Unit 1 Flashcards
proteome
all the proteins expressed by a genome
why is the proteome larger than the number of genes?
alternative RNA splicing and post-translational modification
amino acid link
peptide bonds
primary structure
the sequence in which amino acids are synthesised into the polypeptide
types of secondary structure
alpha helixes, parallel or anti-parallel beta sheets, turns
what holds together the secondary structure?
hydrogen bonding in the backbone of the protein strand
classes of R groups
- positively charged (amine nh2)
- negatively charged (carboxyl)
- polar (hydroxyl)
- hydrophobic (hydrocarbon)
ligand
substance that can bind to proteins
what happens when a ligand binds to a protein binding site or when a substrate binds to an
enzyme’s active site?
the conformation of the protein changes which causes a functional change
prosthetic group
non-protein unit bound tightly to a protein which is necessary for its function
what can interations of R groups be influenced by?
temperature and pH
possible interactions in tertiary structure
hydrophobic interactions, ionic bonds, hydrogen bonds
in which proteins can quartenary structure exist?
proteins with several connected polypeptide subunits
in archaea, how do bacteriorhodopsin molecules generate potential differences?
by absorbing light to pump protons across the membrane and the resulting
diffusion of hydrogen ions back across the membrane drives ATP synthase.
In plants, what does the light absorbed by photosynthetic pigments within protein
systems do?
drives an electron flow that pumps hydrogen ions across the thylakoid membrane of the chloroplast and the resulting diffusion of hydrogen ions back across the membrane drives ATP synthase
what forms rhodopsin?
opsin and retinal
what does different forms of opsin do in cone cells?
give sensitivity to specific wavelengths of light (red, green, blue or UV)
what does rhodopsin and the protein cascade do in rod cells?
absorbs a wider range of wavelengths, and a
greater degree of amplification by the protein cascade results in sensitivity at low light intensities
what amplifies light signals in eyes?
a cascade of proteins
Process of a nerve impuulse being generated once rhodopsin is excited by a photon of light
Excited rhodopsin activates G-proteins
which activate many enzyme molecules. The enzyme molecules cause the closure of ion channels by catalysing the removal of molecules that keep channels open. The inward leakage of positive ions is halted so the membrane potential increases. Hyperpolarisation (increasing charge) stimulates a nerve impulse.
what are membranes made of?
a bilayer of phospholipid molecules and a
patchwork of protein molecules.
where are hydrophyllic R groups in a protein?
surface of a soluble protein found in the cytoplasm
where are hydrophobic R groups in a protein?
they cluster at the centre of a protein to form a globular structure
peripheral proteins
- proteins that temporarily attach to the cell membrane
- have less hydrophobic R groups interacting with phospholipids
examples of integral transmembrane proteins
channels, transporters, receptors
how are integral proteins held in place within the phospholipid bilayer?
regions of hydrophobic R groups allow strong hydrophobic interactions that hold the integral proteins in place
in eukaryotes, how is nucleosome packing of DNA in chromosomes formed?
positively charged histone proteins bind to negatively charged sugar phosphae backbone of DNA, DNA wraps around histone proteins to form nucleosomes
induced fit
correct substrate starts to bind resulting in a temporary change in the shape of the active site increasing the binding and interaction with the substrate, activation energy is lowered for this reaction
where do modulators bind on allosteric enzymes?
secondary binding site
effect of modulator binding
conformation of the enzyme changes and this alters the affinity of the active site for the substrate
positive and negative modulators effect
positive modulators increase the enzyme’s affinity whereas negative modulators reduce the enzyme’s affinity for the substrate.
cooperativity
changes in binding at one subunit alter the affinity of the remaining subunits
cooperativity in oxygen in haemoglobin
In haemoglobin, when one of the subunits binds a molecule of oxygen, the
second binds more easily, and so on
main factors which will affect haemoglobin’s ability to bind oxygen
temperature and pH
kinase
phosphorylation- attaches a phosphate group to a protein
phosphatase
dephosphorylation- removes a phosphate group from a protein
process of muscle contraction
-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 forwards and rebinds
-The rebinding releases the ADP and a
phosphate and drags the myosin along the actin filament.
what uses ATP for phosphorylation?
