week 1-4 summative test
Metabolic processes that cells undergo which make ATP
glycolysis, oxidative phosphorylation, krebs cycle
Metabolic processes that cells undergo which use ATP
DNA,RNA synthesis, active transport, muscle contraction, etc
why ATP is a relatively large molecule considering the size of the high energy phosphate bond.
Allows for large number of weak interactions
Understand why biological systems never destroy a covalent bond but make another one.
Biological systems are stable molecules
What is derived from the breaking of covalent bonds to make ATP?
electrons
Why is an atom's electronegativity important in oxidative respiration?
A more electronegative atom pulls the electrons to itself and is beneficial for the role of electron acceptors in oxidative phosphorylation and hence in doing so generates more energy for ATP production as a product in respiration
Give two reasons why weak non-covalent bonds are essential to biological life.
-Broken easily to be used for use in biological processes like copying of DNA, etc
-Great specificity - key to life
-Stability - secondary structure of protein and holding of complementary strands in DNA
Why do we carry oxygen on proteins (haemoglobin) in our blood?
Oxygen is insoluble in aqueous environment.
Haemoglobin contains iron that can pick up oxygen and deliver it around the body.
Explain what & why hydrophobic interactions are essential to biological life.
hydrogen bonds, important in protein folding for keeping the proteins stable and biologically active.
the concept of pH
concentration of H+ ions.
pH scale
acidity (1-6) basicity (7-14)
A logarithmic scale that reflects the hydronium ion concentration in solution.
role of pH in fluctuations
removes H+ or OH- ions in environment to ensure minimal pH changes
3 major biological buffering systems that exist in saliva
carbonic acid, phosphate ions, proteins/enzymes
carbonic anyhdrase function
carbonic anhydrase decreases the concentration of H+ ions when the concentration of carbonic acid gets too high, it assists the removal of H+ by catalysing the equation
H2CO3 → H2O + CO2
3 general causes for lowering the pH in the mouth.
food, drinks, bacteria which results in the release of acid
Explain the role of a buffer and how it affects fluctuations in pH.
-buffer removes H+ or OH- ions in the environment to ensure minimal pH changes.
-buffer consists of a weak acid/base and its salt.
Define the differences between a strong and weak acid.
strong acid dissociates completely in water while a weak acid dissociates partially in water.
Define a hydronium ion.
When acid releases a proton to H2O (H+ + H2O → H3O+)
What is pH a measurement of? How is it written mathematically?
-pH is a measurement of the concentration of H+.
-(pH = -log [H+] , [H+] = 1 x 10^-pH)
Explain why biological buffers only work efficiently if their pKa (strength of acid) is between 6 - 7.
need 50% of each, buffer becomes exhausted below and no more H3O+ above
Explain how a weak acid (such as carbonic acid) acts as a buffer when an acid or base is present in the environment. Use equations to explain your answer.
H2CO3 ↔ H+ + HCO3
What other biological compounds which do not primarily act as pH buffers can also buffer pH changes?
-phosphate ions and their derivatives
and
-proteins (9.9)
What role does carbonic anhydrase play in maintaining a neutral pH in the mouth?
-enzyme that decreases the conc of H+ when concentration of H2CO3 gets too high.
-catalyses (H2CO3 → H2O + CO2)
Define the concept of homeostasis, and the key targets of control.
Homeostasis: Maintenance of a ‘relatively constant’ internal environment
’relatively constant’ = dynamic steady state.
Concentration of:
▪ Nutrients
▪ O2 /CO2
▪ Waste products
▪ Water
▪ Salts
▪ Electrolytes
o pH
o Volume & pressure
o Temperature
positive and negative feedback loops.
-Positive feedback loops: amplifies an initial change (eg. blood clotting & contractions during labour)
-Negative feedback loops: opposes an initial change in 3 diff ways (restoration of homeostasis, antagonistic loops, receptor feedback loops)
Discuss some of the pathophysiological consequences when homeostatic systems go wrong.
