microbiology Flashcards
what is molecular cell biology
The study of molecular mechanisms at the cellular level and how such observations relate to cell function
what is a biomarker
A characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention
what is translational research
Applying basic research to a clinical setting
what is stratified medicine
We identify subgroups of a population with exhibit distinct characteristics of disease
what is personalised medicine
A tailor-made clinical model whereby therapy is delivered on an individualised basis
what is physiology
studies the characteristics (chemical, physical and mechanistic) that contribute to function and the processes of life.
what is pathophysiology
studies pathology in the context of physiology. For example, this could be disease process or injury
what is negative feedback
is the process where biological systems maintain defined constant conditions in response to an altering environment.
what is positive feedback
the process of amplifying change
what is a solution
solute dissolved in a solvent
what is diffusion
the movement of a molecule down a concentration gradient, from an area of its high concentration to an area of its low concentration.
what is simple diffusion
molecules move directly across the membrane without the aid of a carrier protein
what is facilitated diffusion
passive movement down a concentration gradient with the help of carrier proteins
what is the equation for rate of diffusion
(surface area x concenctration gradient) / length of diffusuon pathway
what is osmosis
Osmosis is the process by which water molecules pass through a semipermeable membrane, from a less concentrated solution into a more concentrated one.
what is a hypotonic environment
when more water is on the outside
what is hypertonic
when more water is on the inside
what is active transport
the movement of molecules from an area of lower concentration to higher concentration
what is co transport
Some membrane proteins involved in facilitated diffusion or active transport can carry multiple molecules or ions at once
what is a symporter
when molecules move in the same direction through a facilitator protein
what is an antiporter
when molecules move in different directions through a facilitator protein
what is carbonic anhydrase
is an enzyme that catalysis the reaction of H2O and CO2 to generate carbonic acid and subsequently bicarbonate.
what is voltage
is the potential difference between two points in an electrical field
what are features of excitable cells
Excitable cells can produce OR respond to electrical signals
Excitable cells can propagate action potentials
which cells are excitable
neurons, skeletal muscle cells, smooth muscle cells, cardiac myocytes
what is the features of a cell membrane
- Hydrophilic phosphate head groups orientate toward the aqueous internal / external environments
- Hydrophobic lipid tails orientate towards each other.
- Cholesterol alters the fluidity of the plasma membrane.
- One of the most common lipids in the PM is phosphatidylcholine
what are examples of membrane proteins on the cell membrane
- Catalysts – enzymes.
- Transporters, pumps and ion channels.
- Receptors for hormones, local mediators and neurotransmitters.
- Energy transducers.
what is the function of a cell membrane
- Forming a continuous, highly selectively permeablebarrier
- Allowing the control of an enclosed chemical environment
- Communication
- Recognition
- Signal generation
what is the permeability of gases in the cell membrane
permeable
what is the permeability of small uncharged polar molecules in the cell membrane
ethanol is permeable but water and urea are slightly permeabe
what is the permeability of large uncharged polar molecules in the cell membrane
impermeable
what is the permeability of charged polar molecules in the cell membrane
impermeable
what is the permeability of ions in the cell membrane
impermeable
what does the RER do
takes developing proteins from the cytosol and continues their development prior to completion in the golgi apparatus.
which proteins do the RER develop
- Secretion into the extracellular matrix e.g. mucus and enzymes.
- Association with the cell membrane e.g. receptors and channels
- Membrane bound vesicles e.g. enzymes of lysosomes.
what does the SER do
The smooth endoplasmic reticulum is important in the synthesis of lipids, phospholipids and steroids.
what does the golgi apparatus do
The golgi apparatus modifies proteins and lipids that it receives from the endoplasmic reticulum. These biochemicals leave the golgi byexocytosisbefore being delivered to differentintracellularorextracellulartargets.
what is protein processing in the golgi
carbohydrate regions of glycoproteins are altered by addition, removal or modification of carbohydrates.
what is protein processing in the golgi
dds phosphate groups and glycoproteins to lipids from the endoplasmic reticulum (such as cholesterol) to create the phospholipids that make up the cell membrane.
what are lysosomes
are acidic membrane-bound organelles found within cells,
Lysosomes contain numerous hydrolytic enzymes which catalyse hydrolysis reactions.
what is the structure of mitochondria
Mitochondria have an inner and outer membrane, with an intermembrane space between them
what is the function of the mitochondria
The mitochondrion is the site of ATP synthesis for the cell
Store caspases responsible for triggering apoptosis.
