cells and proteins Flashcards
what is the proteome?
the entire set of proteins expressed by a genome
why is the proteome larger than the number of genes?
alternative RNA splicing - more than one protein can be expressed by a single gene
- post translational modification
what do genes that don’t code for proteins do?
transcribed to produce tRNA, rRNA, and other RNA molecules that control the expression of other genes
conditions under which can affect the set of proteins expressed by a gene
- metabolic activity of the cell
- cellular stress
- response to signalling molecules
- diseased vs healthy cells
what is the purpose of the system of internal membranes in eukaryotic cells?
increases the total area of membrane available for cellular functions
endoplasmic reticulum
- forms a network of membrane tubules continuous with the nuclear membrane
- is involved in the synthesis of proteins and lipids
- involved in transporting completed proteins to the golgi apparatus
smooth vs rough ER
rough = has ribosomes on its cytosolic face
smooth = lacks ribosomes
golgi apparatus
- series of flattened membrane discs
- involved in the transport and modification of proteins
lysosomes
membrane-bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids, and carbohydrates
vesicles
transport materials between membrane compartments
lipid production
synthesised in smooth ER and inserted into its membrane
where does all protein synthesis begin?
cytosolic ribosomes
what do transmembrane proteins do?
they carry a signal sequence which halts translation, and directs the ribosome synthesising the protein to dock with the ER, this is what forms the rough ER.
what is a signal sequence?
- a short stretch of amino acids at one end of the polypeptide
- determines the eventual location of a protein in a cell
what happens after the ribosome docks with ER?
translation continues and the protein is inserted into the membrane of the ER
what happens once the proteins are in the ER?
they are transported by vesicles that bud off from the ER and fuse with the golgi apparatus
what happens as proteins move through the golgi apparatus?
they undergo post-translational modification
what is the major modification taking place in the golgi?
the addition of carbohydrate groups to proteins. enzymes catalyse the addition of various sugars in multiple steps to form the carbohydrates
movement of proteins between membranes - after carbohydrate groups are added
- molecules move through the golgi discs in vesicles that bud off from one disc and fuse to the next one
- vesicles that leave the golgi apparatus take proteins to the plasma membrane and lysosomes
- vesicles move along microtubules to other membranes and fuse with them within the cell
examples of secreted proteins
peptide hormones and digestive enzymes
what happens to secreted proteins?
- translated in ribosomes on rough ER and enter its lumen
- they move through the golgi apparatus and are packaged into secretory vesicles, which fuse with the plasma membrane, releasing the proteins from the cell
proteolytic cleavage
- form of post-translational modification
- process of breaking the peptide bonds between amino acids
when is proteolytic cleavage required?
in secreted proteins that are synthesised as inactive precursors and require proteolytic cleavage to produce active proteins
e.g. prevents digestive enzymes from becoming active in an inappropriate location and causing damage to the cell
amino acid structure
- same basic structure as each other, differing only in the R groups
- R groups vary in size, shape, charge, hydrogen bonding capacity and chemical reactivity
groups in an amino acid
amino group - NH2, alkaline and slightly positive
acid group - acidic and slightly negative
protein structure
- polymers of amino acid monomers
- amino acids are linked by peptide bonds
- the OH group of one amino acid bonds to the H from the NH2 group on another amino acid (condensation reaction)
what is a heteropolymer?
made up of different monomers - proteins are an example as they are made of different amino acids (they are similar but not the same)
classifications of R groups
- acidic (negative)
- basic (positive)
- polar
- hydrophobic
acidic R groups
contain an additional acid (COOH) group
basic R group
contains additional amino group
polar R group
contains uncharged, different functional groups - often O/H
hydrophobic R groups
usually contain hydrocarbon chains
what determines protein structure?
amino acid sequence
primary structure
sequence in which amino acids are synthesised into a polypeptide
secondary structure
- hydrogen bonding along backbone of protein strand results in regions of secondary structure
- 3 types: alpha helix, beta sheets, turns
tertiary structure
- folding of polypeptide chains gives a more complex 3D structure
- stabilised by interactions between R groups: hydrophobic, ionic bonds, LDFs, hydrogen bonds, disulfide bridges
what is a disulfide bridge?
covalent bonds formed between R groups, containing sulfur
quaternary structure
- exists in proteins with 2 or more connected polypeptide chains
- describes the spacial arrangements of the subunits
what is a prosthetic group?
a non-protein unit tightly bound to a protein and is necessary for its function
what happens to proteins when temperature increases?