-When antagonistic loop homeostasis goes wrong, diabetes mellitus results
-When restoration of homeostasis goes wrong, rickets results
Negative feedback loops
Restoration of Homeostasis (conventional way)
Antagonistic loops (glucose homeostasis)
Receptor Feedback loops (metabolic homeostasis)
Understand the difference between homopolysaccharides and heteropolysaccharides and what roles they generally play.
homo: single mono unit → storage forms
hetero: polymer with 2 or more mono units → extracellular support matrix
Have a broad understanding of the meaning of the configuration (a or b) of the glycosidic linkage in di- or poly-saccharides.
a glycosidic bond → H group is above the C1
b glycosidic bond → H group is below the C1
Know what hyaluronic acid is and its general role(s).
hyaluronic acid is a polymer that gives cartilage and tendons toughness and flexibility.
Understand what makes polysaccharides such as glycogen relatively insoluble and know what the biological advantage is for bacteria and mammals.
-this is due to the extensive branching & hence unable to form hydrogen bonds with water
-can be broken down into monosaccharides easily due to many sites for enzyme action
-has little effect on the osmotic strength of the cell.
the terms indicating what branching is and how it relates to the monosaccharide molecules involved. Eg a1 4 linkage and a1 6 branching.
carbon 1 linked to carbon 4 of the next monosaccharide → linkages in straight chains
carbon 1 linked to carbon 6 of the next monosaccharide → linkages at branch points
the structure of glycogen and how its structure assists with storage and the fight and flight response.
glycogen has a tightly coiled structure and highly branched, this means that it can be easily broken down into monosaccharides faster due to the many sites for enzymes to act on.
what tissues in the body is glycogen stored?
muscle, liver
peptidoglycan and the role it plays in bacteria and what lysozyme does to it
peptidoglycan are polymers that lay side by side in the cell wall of bacteria and are cross-linked by short peptides.
By hydrolysing the glycosidic bonds between NAG and NAM in peptidoglycan and hence killing the bacterial cell
the structure of proteoglycans and the role they play in extra-cellular matrix.
extracellular protein/carbo called Aggrecans (core protein) attached non-covalently to hyaluronic acid
structural integrity
Understand the difference between glycoproteins and proteoglycans and lipo-polysaccharides.
glycoproteins: globular protein molecules with branched chains of monosaccharides covalently attached
proteoglycans: non-covalently bonded proteins called aggrecans to hyaluronic acid
lipo-polysaccharides: covalently bonded lipid to polysaccharide
Structure of the saturated fatty acid
straight hydrocarbon chain (no double bond)
structure of the unsaturated fatty acid
hydrocarbon chain with a kink (due to double bond)
structure of the triglyceride
1 glycerol + 3 fatty acid chains with removal of H2O group
monounsaturated and polyunsaturated fatty acid
mono: one double bond, poly: more than one double bond
structure of w 3 fatty acid
double bond 3 carbons from the omega carbon
strucure of w 6 fatty acid
double bond 6 carbons from the omega carbon
shingolipid
one polar head and 2 non-polar tails
phospholipid
one polar head and one non-polar tail
structural changes produced by the inclusion of a double bond in the carbon chain of a fatty acid
double bond results in a kink in the straight hydrocarbon chain
what effect the double bond kink will have on the physical properties of the fat at room temperature.
less packed together and hence more fluidity and hence permeability
Why the structure triglycerides allows for the storage of fat in adipose tissue.
-C-C and C-H bonds are non-polar and hence cannot form any hydrogen bonds with surrounding water molecules and hence is insoluble in water, hence does not affect water potential of the cell.
-C-C and C-H bonds release more energy when broken and hence for the same amount of fat stored as carbohydrates, fats release more energy and hence serves as a good storage in small amounts → lighter and takes up less space
what does amphipathic mean?