Are able to transiently store calcium contributing to calcium homeostasis.
what is the role of the cytoskeleton
Is involved in the processes such as mitosis
Acts as a highway for intracellular vesicles
Provides support to the plasma membrane
Enables cellular locomotion
Controls the shape of the cell
what are the primary filament systems of the cell cytoskeleton
microtubules
actin filaments
intermediate filaments
what do stem cells divide into
DNA vs RNA
what are features of stem cells
They can divide indefinitely
Are not terminally differentiated
Daughters have a choice: differentiate or remain a stem cell
what are introns
. Introns are removed by RNA splicing as RNA matures, meaning that they are not expressed in the final messenger RNA (mRNA) product
what are exons
exons go on to be covalently bonded to one another in order to create mature mRNA.
why do large variations of the genome exist
mechanisms of disease
targeted therapeutics
gene therapy
predictive use (testing and reproductive ethics)
what are purines
adenine and guamine
what are pyrimidines
cytosine
uracil
thymine
what is the structure of DNA
- DNA is a double helix formed by base pairs attached to a sugar-phosphate backbone.
- Sugars are connected via phosphate groups
- This phosphodiester bond occurs between the 3’ and 5’ carbon atoms
- The helix is antiparallel
- Opposite bases on each strand compliment each other.
- The outer edges of the bases are exposed in the major and minor grooves.
how many hydrogen bonds do AT have
2
how many hydrogen bonds do CG have
3
what are the stages of the cell cycle
g1
s
g2
m
what happens during the g1 phase
cell increases in size
cellular contents are duplicated
what happens during the s phase
dna replication
what happens during the g2 phase
cell grows more
organelles and proteins develop in preperation for cell division
what happens during the m phase
mitosis followed by cytokensis
formation of two identical daughter cells
how is the cell cycle regulated
This cycle is also closely regulated by cyclins which control cell progression by activating cyclin-dependent kinase (CDK) enzymes.
what happens during prophase (mitosis)
Each chromosome is made of two genetically identical chromatids, joined by a centromere. mitotic spindles begin to form.
The spindles attach to the centrosome.
the centrosomes begin to move in opposite directions.
what happens during metaphase (mitosis)
the chromosomes align at the metaphase plate. The centrosomes are located at opposite ends of the cell.
the cell will check that all the chromosomes are aligned along the metaphase plate.
what happens during anaphase (mitosis)
sister chromatids are pulled to opposite ends of the cell.
The spindle fibres contract, breaking the chromatids at the centromere and moving them to opposite poles of the cell.
what happens during telophase (mitosis)
reformation of two nuclei
The chromosomes decondense and the mitotic spindles fibres are broken down.
what happens during cytokinesis (mitosis)
Cytokinesis is the division of the cytoplasm to form two new cells.
what happens during initiation of DNA replication
DNA synthesis is initiated at origins which have specific coding regions.
DNA helicase unwinds the double helix by hydrolysing the ATP used to form the bonds between the nucleobases
DNA primase synthesises a small RNA primer, which acts as a ‘kick-starter’ for DNA polymerase.
what happens during elongation of DNA replication
Once DNA Polymerase has attached to the two unzipped strands of DNA it is able to start synthesising new strands of DNA by adding free nucleotides to the 3’ end.
One of the template strands is read in a 3’ to 5’ direction, therefore the new strand will be formed in a 5’ to 3’ direction.
what happens during termination of DNA replication
The process of expanding the new DNA strands continues until there is either no more DNA template strand left to replicate.
what it meiosis
the process of cell division by which gametes are made
what is meiosis I
In meiosis I, homologous chromosomes are separated into two cells
what happens in prophase I (meiosis)
chromosomes replicate to form sister chromatids. The nuclear envelope disintegrates and the chromosomes begin to condense.
