accumulation of protons is crucial for chemiosmosis

Chemiosmosis: ATP synthase spans fro the intermembrane space to the mitochondria matrix, protein gradient powers ATP synthase

Adenosine triphosphate (ATP)

Enables controlled release of energy, cell continuously uses and regenerates ATP

Photosynthesis

Light reactions occur in the thylakoid membrane, carbon fixation occurs in the stroma

The light reactions

1. Photosystems are protein complexes that contain the chlorophyll 2. Chlorophyll absorbs light energy 3. Light energy absorbed by chlorophyll produces high energy electrons 4. High energy electrons travel through the photosynthetic electron transport chain

Chloroplast

Contain DNA, ribosomes and are able to make their own proteins

The nuclear pore complex

Controls movement of molecules out of or into the nucleus

Out: mRNA, tRNA and ribosomes

In: control signals, building materials and energy

Within the nucleus

Inner surface of nuclear envelope lined by nuclear lamina, composed of intermediate filaments, maintain nucleus shape, organise the packing of the DNA

Nucleolus

Prominent nuclear structure with non-diving cells, two or more nucleoli per cell, responsible for making ribosomal RNA which combines with proteins to produce ribosomes

DNA organisation within the nucleus

DNA a nucleotide polymer, DNA double helix, helix interacts between the specific proteins histones, DNA strand coiled to form fibre, coil again in cell division to form metaphase chromosomes (karyotype)

Euchromatin and Heterochromatin

Euchromatin: less dense, contains genes being used by that cell

Heterochromatin: more dense, contains genes not being used by that cell

Dynamic relationship

Chargaff discovery

Significant DNA variation between species thus DNA could be the genetic material.

Chargoff' Rules

First rule: A = T and G = C

Second rule: the composition of DNA varies between species

DNA structure

Double stranded helical molecule with particular features

X-ray diffraction patter of DNA

Bases perpendicular to the length of the DNA molecule

Formation of the Phosphodiester Bond

The hydroxyl group (OH) on the 3rd carbon of one nucleotide reacts with the phosphate group attached to the 5th carbon on another nucleotide

Each strand has a direction, the two strands are antiparallel

The Watson-Crick model of DNA structure

Sugar phosphate backbone is on the outside, bases on the inside, stabilised by hydrogen bonds, two polynucleotide strands are oriented in opposite directions

Watson-Crick model provides

A stimulus for deciphering the genetic code, possible mechanism for the replication of DNA

Eukaryotic DNA replication

Multiple large linear chromosomes (23)' multiple origins of replication, bidirectional

Direction of DNA synthesis

DNA always synthesised in the 5' -> 3' direction, parental template strands are run in the 3' -> 5' direction

What is needed to make a DNA copy

Progressive addition of new nucleotides (DNA polymerase III), a starting point for nucleotide addition (Primase enzyme makes RNA primer), unwinding of the helical double-stranded DNA to give two parental templates ( helicase), release of tension generated by unwinding the DNA helix (topoiaomerase nicks and rejoins DNA strands), prevention of unwound double-stranded helical DNA ( single-stranded DNA binding protein, DNA polymerase I removes RNA primer and fills the gap with DNA nucleotides), joining of ends of newly synthesised fragments together (DNA ligase)

Replication of semi-discontinuous

Leading strand: continuously synthesised in its 5' -> 3' direction

Lagging strand: discontinuously synthesised in its 5' -> 3' direction as Okazaki fragments

Primase

Enzyme (type of RNA polymerase) makes aRNA primer = starting point for DNA polymerisation

DNA polymerase III (Pol III)

Needs an OH group which the phosphate group of the incoming nucleotide can be attached to, only makes 5' to 3' DNA synthesising a new DNA strand complementary to the parental template strands, cannot bind to single stranded DNA

DNA polymerase I

Removes RNA primers (RNase H) and fils the gap with DNA nucleotides

DNA Ligase

Joins the new synthesised Okazaki fragments together (creates phophodiester bonds)

DNA Pol I arrives out two activites

1. RNase activity: endonuclear enzyme that recognises DNA : RNA hybrids and degrades the RNA part

2. DNA polymerase activity: synthesises DNA by adding nucleotides (complementary to the parental DNA template of the lagging strand)

Repair of DNA errors

1. During replication : exonuclease

2. After replication : endonuclease

Durning replication

High accuracy, DNA pol III has a proofreading mechanism, check the newly inserted nucleotide bases against the template

After DNA replication

Variety things can cause damage and errors

Incorrectly inserted bases not corrected by Pol III, radiation damage, chemical modification of bases

Importance I'd correcting DNA errors

If not corrected the error becomes part of the DNA template, permanent change, mutation