molecular biology Flashcards
macromolecules
proteins
carbohydrates
lipids
nucleic acids
metabolism
is the web of all the enzyme-catalysed reactions in a cell or organism
anabolism
the synthesis of molecules from small to larger molecules, condensation
catabolism
the breaking down of molecules, hydrolysis
organic compounds
carbon
carbon properties
can form 4 bonds can bond to functional bonds can form covalent bonds can for double and triple bonds can form chains or rings
carbohydrates form from
CHO
proteins form from
CHON
lipids form from
CHO
nucleic acids
CHONP
monomer of carbohydrates
monosaccharides
monomer of proteins
amino acid
monomer of lipids
fatty acids
monomer of nucleic acid
nucleotide
vitalism
a doctrine that dictated that organic molecules could only be synthesised by living systems
falsification of vitalism
synthesis of urea
water
H2O
two hydrogen atoms covalently bonded to oxygen atoms
properties of water
cohesion
adhesion
solvent properties
thermal properties
polarity of water
water is polar due to the slight difference in electronegativity
heat properties of water
Water has the capacity to absorb significant amounts of heat before changing state
This is due to the extensive hydrogen bonding between water molecules – the H-bonds need to be broken before a change in state can occur and this requires the absorption of energy (heat)
difference in water and methane
water: polar intermolecular hydrogen bonds higher boiling and melting point higher specific heat capacity higher heat vaporization higher heat of vaporization higher heat of fusion
methane:
non polar
weak dispersion forces
sweat
use of water as a coolant as
The change of water from liquid to vapour (evaporation) requires an input of energy
This energy comes from the surface of the skin when it is hot, therefore when the sweat evaporates the skin is cooled
Because water has a high specific heat capacity, it absorbs a lot of thermal energy before it evaporates
Thus water functions as a highly effective coolant, making it the principal component of sweat
cohesion
ability of the same molecule to stick together
adhesion
ability different molecules to stick together
surface tension
cohesion
The hydrogen bonding between water molecules allows the liquid to resist low levels of external force (surface tension)
The high surface tension of water makes it sufficiently dense for certain smaller organisms to move along its surface
capillary action
adhesion properties allows water to defy the movement of gravity.
solvent properties
give an example
water can dissolve any molecule with ions and electronegative atoms (polarity)
for example: NaCl
polysaccharides
multiple monosaccharides joined together
disaccharides
2 monosaccharides
what are carbohydrates
sugars
monosaccharides
glucose
galactose
fructose
disaccharide
sucrose
maltose
lactose
polysaccharides
glycogen
cellulose
starch
cellulose
found in cell walls of plants made of B-glucose (1-4 arrangement)
starch
energy storage polysaccharide found in plants
It is composed of α-glucose subunits (bound in a 1-4 arrangement) and exists in one of two forms – amylose or amylopectin
amylose
is a linear (helical) molecule
amylopectin
is branched (contains additional 1-6 linkages)
glycogen
energy storage polysaccharide formed in the liver in animals
It is composed of α-glucose subunits linked together by both 1-4 linkages and 1-6 linkages (branching)
types of fatty acids
saturated
monounsaturated
polyunsaturated
unsaturated
contains 1 or more double bonds
types of unsaturated fats
cis: bent, hydrogen on the same side
trans: straight, hydrogen on different sides
what are triglycerides
polymer of lipids, formed by condensation of three fatty acids and 1 glycerol
function of triglycerides
store long term energy
bad fats
saturated and trans
regulating blood cholesterol level
Low density lipoproteins (LDL) carry cholesterol from the liver to the rest of the body
High density lipoproteins (HDL) scavenge excess cholesterol and carry it back to the liver for disposal
types of fats affect cholesterol
saturated and trans increase LDL, therefore high cholesterol
cis increase HDL, lowering cholesterol levels
risks of cholesterol
hardening and narrowing of arteries
The accumulation of fat within the arterial walls lead to the development of plaques which restrict blood flow
If coronary arteries become blocked, coronary heart disease (CHD) will result – this includes heart attacks and strokes
lipid health claims
Diets rich in saturated fats and trans fats increase the risk of CHD
Diets rich in monounsaturated and polyunsaturated (cis) fats decrease the risk of CHD
difference in carbohydrates and lipids
both store energy, however carbohydrates is short term energy storage meanwhile lipids are used for long term energy storage. carbohydrates: store half the ATP stronger effect on osmotic pressure water soluble readily digested lipids: stores twice as much ATP less effect on osmotic pressure hydrophilic less easily digested
body mass index
mass in kg/ (height in m)^2
types of lipids
steroids triglycerides phospholipids waxes glycolipids
amino acids components
An amine group (NH2)
A carboxylic acid group (COOH)
A hydrogen atom (H)
A variable side chain (R)
polypeptides
multiple amino acids joined together
denaturation
a structural change in a protein that results in the loss (usually permanent) of its biological properties, unfolded protein
what causes the denaturation of protein
pH- Changing the pH will alter the charge of the protein, which in turn will alter protein solubility and overall shape
temperature-High levels of thermal energy may disrupt the hydrogen bonds that hold the protein together
gene sequencing is converted into a polypeptide by:
transcription-making an mRNA transcript based on a DNA template (occurs within the nucleus)
translation-using the instructions of the mRNA transcript to link amino acids together (occurs at the ribosome)
what is a proteome
all of the proteins produced by a tissue, cell, or an organism.