ATPases
what can the addition or removal of phosphate from particular R groups can be used to cause?
reversible conformational changes in proteins, common form of post-translational modification
what does the phospholipid bilayer act as a barrier to?
ions and most uncharged polar molecules
where are the receptor molecules for hydrophyllic proteins?
on the surface of the cell
where are the receptor molecules for hydrophobic proteins?
within the nucleus as hydrophobic signals can pass through membranes
small molecules that can pass through the phospholipid bilayer
carbon dioxide and oxygen
how do cells perform specialised functions?
different cell types and different cell compartments have different channel and transporter proteins
passage of molecules through channel proteins is
passive
types of gated channels
- ligand gated channels- controlled by specific ligand binding to protein
- voltage gated channels- controlled by changes in voltage
types of transporter proteins
- facillitated transport- simultaneuosly transports 2 types of molecules
- active transport- transports molecules against concentration gradient
examples of gated channels
sodium channel and potassium channel
examples of transporter proteins
facilitated- glucose symport
active- Na/K-ATPase
transcription factor
proteins that have binding sites that are specific to particular sequences of DNA and when bound to can either stimulate or inhibit initiation of transcription
where does the energy for conformational change in active transport come from?
hydrolysis of ATP
Functions of the sodium-potassium pump
◦ maintaining the osmotic balance in animal cells;
◦ generation of the ion gradient for glucose symport in the small intestine
◦ generation and long-term maintenance of the ion gradient for resting potential in neurons
◦ generation of the ion gradient in kidney tubules
signal transduction can result in:
activation of enzymes or G-proteins,
a change in uptake or secretion of molecules, rearrangement of the
cytoskeleton or activation of proteins that regulate gene transcription
Process of sodium potassium pump
-The sodium-potassium pump has high affinity for sodium ions inside the cell, therefore binding occurs.
-Phosphorylation by ATP causes the conformation of the protein to change.
-The affinity for ions changes, resulting in sodium
being released outside of the cell.
-Potassium ions from outside the cell bind to the sodium-potassium pump.
-Dephosphorylation occurs, which causes the conformation of the protein to change.
-Potassium ions are taken into
the cell and the affinity returns to the start.
resting potential
membrane potential of a neuron that is not transmitting signals
depolarisation
membrane potential of neuron increase
action potential
a signal that carries information along axons, is achieves if depolarisation change is big enough
Process of Nerve Transmission
-An appropriate signal molecule like neurotransmitter, triggers the opening of ligand-gated ion channels.
-If sufficient ion movement occurs, then voltage-gated ion channels will open and the effect travels along the length of the nerve.
-Once the wave of depolarisation has passed, these channel proteins close and others open to allow the movement of ions in the opposite direction to
restore the resting potential.
receptor molecules of target cells
proteins with a binding site for a signal molecule
in a multicellular organism, can different cell types show a tissue-specific response to the same signal?
Yes
Hydrophobic signalling molecules examples
steroid hormones and the thyroid
hormone thyroxine
How does thyroxine increase metabolic rate?
When thyroxine binds to the receptor protein, conformational change prevents the protein binding to
the DNA, allowing transcription of the gene for Na/KATPase, resulting in an increase in metabolic rate
How does thyroxine decrease metabolic rate?
Thyroxine receptor protein binds to DNA in the absence of thyroxine and inhibits transcription of the gene for Na/K-ATPase
Process of hormone signalling
The receptor proteins for steroid hormones are transcription factors. Once the hormone signal has bound to the receptor can the transcription factor bind to gene regulatory sequences of DNA which allows transcription to occur
hydrophyllic signalling molecules examples
peptide hormones and neurotransmitters
cause of Type 1 diabetes
lack of insulin production
cause of Type 2 diabetes
loss of insulin receptor function
Transduced hydrophilic signals often involve
cascades of G-proteins or phosphorylation by kinase enzymes
transmembrane receptor signalling process
transmembrane receptors change conformation when the ligand binds outside the cell; the signal molecule does not enter the cell, but the signal is transduced across the membrane of the cell
effect of binding of the peptide hormone insulin to its receptor
triggers recruitment of GLUT4 glucose transporters to the cell membrane of fat and muscle cells which facilitates the uptake of glucose into the cells
another thing that can trigger GLUT4 recruitment
exercise, can help people with Type 2 diabetes
where is the receptor for ADH?
collecting duct of kidney
effect of ADH binding to it’s receptor
triggers recruitment of the channel protein aquaporin 2 (AQP2)
aquaporins provide
highly efficient route for water to move across membranes
Recruitment of AQP2 allows
control of water balance in terrestrial vertebrates
what can failure to produce ADH or insensitivity of it’s receptor lead to?
diabetes insipidus
what does the cytoskeleton of a cell do?
provides mechanical support and shape to cells
what are microtubulins made of?
hollow straight rods of globular proteins called tubulins
what do microtubules do and form?
govern the location and movement of membrane-bound organelles and other cell components and form spindle fibres
where do microtubules and spindle fibres radiate from?