-amphiphatic means that the molecule consists of both polar and non-polar components.
give an example of a fat molecule that is amphipathic.
phospholipid
What role does cholesterol play in cell membranes?
maintain fluidity
Describe the general structure and chemistry of amino acids.
amine group, R group, central carbon atom, H atom, carboxyl group
Describe how amino acids are classified
essentials, non-essentials and R groups
4 levels of protein architecture
-primary (amino acid sequence)
-secondary (sub-structures: alpha helix and beta sheet)
-tertiary (three-dimensional structure)
-quarternary (complex of protein molecules)
Describe the general structure and chemistry of nucleotides
-nitrogenous base (A,T,G,C)
-phosphate group
-5 C pentose sugar
the types of nucleic acids and their functions
-DNA: template for RNA synthesis and DNA rep
-RNA: multiple functions but predominantly transfer information from DNA to ribosomes
the types of reactions involving nucleic acids
DNA rep, transcription, translation
What components make up a functional enzyme?
apoenzyme, co-factors, co-enzymes (inorganic ions)
prosthetic groups
co-factors and co-enzyme
How would you describe the type of interactions which occur between the enzyme and its substrate?
weak and numerous
What enables an enzyme to bind specifically to its substrate?
numerous weak non-covalent bonding → specificity of binding
How do enzymes increase the reaction rate?
enzymes catalyse the reactions by lowering the activation energy of the reaction
What type of kinetics do un-regulated enzymes follow?
Michaelis Menten Kinetics = Saturation Kinetics
How can enzymes be used diagnostically?
lactate dehydrogenase and cabronic anhydrase
What is the relationship between the Km of an enzyme and its affinity for substrate?
the lower the Km, the higher the affinity for the substrate
what is Km?
Km is the concentration of enzyme needed to reach half of the Vmax
What are 2 differences between regulated enzymes and non-regulated enzymes?
-non-regulated enzymes follow the Michaelis Kinetics while regulated enzymes do not.
-non-regulated enzymes have a Km and Vmax while regulated enzymes do not.
Do regulated enzymes follow Michaelis Menton kinetics? Explain your answer.
No. They are not dependent on substrate concentration but the presence of regulator.
What usually determines the activities of regulated metabolic pathways in cells?
regulated enzymes. feedback inhibition.
What is feedback inhibition?
end product influences the activity of enzyme in its own metabolic pathway.
Name three types of regulation which affects the activity of regulated enzymes?
-allosteric
-covalent modification
-modification of zymogens (proteolytic cleavage)
Broadly explain how allosteric enzymes and zymogens are controlled?
-allosteric enzymes - modulator binding
-zymogens - proteolytic cleavage
Can zymogens be controlled after activation? Explain your answer?
Yes. By the binding of an inhibitor to the enzyme active site.
What is an isozyme?
multiple enzymes which have different detailed structure but show reactivity to the same substrate.
example of an isozyme
lactate dehydrogenase
Describe the process of covalent modification in enzyme activation. Is it a reversible process?
Yes. Separate enzymes are involved in removing or adding the modifying group, ie. break covalent bond.
Describe why lactate dehydrogenase isozymes appear in the blood following a heart attack.
Lactic acid is present in the heart, all isozyme types catalyse:
Lactate + NAD → Pyruvate + NADH
Could the appearance of LDH isozymes in the blood indicate that a patient may have acute hepatitis? Why?
when a muscle as been torn, there is an increase in LDH5 (MMMM) since the muscle subunits are associated with the muscle
2 common functions of the microfilament, microtubule and intermediate filaments
give shape to the cell and intracellular movement of organelles and inclusions
microfilament structure and function and eg.
structure: composed of actin subunits
function: give the cell shape, mechanical support, muscle contraction, locomotion and phagocytosis
microtubules structure and function and eg.