- interactions of R groups are disrupted
- proteins unfold and denature
what happens to proteins when pH changes?
- charges on acidic and basic R groups are affected
- ionic interactions between charged groups are lost, changing the conformation of the protein until it becomes denatured
what is a ligand?
a substance that can bind to a protein
what allows ligands to bind?
R groups that are not involved in protein folding
what happens when a ligand binds to a protein’s active site?
the conformation of the proteins changes, causing a functional change which can activate or deactivate the protein
where do allosteric interactions occur?
between spatially distant sites - somewhere other than the active site of the protein
what can cause the activity of allosteric enzymes to vary?
changes in substrate concentration
affinity definition
attractive force and binding of atoms in molecules; the tendency to combine and form bonds in a chemical reaction
what regulates the activity of enzymes when they bind to the allosteric site?
modulators
what happens after the modulator binds?
the conformation of the enzyme changes, which alters the affinity of the active site of the substrate
positive modulators
increase enzyme’s affinity for substrate
negative modulators
reduce enzyme’s affinity for substrate
how does haemoglobin show cooperativity in bonding?
as one molecule of oxygen binds to one of the four haem groups, it increases the affinity of the other three haem groups in the haemoglobin, making the binding of oxygen more likely
what is phosphorylation?
addition of a phosphate group, adding negative charges
- form of post-translational modification
- can be used to cause reversible conformational changes
what is dephosphorylation?
removal of a phosphate group
kinases
- catalyse the transfer of a phosphate group to other proteins
- terminal phosphate of ATP is transferred to specific R groups
phosphatase
- catalyse dephosphorylation of proteins
- changes conformation of the protein as a result of charge interactions
membrane structure
- composed of proteins embedded within a phospholipid bilayer
- fluid mosaic model
phospholipid structure
composed of a hydrophilic head and hydrophobic tail
2 types of membrane proteins
integral and peripheral
integral membrane proteins
- held within phospholipid bilayer by strong hydrophobic reactions between regions of hydrophobic R groups
peripheral membrane proteins
have hydrophilic R groups on their surface and are bound to the surface of membranes by hydrogen bond interactions
3 roles of membrane proteins
1 - movement of molecules across membranes
2 - transmission of extracellular signals i.e. signal transduction
3 - detecting and amplifying stimuli
which molecules can pass through the phospholipid bilayer
hydrophobic molecules & small, uncharged polar molecules
which molecules can’t pass through the phospholipid bilayer
large, uncharged polar molecules & ions
what is facilitated diffusion?
passive transport of substances across the membrane through specific transmembrane proteins
2 types of transmembrane proteins?
channels & transporter proteins
channel proteins
- multi-subunit proteins with water filled pores that extend across the membrane
- either gated or ungated
gated channel proteins
- change conformation to allow or prevent diffusion
ligand gated = controlled by binding of signal molecules, allow passage of solutes
voltage gated = controlled by changes in ion concentration
transporter proteins
- bind to the specific substance and undergo a conformational change to transfer the solute across
- alternate between 2 conformations so that the binding site is sequentially on one side of the bilayer and then the other
- can operate passively or actively
active transport
- uses pump proteins to transfer substances across the membrane, against their concentration gradient
- pumps that mediate active transport are coupled to an energy source
what do some active transport proteins do?
hydrolyse ATP directly, these proteins are called ATPases
when is a membrane potential created?
when there is a difference in electrical charge on the 2 sides of the membrane
electrochemical gradient
- formed in solutes carrying a net charge when the concentration gradient and electrochemical potential difference combine
where do ion pumps get energy from?
the hydrolysis of ATP
what do sodium-potassium pumps do?
actively transport sodium ions out of the cell and potassium ions into it
how many sodium and potassium ions are transported in and out of the cell per ATP hydrolysed?
potassium - 2
sodium - 3
what do multicellular organisms use to signal between each other?
extra-cellular molecules
examples of extra-cellular signalling molecules
hormones (steroid + peptide), neurotransmitters
what are receptor molecules on target cells?
proteins with a binding site for a specific signal molecule.
binding changes the conformation of the receptor, which initiates a response within the cell
extracellular signalling - steps
- specific signalling molecules released as a result of a change in internal state
- signalling molecules carried to target cells
- signalling molecule binds to the receptor and causes conformational change, and is linked to a change in the internal state of the cells
variation in responses
different cell types may show a specific and different tissue response to the same signal
steroid hormones
lipophilic (fat-loving), meaning they can freely diffuse across the plasma membrane of a cell.