centrosome
the cell cycle
interphase (G1, S, G2), prophase, metaphase, anaphase, telophase, cytokinesis
prophase
each duplicated chromosome appears as two identical
sister chromatids which are joined at the centromere
metaphase
the chromosomes line up on the metaphase plate in the middle of the cell and each of the sister chromatids in each chromosome is attached to microtubules from opposite ends of the parent cell the kinetochore
anaphase
the paired centromeres of each chromosome separate
and the chromatids begin moving apart as the spindle shortens
telophase
the cell lengthens and a nuclear membrane forms around each set of chromosomes, the chromosomes start to uncoil
cytokinesis
takes place during telophase, involves the separation of the cytoplasm into two daughter cells
checkpoints in cell cycle
G1, G2 and M
what happens if go ahead signal is not reached at G1 checkpoint?
the cell switches to a nondividing state called the G0 phase
uncontrolled decrease in the rate of cell cycle leads to
degenerative disease
uncontrolled increase in the rate of cell cycle leads to
tumour formation
proliferation gene
codes for proteins that promote cell division eg. cyclin dependant kinase (CDK)
anti-proliferation gene
codes for proteins that restrict cell division eg. retinoblastoma (Rb) and p53
biological control
includes using more suitable strain of microorganism eg. less virulent
dilution series
stepwise dilution of a stock dilution, often performed by diluting 1cm3 with 9cm3 of water and then repeating the process with newly produced solution
standard curve
used to determine the concentration of an unknown solution
pH buffer
solution whose pH changes very little when strong acid or base is added
equipment that can be used to measure liquid volumes
cylinders, pipettes, burettes, syringes, autopipetters
how to measure pH?
meter or indicator
colorimeter
used to quantify the concentration of a pigmented solution
substances can be separated according to
solubility, size, shape, or charge
centrifugation
allows substances to be separated according to their size and density, largest and densest separate first and form a pellet at the bottom and liquid above the pellet is called the supernatant
chromatography types
- paper chromatography- seperates components using a solvent drawn up chromatography paper
- thin layer chromatography
- affinity chromatography- relies on binding interactions between the protein of interest and ligand
protein electrophoresis
uses current flowing through a buffer to seperate proetins according to size and charge
iso-electric point
overall neutral net charge and precipitate out of solution
ELISA
uses antibodies that are linked to reporter enzymes to cause a colour change in the presence of a specific antigen
applications of ELISA
diagnostic tests for HIV and food allergens
protein blotting
proteins are separated and transferred to a membrane which is probed for the protein of interest using a specific antibody that is linked to a detectable label, this label may be a reporter enzymes to cause a colour change in the presence of a the target protein
immunohistochemistry
antibodies are used to detect the presence of a particular antigen within a tissue sample
how are hybridomas formed?
fusion of a B lymphocyte with a myeloma cell using polyethylene glycol
fluorescence microscopy
specific protein structures have fluorescent markers added to them and structures are visualised using a fluorescent microscope
haemocytometry
known volume of cell culture is added to haemocytometer which is viewed under a microscope to perform cell counts to estimate the number of cells in a sample
flow cytometry
allows scientists to detect, count and analyse cells one by one as they flow past a detector in solution
what dyes can be used to show cells for cell counts (viable and total)?
methlyne blue or trypan blue dye
comparison of primary cell lines to tumour cell lines
primary cells have limited lifetimes whereas tumour cells grow and divide indefinitely in cell culture
culture media contains
requirement of a cell
complex culture media contains
growth factors from serum
aseptic technique aim
keep bacteria free from contamination by microorgansims such as bacteria
examples of aseptic technique
sterilisation of equipment, containers and materials, disinfection of the working area and wearing a lab coat
event that triggers p53
DNA damage
what happens as cell size increases during G1?
cyclin proteins accumulate and combine with Cdks and activate them
what do active Cdks cause?
phosphorylation of proteins that stimulate the cell cycle, if a sufficient threshold of phosphorylation is reached the cell cycle moves on to the next stage, if not the cell is held at a checkpoint
how does active G1 Cdks cause DNA replication in the S phase?
G1 Cdk phosphorylates a transcription factor inhibitor, Rb protein
what can p53 cause?
stimulate DNA repair, arrest the cell cycle or cause
apoptosis
caspases
DNAases and proteinases
apoptosis is triggered by
cell death signals that activate inactive forms of caspases that destroy the cell
cell death signals that originate outwith the cell (eg from lymphocytes)
bind to a surface receptor protein to activate a protein cascade that produces active caspases
absence of cell growth factors can
initiate apoptosis
action of caspases in cell destruction
activate other caspases and digest other proteins
tertiary structure
folded polypeptide shape