structure: hollow tubular strucuture made out of tubulin
function: transport of organelles and inclusions within the cell, subunits for specialised organelles and cellular structures
eg. centriole
cilia structure and function
structure: hair-like structures that act as escalators
function: beat in unison, creates a unidirectional current
microvilli structure and function
structure: finger-like protrusions
function: increase surface area for absorption
Intermediate filaments structure and function
structure: Different protein subunits in cells of different tissues
function: General structural support NOT movement
cell polarity
differential distribution of cell membrane and organelle specialisation to facilitate cellular function
cell polarity in cell surfaces
apical: microvilli
lateral: concentration gradient
basal: heidesmosomes
Specialisations on lateral surfaces between epithelial cells
Desmosomes, Heidesmosomes, tight junction, gap junction
Desmosomes
'spot welds' intermediate filaments that span the cell
Gap junctions
hollow protein channels for small molecules to pass
Tight junctions
adjacent cell membranes fuse together, seals the intercellular passage from fluids and other substances
Heidesmosomes
half a desmosome, anchor cells to the base membrane
Passive transport (Facilitated diffusion, Diffusion, Osmosis)
movement of small ions and molecules across membranes without use of energy
active transport (primary, secondary and bulk transport)
with use of energy
BULK TRANSPORT
Pinocytosis and Phagocytosis
Pinocytosis
‘cell drinking’, endocytosis of fluid, smaller vesicle formed, no merger with lysosome
Phagocytosis
large particle taken into cell, microbe enclosed in vesicle, lysosome fuses with the vesicle
nucleus morphology & cell identification.
-spindle: compaction of the chromatin for protection, high flexibility and with differentiation the cells become more rigid
-lobulated: increases flexibility, easier to deform nucleus, pass through gaps between the EC and CT matrix
less lobes means shorter lifespan and less flexility BUT stronger structural support
Euchromatin
uncoiled, less dense region (transcribing) → protein synthesised
Heterochromatin
tightly coiled, denser region (non-transcribing) → protein not synthesised
Apoptosis
(programmed naturally) → still functional cells and contents not released
Necrosis
(by external factors) → non-functional cells and contents are released (autolysis)
Pyknosis
nuclear shrinkage
Karyohexis
nuclear fragmentation
Karyolysis
nuclear fade
the differences between eukaryotes and prokaryotes in respect to their chromosomes, cell wall, size, organelles, ribosomes and nucleus. (6 points)
-eukaryotes:
1) double stranded, linear DNA
2) no cell wall
3) larger in size
4) have organelles
5) 80S ribosomes
6) have nucleus
-prokaryotes
1) single stranded, circular DNA
2) cell wall
3) smaller in size
4) no organelles
5) 70S ribosomes
6) no nucleus
2. Order viruses, bacteria and eukaryotes by size, from the largest to the smallest.
-eukaryotes
-bacteria
-viruses
Name four ways (excluding DNA technology) in which bacteria can be classified into species.
-SHARED PROPERTIES
1) characteristic surface macromolecules
2) visible properties
3) physiological properties
4) PHYLOGENETIC:
What colour are Gram negative (G-ve) bacteria and what colour are Gram positive (G+ve) bacteria?
-Gram negative: red/pink
-Gram positive: blue/violet
What shape are streptococci bacteria?
spherical (chain of cocci)
What shape are bacilli bacteria?
cylindrical
What is a capsule or slime layer and give one advantage it provides to bacteria.
-polysaccharides formed outside cell wall
-prevents the cell from being identified by antibodies and hence survives
What structure allows certain bacteria to move towards nutrients or favourable environmental conditions?
flagella
Fimbrae (pili) are involved in what two processes?
-transfer of DNA from host to recipient (increasing resistance)
-surface attachment
What is the main function of the rigid cell wall found in bacteria?
stop cell from exploding
What are the differences (peptidoglycan and structure) in the cell walls between Gram positive and Gram negative bacteria.
-Gram positive: thick peptidoglycan
-Gram negative: thin peptidoglycan between the outermembrane and cell membrane
Describe the structure of peptidoglycan and how antibiotics such as penicillin target its structure.
complex penicilin targets the enzyme transpeptidase by inhibiting it → break the peptides → cross-linking of peptidoglycan prevented
What are teichoic acids and what type of bacteria (G+ve or G-ve) contains them?