Spindle fibres appear
crossing over on the chiasmata
what happens in metaphase I
homologous chromosomes align along the equator of the cell.
independent assortment occurs
what is crossing over
To further increase genetic diversity, homologous chromosomes exchange small parts of themselves, such that one chromosome contains both maternal and paternal DNA
the points at which this occurs on a chromosome is the chiasmata.
what is independent assortment
this is when maternal and paternal chromosomes line up and randomly align themselves on either side of the equator.
what happens during anaphase I
each of the homologous chromosomes get pulled towards opposite poles of the cell as the spindle fibres retract. This equally divides the DNA between the two cells which will be formed.
what happens during telophase I
the nuclear envelope reforms and spindle fibres disappear
what happens during cytokinesis I
the cytoplasm and cell divide resulting in two cells that are technically haploid – there is one chromosome and two chromatids for each chromosome (2c, n).
what happens during prophase II
The nuclear envelope disintegrates and the chromosomes begin to condense.
Spindle fibres appear
what happens during metaphase II
chromosomes line up in single file along the equator of the cell.
what happens during anaphase II
sister chromatids are pulled to opposite poles of the equator
what happens during telophase II
the nuclear envelope reforms and spindle fibres disappear
what happens during cytokinesis II
the cytoplasm and cell divide producing 2 non-identical haploid daughter cells.
what do recombination errors lead to
gene duplications (or loss)and to inversions and translocations
what is turner syndrome
XO female, reduced height, underdeveloped ovaries, and may have neck webbing, heart and kidney defects
what is Klinefelter syndrome
XXY male, reduced fertility, may affect general development
where can dna damage occur
germline or soma
what are mutations
- Changes in the DNA
- Source of all genetic variation
- Random and can be harmful, neutral or advantageous
- Mutation rates are generally low
what are routes of DNA repair
- Polymerases involved in DNA replication have 3’-5’ exonuclease activity, this allows proof reading
- Base excision repair (BER), nucleotide excision repair (NER) and mismatch repair (MMR) systems that act throughout cell life repairing DNA damage
- A specific system exists to repair double stranded breaks, this is related to the system that allows recombination
what are mitochondrial diseases
Mutations in mitochondrial genes can also cause a range of maternally-inherited diseases
what is Leber’s hereditary optic atrophy (LHON)
a midlife, acute or subacute, painless, central vision loss that results from one of arrange of mtDNA mutations
what is myoclonic epilepsy
mutation at nucleotide that results in a defect in translation of all mtDNA-encoded genes
what is cystic fibrosis
CTRF protein Cl- channel is expressed in a number of epithelial tissues and mutations may be in the form of blocked channels or few channels on the membrane surface.
what is xerderma pigmentosum
is an autosomal recessive dissorder
what is DNA transcription
the process by which the genetic information contained within DNA is re-written into messenger RNA (mRNA) by RNA polymerase. This mRNA then exits the nucleus, where it acts as the basis for the translation of DNA. By controlling the production of mRNA within the nucleus, the cell regulates the rate of gene expression.
what is the initiation of DNA transcription
Transcription is catalysed by the enzyme RNA polymerase, which attaches to and moves along the DNA molecule until it recognises a promoter sequence.
Once bound to the promoter sequence, RNA polymerase unwinds a portion of the DNA double helix, exposing the bases on each of the two DNA strands.
what are transcription factors
Transcription factors are proteins that control the rate of transcription; they too bind to the promoter sequences with RNA polymerase.
what is the elongation of DNA transcription
One DNA strand (the template strand) is read in a 3′ to 5′ direction, and so provides the template for the new mRNA molecule. The other DNA strand is referred to as the coding strand.
RNA polymerase uses incoming ribonucleotides to form the new mRNA strand. It does this by catalysing the formation of phosphodiester bonds between adjacent ribonucleotides
what is the termination of DNA transcription
Elongation continues until the RNA polymerase encounters a stop sequence. At this point, transcription stops and the RNA polymerase releases the DNA template.
what is splicing
Splicingallows the genetic sequence of a single pre-MRNA to code for many different proteins, conserving genetic material.