- they bind to receptors in either the cytoplasm or nucleus of the target cells
- hormone-receptor complex moves to the nucleus where it bonds to specific sites on DNA and affects gene expression
- specific DNA sites are called hormone response elements (HREs), binding here influences the rate of transcription
peptide hormones
hydrophilic & lipophobic, meaning they cannot freely cross the plasma membrane.
they bind to receptors on the surface of the cell
neurotransmitters (basic info)
- chemical messengers
- transmit their messages over a much shorter distance than hormones
- carry messages across a synapse
hydrophobic signalling molecules
- able to directly diffuse through the phospholipid bilayer
- once inside the cell, they can bind to intracellular receptors
- these receptors are transcription factors
hydrophilic signalling molecules
- bind to transmembrane receptor
- receptors change conformation once ligand binds
- signal molecule is tranduced across the plasma membrane; transmembrane receptors act as signal transducers by converting the extracellular ligand-binding event into specific intracellular signals, altering the behaviour of the cell
transduction
- involves a series of reactions that occur inside the cell through a signal transduction pathway
- transduced hydrophilic signals often involve G-proteins or cascades of phosphorylation by kinase enzymes
G-proteins
- relay signals from activated receptors to target proteins, such as enzymes and ion channels
- family of proteins that act as molecular switches inside cells, involved in transmitting signals from a variety of stimuli outside a cell to its interior
transduction by phosphorylation cascades
- involves a series of events with one kinase activating the next in the sequence, and so on
- can result in the phosphorylation of many proteins
GLUT4 proteins
- glucose transporters
- binding of insulin to its receptor triggers phosporylation of the receptor, starting a cascade within the cell
- eventually leads to GLUT4-containing vesicles being transported to the membrane to increase GLUT4 activity in the membrane
what is a transcription factor?
proteins that, when bound to DNA, can either stimulate or inhibit initiation of transcription
what is resting membrane potential?
a state where there is no net flow of ions across the membrane
what does the transmission of a nerve impulse require?
changes in the membrane potential of a neuron’s plasma membrane
what is an action potential?
a wave of electrical excitation along a neuron’s plasma membrane
what does binding of a neurotransmitter to its receptor trigger?
the opening of ligand-gated ion channels at a synapse
what occurs after the ion channels at the synapse open?
positive ions enter the cell, depolarising the plasma membrane.
if there is sufficient ion movement then the membrane is depolarised beyond a threshold value and voltage-gated sodium channels open, allowing sodium ions to enter the cell down their electrochemical gradient
what happens after sodium ions enter the cell?
a rapid and large change in membrane potential occurs.
sodium channels become inactivated a short time after opening, and voltage-gated potassium channels open, allowing potassium ions to move out of the cell to restore the resting potential
what does depolarisation of one patch of membrane do?
causes neighbouring regions to depolarise and go through the same cycle
what happens when the action potential reaches the end of the neuron?
vesicles containing neurotransmitter fuse with the membrane, releasing the neurotransmitter, stimulating a response in a connecting cell
photoreceptor proteins
- light sensitive
- can sense and respond to light
- found across all 3 domains of life
photoreceptors in animals
- found in retinas
- 2 types: rods & cones
- retinal combines with opsin (membrane protein) to form these photoreceptors
rods
- function in dim light
- don’t allow colour vision
- contain retinal-opsin complex rhodopsin
how rod cells work (1)
- retinal absorbs a photon of light
- rhodopsin changes conformation to photoexcited rhodopsin
- cascade of proteins amplifies the signal
- a single photoexcited rhodopsin activates hundreds of molecules of a G protein called transducin
- each activated G protein activates 1 mole of the enzyme phosphodiesterase (PDE)
how rod cells work (2)
- PDE catalyses the hydrolysis of a molecule called cyclic GMP (cGMP), each active PDE breaks down thousands of cGMP molecules per second
- reduction in cGMP concentration affects the function of ion channels in the membrane of rod cells
- the inward leakage of positive ions is halted, so membrane potential increases, triggering a nerve impulse in neurons in the retina
what results in rod cells being able to respond to low intensities of light?