-polymers of glycerol/libitol that gives the cell a -ve charge to attract and allow passages of cations, G+ve bacteria
What are the two main components of lipopolysaccharide? What bacteria (G+ve or G-ve) contains LPS?
complex lipid a + polysaccharide, G-ve bacteria
What role do granules play in bacterial cells?
cellular storage materials
Describe in general what an endospore is and what advantage it provides.
spore-like formations in the cell (like a plant seed) → germinated only when needed to be → resistant to unfavourable conditions
Why are penicillin antibiotics more effective against Gram positive bacteria in general?
no outermembrane with lipopolysaccharides like in Gram negative bacteria → hence easier to destroy the peptidoglycan cell wall
Explain the role of the membrane as a barrier with selective permeability.
maintain differences in ionic concentration inside and outside of the cell
Describe the roles of the major classes of transporters and ion channels in regulating cell function.
allow large molecules and ions to pass through/ leave the cell
Explain the ionic basis of the resting membrane potential.
-K+ leaks from the inside to outside of the cell and generates a negative charge inside vs outside
membrane polarized → voltage acquired
the structure of DNA at different organisational levels
-coiling of the long linear strand of chromosome to protect DNA from damage (not actively transcribing DNA anymore) → before cell division
-uncoiling for enzymes to get access to code
-PACKING IN NUCLEUS: DNA and associated proteins → form a granular thread → nucleosomes (cluster of eight proteins, histones, serve as spools to protect and organise DNA) → supercoils - preparation for cell division
the concept of redundancy in the genetic code
-often 2-3 codons code for the same amino acid (redudancy) → decreases chances of mutation
-’wobble’ base → although the third base changes, no change in amino acid code → resilience/buffering capacity
simple pedigree interpretation
sex-linked inheritance: mother to son
autosomal inheritance: father to son (since the female is needed to pass the trait from X chromosome)
the requirement for cells to grow and divide
-Cell is large enough
-DNA replicated
-Adequate supply of nutrients
-Growth factor stimulated
-Open space in tissue
the different phases of the cell cycle, and what role the cell is playing in each
**INTERPHASE**
-G0: non-dividing stage (exit from cell cycle)
-G1: cells metabolically active, duplicated organelles and cytosolic components (infrastructure)
-S: DNA and centrosome replicated (replication)
-G2: Cell growth continues, enzymes and other proteins are synthesised
**MITOTIC**
-Prophase: Individualisation of chromosomes, initiation of mitotic spindle, rupture of nuclear envelope
-Metaphase: Chromosomes arranged in equatorial plane, spindle completed, disappearance of nuclear envelope and nucleolus
-Anaphase: Longitudinal splitting of chromosomes and migration to poles
:Aggregation of chromosomes at the poles, beginning of cell division, initiation of cleavage furrow
-Telophase: Nuclear reinstitution, nuclear envelope and nucleolus formation, end of cell division
-Cytokineses: contractile ring forms cleavage furrow
relationship between mitosis and cytokinesis
mitosis is when the cell divides while the cytokinesis is when the cytoplasm of the cell divides and the cell cycle ends, with each chromosome consisting of a single chromatid.
different cells of the oral cavity
oral epithelium, nerve cells, salivary cells, bone cells
how are proteins synthesized
the central dogma (transcription followed by translation)
DNA →(transcription) mRNA → (translation) protein
how alternative splicing can give rise to protein complexity (20,000 genes->200000 proteins)
-Alternative splicing involves the excising of introns and splicing of exons from the pre-mRNA strand in different ways to form the mature mRNA.
-With multiple introns and exons, splicing may occur in a number of ways, creating polypeptides, and hence many different proteins
-same gene expressed in different cell types and produce many different polypeptide products
the relationship between the genetic code and the amino acid sequence of a polypeptide
-genetic code (message) is transported out of the nucleus and outside of the nucleus, the message must be translated from nucleic acid code to amino acid code