Removal ofintrons(non-coding sequences) viaspliceosome excision
Joining together ofexons(coding sequence) byligation
what is DNA translation
is the process by which the genetic code contained within a messenger RNA (mRNA) molecule is decoded to produce a specific sequence of amino acids in a polypeptide chain.
what is the initiation of DNA translation
thestart codonis recognised.
the small 40s subunit of the ribosome binds. Subsequently, the larger 60s subunit binds to complete theinitiation complex.
what is the elongation of DNA translation
The ribosome hastwo tRNA binding site; thePsite which holds thepeptide chain and theAsite whichaccepts the tRNA.
While tRNA occupies the P site, the tRNA that is complementary to the next codon binds to the A site,
The ribosome thentranslocatesalong the mRNA molecule to the next codon
what is termination of DNA translation
One of the threestop codonsenters the A site. The small and large subunits of the ribosomedissociate
what are microRNA’s
micro RNAs (miRNA) are non-coding RNAs that play a critical role in gene expression.
what do amino acids consist of
- the amino group
- carboxyl group
- the R group
what is the chemistry of non-polar aliphatic r groups
hydrophobic
what is the chemistry of aromatic r groups
hydrophobic but functional groups may alter polarity
what is the chemistry of polar r groups
polar uncharged hydrophllic
what is the chemistry of polar r groups
polar uncharged hydrophllic
what is the chemistry of positively charged r groups
basic
hydrophilic and possess a significant charge at pH 7
what is the chemistry of negatively charged r groups
acidic
hydrophilic and possess a significant charge at pH 7
what are features of the protiens primary strucutre
multiple amino acids bound together via strongcovalent peptide bondsto form apolypeptide chain.
The peptide bond has a partial double bond character
what mutations form from a proteins’ primary structure
can affect protein folding in the subsequent stages of protein structure, leading to problems with the protein’s function.
what bonds come from the primary structure of a protein
electrostatic attraction
London forces
hydrogen bonds
interchain disulfide bonds
intrachain disulfide bonds
what is the secondary structure of a protein
folding of polypeptide chains by hydrogen bonds between the hydroxyl (OH) group and the hydrogen molecule of the adjacent amino acid
what is an alpha helix
a coil formed by hydrogen bonds between the carbonyl group and the amino group
The strong bonds and stability of this structure gives it a strong tensile strength
what is a beta-pleated sheet
is formed by hydrogen bonds between the carboxyl group of one amino acid on one sheet and the hydrogen molecule of an amino acid on another sheet. The sheets can be in parallel or anti-parallel.
what is a beta-turn
- These connect the polypeptide chains between secondary structures such as ⍺-helices and β-sheets.
- The turn brings about a 180 change in direction for the polypeptide chain.
what is the tertiary structure of a protein?
the folding of the polypeptide chain into aunique 3D structure.
Folding of the polypeptide chain occurs viainteraction between the R groupsof amino acids.
what is protein denaturation?
disruption to the bonds between R groups. This causes the structure to lose its shape, resulting in a loss of function
what bonds are present in the tertiary strucutre
hydrostatic
electrostatic
covalent disulphide
hydrophobic
what is a hydrostatic bond
forms between the hydroxyl (OH) group and an adjacent hydrogen molecule, providing a strong bond between polar R groups.
what is a electrostatic bond
forms between positive and negative charge. They can be disrupted by presence of other charged molecules near them.
what is a covalent disulphide bond
form between sulphide groups within the R group of amino acids. They usually occur between two cysteine amino acids, which contain sulphur within their R groups.
what is a hydrophobic bond
form between non-polar groups and commonly involve the benzene group.
what is the quaternary protein structure
he combination of multiple polypeptide chains that link together to form a functioning unit. It is formed via bonds between the R groups of different amino acids within the polypeptide chains,
what factors affect protein folding
- Hydrogen bonds between groups form cooperatively:
- Ionic interactions / salt bridges: strength increases if salt bridge formed within more hydrophobic interior of a protein
- Disulphide bonds: additional covalent bonds that join together different parts of the polypeptide to help form the final 3-D structure of the protein.
what are protein domains
- Proteins may fold into multiple domains
- Domains usually have a distinctive function or role.
- Such roles include: DNA binding, protease, spanning plasma membranes
- Domains can often be “found” in the primary sequence as SEQUENCE MOTIFS
what are chaperone proteins?
proteins that help other proteins fold correctly