what are the functions of protein?
catalysis muscle contraction membrane transport cell to cell communication cell adhesion transport of nutrients and gas hormones receptors packing of DNA Immunity blood clotting tonsil strengthening cytoskeletons
what is an enzyme?
a globular protein which acts as a biological catalyst by speeding up the rate of a chemical reaction
what is the active site?
the region on the surface of the enzyme which binds to the substrate molecule
The rate of enzyme catalysis can be increased by improving the frequency of collisions via:
Increasing the molecular motion of the particles (thermal energy can be introduced to increase kinetic energy)
Increasing the concentration of particles (either substrate or enzyme concentrations)
enzyme activity
- substrate binds to active site of the enzyme
- while the substrates are bound to the active site they change into chemical reactions.
- the products separate from the active site, leaving it vacant for other substrates to bind again
factors that affect enzymatic activities:
temperature
pH
substrate concentration
how does temperature affect enzymatic activity
- Low temperatures result in insufficient thermal energy for the activation of an enzyme-catalysed reaction to proceed
Increasing the temperature will increase the speed and motion of both enzyme and substrate, resulting in higher enzyme activity
Higher temperatures THAN OPTIMAL TEMPERATURE will cause enzyme stability to decrease, as the thermal energy disrupts the enzyme’s hydrogen bonds
This causes the enzyme (particularly the active site) to lose its shape, resulting in the loss of activity (denaturation)
how does pH affect enzymatic activity
Changing the pH will alter the charge of the enzyme, which in turn will alter protein solubility and overall shape
Changing the shape or charge of the active site will diminish its ability to bind the substrate, abrogating enzyme function
how does substrate concentration affect enzymatic activity
Increasing substrate concentration will increase the activity of a corresponding enzyme
More substrates mean there is an increased chance of enzyme and substrate colliding and reacting within a given period
After a certain point, the rate of activity will cease to rise regardless of any further increases in substrate levels
This is because the environment is saturated with substrate and all enzymes are bound and reacting (Vmax)
measuring enzyme activity
gas production
digestion of a solid
digestion of a liquid
color change
immobilised enzymes are utilised in a wide variety of industrial practices
Biofuels Medicine Biotechnology Food production Textiles Paper
lactose
a disaccharide that is produced in lactating mammals as an energy source for newborns
lactose intolerance
they do not contain lactase. Without lactase, lactose will pass intact into the large intestine, where it is broken down by probiotic bacteria, As part of the bacterial fermentation process, large amounts of gas are produced
This leads to the various ailments associated with lactose intolerance – including abdominal bloating, cramps and flatulence
nucleic acids
the genetic material of the cell and are composed of recurring monomeric units called nucleotides
Each nucleotide is comprised of three principal components:
5-carbon pentose sugar (pentagon) Phosphate group (circle) Nitrogenous base (rectangle)
two types of nucleic acids present in our cells
DNA AND RNA
difference between DNA and RNA
DNA: deoxyribose ATGC double stranded forming a double helix RNA: ribose AUGC one stranded carries a message
what are the three types of RNA
mRNA, rRNA, tRNA
DNA structure
A-T
G-C
strands describes as antiparallel
double helix, twists at intervals every 34 angstrom
orientation: Nitrogenous bases are closely packed together on the inside and phosphates form an outer backbone
DNA replication is a:
semiconservative process:
One strand will be from the original template molecule
One strand will be newly synthesised
two key enzyme of DNA replication
helicase- unzips or unwinds the double strands
DNA polymerase- synthesizes a new strand
HL:
complex system of enzymes for the replication of DNA
helicase
primase-DNA primase generates a short RNA primer (~10–15 nucleotides) on each of the template strands
polymerase 1- Free nucleotides align opposite their complementary base partners (A = T ; G = C)
DNA pol III attaches to the 3’-end of the primer and covalently joins the free nucleotides together in a 5’ → 3’ direction
As DNA strands are antiparallel, DNA pol III moves in opposite directions on the two strands
On the leading strand, DNA pol III is moving towards the replication fork and can synthesise continuously
On the lagging strand, DNA pol III is moving away from the replication fork and synthesises in pieces (Okazaki fragments)
and 3- As the lagging strand is synthesised in a series of short fragments, it has multiple RNA primers along its length
DNA pol I removes the RNA primers from the lagging strand and replaces them with DNA nucleotides
ligase-DNA ligase joins the Okazaki fragments together to form a continuous strand
gyrase-DNA gyrase reduces the torsional strain created by the unwinding of DNA by helicase
Single Stranded Binding (SSB) Proteins-SSB proteins bind to the DNA strands after they have been separated and prevent the strands from re-annealing
These proteins also help to prevent the single stranded DNA from being digested by nucleases
leading versus lagging strand
On the leading strand, DNA polymerase is moving towards the replication fork and so can copy continuously