a very high degree of amplification
cone cells
- different forms of opsin combine with retinal to give different photoreceptor proteins, each with maximum sensitivity to specific wavelengths
- allow colour vision and only function in bright light
cytoskeleton
- gives eukaryotic cells their shape, provides mechanical support and helps maintain organisation within the cell
- consists of different protein structures, including microtubules
microtubules
- hollow cylinders composed of the protein tubulin
- radiate from the microtubule organising centre (MOTC) or centrosome
- control the location and movement of membrane-bound organelles and chromosomes
- form spindle fibres which are active during cell division
formation and breakdown of microtubules
involves polymerisation and depolymerisation of tubulin
what does cell division require?
remodelling of the cytoskeleton
2 stages of cell division
interphase & m-phase
3 parts of interphase
G1 - organelles replicate, protein synthesis occurs
S - replication of nuclear DNA
G2 - second phase of growth, checkpoint
2 processes which occur during m-phase?
mitosis & cytokinesis
4 phases of mitosis
prophase, metaphase, anaphase, telophase
what happens during the prophase?
- DNA condenses in chromosomes which now consist of two sister chromatids
- nuclear membrane breaks down
- microtubules extend from the MTOC and attach to the chromosomes via their kinetochores in the centrmere region
what happens during the metaphase?
chromosomes are aligned at the metphase plate (spindle equator)
what happens during the anaphase?
- separation of sister chromatids
- chromatids are pulled apart by spindle microtubules shorten by depolymerisation
- chromosomes are pulled to opposite poles of the cell
what happens during the telophase?
- chromosomes decondense and the nuclear membranes are formed around each set of chromosomes
what is cytokinesis?
- occurs after mitosis
- involves the separation of the cytoplasm into two daughter cells
3 checkpoints during cell division
G1, G2, metaphase
what is a checkpoint?
they assess the condition of the cell during the cell cycle and halt progression to the next phase until certain requirements are met
cyclins
- involved in regulating the cell cycle
- combine with and activate CDKs, active CDKs regulate progression through the cycle if sufficient phosphorylation occurs.
- if phosphorylation is insufficient then the cycle is halted
G1 checkpoint
- retinoblastoma (Rb) acts as a tumor suppressor by inhibiting the transcription of genes that code for proteins needed for DNA replication
- Rb does this by binding to the transcription factor, preventng the stimulation of transcription
- as CDKs are activated, Rb is phosphorylated and becomes inhibited, causing a conformational change which means it can no longer bind to the transcription factor, therefore allowing the transcription of proteins needed for DNA replication
G2 checkpoint
- success of DNA replication/damage to DNA is assessed
- DNA damage triggers the activation of proteins including p53, which can stimulate DNA repair and cause cell death (apoptosis)
metaphase checkpoint
- progression is halted until the chromosomes are aligned correctly on the metaphase plate & attached to spindle microtubules correctly (at kinetochores)
- this ensures each daughter cell has the correct number of chromosomes
what does an uncontrolled reduction in the rate of the cell cycle cause?
a degenerative disease
what does an uncontrolled increase in the rate of the cell cycle cause?
formation of a tumor
proto-oncogenes
- normal genes, usually involved in the control of cell growth or division
- can mutate to form a tumor-promoting oncogene
what is apoptosis?
programmed cell death
when will cells initiate apoptosis?
in the absence of growth factors
what is apoptosis triggered by?
cell death signals - external or internal
external death signals
come from lymphocytes - they bind to a surface receptor protein and trigger a protein cascade within the cytoplasm
internal death signals
DNA damage - causes activation of p53
what do death signals result in?
the activation of caspases that cause the destruction of the cell by triggering the degradation of any protein molecule