On the lagging strand, DNA polymerase is moving away from the replication fork, meaning copying is discontinuous
Okazaki fragments
the short fragments copied on the lagging strand
non-coding DNA
genes that are inactivated
types of non-coding dna
satellite DNA, telomeres, introns, ncRNA genes and gene regulatory sequences
nucleosome
the DNA is packaged with histone proteins to create a compacted structure
function of nucleosomes
Nucleosomes help to supercoil the DNA, resulting in a greatly compacted structure that allows for more efficient storage
Supercoiling helps to protect the DNA from damage and also allows chromosomes to be mobile during mitosis and meiosis
what does a nucleosome consist of
A nucleosome consists of a molecule of DNA wrapped around a core of eight histone proteins (an octamer)
telomerase
Telomeres can be lengthened by the enzyme telomerase, allowing for continued cell division past the Hayflick limit
Permanent activation of telomerase can cause cells to become immortal and leads to cancer (uncontrolled cell division)
transcription
the process by which an RNA sequence is produced from a DNA template
HL three main parts of transcription
promoter=The promoter functions as a binding site for RNA polymerase (the enzyme responsible for transcription)
coding sequence -After RNA polymerase has bound to the promoter, it causes the DNA strands to unwind and separate
The region of DNA that is transcribed by RNA polymerase is called the coding sequence
terminator - RNA polymerase will continue to transcribe the DNA until it reaches a terminator sequence
transcription process
RNA polymerase separates the DNA strands and synthesises a complementary RNA copy from one of the DNA strands
When the DNA strands are separated, ribonucleoside triphosphates align opposite their exposed complementary base partner
RNA polymerase removes the additional phosphate groups and uses the energy from this cleavage to covalently join the nucleotide to the growing sequence
Once the RNA sequence has been synthesised, RNA polymerase detaches from the DNA molecule and the double helix reforms, transcription happens from 5’–> 3’
three post-transcriptional events
capping
Polyadenylation
Splicing
capping
Capping involves the addition of a methyl group to the 5’-end of the transcribed RNA
The methylated cap provides protection against degradation by exonucleases
Polyadenylation
Polyadenylation describes the addition of a long chain of adenine nucleotides (a poly-A tail) to the 3’-end of the transcript
The poly-A tail improves the stability of the RNA transcript and facilitates its export from the nucleus
Splicing
removal of introns
alternative splicing
removal of exons
SL: genetic codes
the set of rules by which information encoded within mRNA sequences is converted into amino acid sequences (polypeptides) by living cells
codons
The mRNA sequence is read by the ribosome in triplets of bases
HL: Regulatory proteins bind to DNA sequences outside of the promoter and interact with the transcription factors
activator proteins- increases rate of transcription
silencer protein- decreases rate of transcription
control elements
The DNA sequences that regulatory proteins bind to
types of chromatin
heterochromatin
euchromatin
heterochromatin
When DNA is supercoiled and not accessible for transcription
euchromatin
When the DNA is loosely packed and therefore accessible to the transcription machinery
epigenetic
the study of changes in phenotype as a result of variations in gene expression levels
translation
the process of protein synthesis in which the genetic information encoded in mRNA is translated into a sequence of amino acids on a polypeptide chain
ribosomes
Ribosomes are made of protein (for stability) and ribosomal RNA (for catalytic activity)
what do ribosomes consist of
The small subunit contains an mRNA binding site
The large subunit contains three tRNA binding sites – an aminoacyl (A) site, a peptidyl (P) site and an exit (E
steps of translation
initiation
elongation
termination
translocation
when the peptide chain moves to p site and theater one is decayed to the E site
polysome
a group of two or more ribosomes translating an mRNA sequence simultaneously
cell respiration
the controlled release of energy from organic compounds to produce ATP
types of cell respiration
Anaerobic respiration involves the partial breakdown of glucose in the cytosol for a small yield of ATP
Aerobic respiration utilises oxygen to completely break down glucose in the mitochondria for a larger ATP yield
what is ATP (adenosine triphosphate)
a high energy molecule that functions as an immediate source of power for cell processes
glycolysis
Glycolysis breaks down glucose (6-C) into two molecules of pyruvate (3C), and also produces:
- Hydrogen carriers (NADH) from an oxidised precursor (NAD+)
- A small yield of ATP (net gain of 2 molecules)
the pyruvate is converted into
in animals–> lactic acid
plants–>ethanol and carbon dioxide
what energy storage will undergo anaerobic respiration
carbohydrates
where does Aerobic cell respiration take place and what does it require
requires the presence of oxygen and takes place within the mitochondrion
what does aerobic respiration consist of
consists of the link reaction, citric acid cycle (or Krebs cycle) and the electron transport chain
respirometer
a device that determines an organism’s respiration rate by measuring the rate of exchange of O2 and CO2
factors that affect the rate of respiration
temperature, hydration, light (plants), age and activity levels
