BIOCHEMISTRY Flashcards
define an atom
smallest unit of an element
what does an atom contain
nucleus (protons & neutrons)
electrons
what is within a nucleus
protons
neutrons
what charge are protons
positive
what charge are neutrons
neutral
what charge are electrons
negative
what is the atomic number
number of protons
what is atomic mass measured in
Daltons (Da)
what is atomic mass
gives us the mass of one of the elements atoms
how many elements known to make up living organisms
26
what is covalent bonding
the bond formed when atoms share electrons
when is a single bond formed
when each atom contributes one electron
when is a double bond formed
when each atom contributes 2 electrons
what do organic molecules contain
carbon
what do inorganic molecules contain
NO CARBON (eg water)
what is a molecule
atoms joined via covalent bonds
what is molecular formula
symbols
eg H20
what is structural formula
drawn out with C and H and lines
do molecules have a charge
no they are neutral
do ions have charge
yes
what is an anion
some atoms are more stable with more electrons than protons
therefore ion carries a negative charge
what is a cation
some atoms carry less electrons than protons
therefore ion carries a positive charge
what is a radical
when a molecule has an unpaired electron
what pH is acidic
1-7
what pH is neutral
7
What pH is alkaline
7-14
what are the 4 biomolecules
proteins
nucleic acids
carbohydrates
lipids
what are inorganic substances
water
Ions (sodium, potassium, chloride, calcium, magnesium, bicarbonate, hydrogen phosphate)
what does a lysosome do
breakdown of proteins and other molecules
what does the nucleus do
contains DNA
what does RNA do
transcription & translation of proteins
What do ribosomes do
proteins production
what does the endoplasmic reticulum do
synthesis and storage
what does Golgi apparatus do
secretion of proteins
what does mitochondria do
site of metabolic processes
define metabolism
the sum of the chemical reactions occurring in a living organism/ part of it
what is the symbol for entropy
S
what does an increase in order do to entropy
decrease in entropy
what does a decrease in order do to entropy
increase in entropy
What is delta G
Free energy
What is the free energy equation
deltaG = DeltaH - TdeltaS
what is delta H
enthalpy (bond energy)
What is T delta S
Temp x entropy
what effects deltaG
Temperature
Pressure
Conc of reactants & products
pH
What are standard conditions for free energy change reaction
25 degrees
1atm pressure
pH 7
what is exergonic
free energy of products is lower than the reactants
therefore favoured
what is endergonic
free energy of products is higher than reactants
therefore unfavoured
What is equilibrium
dynamic state whereby energy of products and reactants is equal
When a compound accepts oxygen what happens
it is oxidised
When a compound loses oxygen what happens
it is reduced
When a compound loses hydrogen what happens
it is oxidised
catabolism
When a compound accepts hydrogen what happens
it is reduced
anabolism
how many hydroxyl groups do carbohydrates contain
at least 2 hydroxyl groups
what are monosaccharides
simplest carbohydrates
Function of carbs??
offer cells external protection (cellulose)
assist cells in recognising molecules when attached to proteins and lipids
what are ogliosaccharides
when 2-10 monosaccharides link covalently
linkages are glycosidic bonds
what is sucrose made from
glucose and fructose
what is lactose made from
galactose and glucose
what is maltose made from
2x alpha glucose
what are polysaccharides
formed from 10+ monosaccharides
give 2 examples of polysaccharides
cellulose
starch
what do lipids exist as
exist as large tissue (adipose)
what is a common feature of lipids
low solubility in water
what is a saturated fat
single bonds only (palimate)
what is an unsaturated fat
single and double bonds
what are fatty acids linked by
ester bonds
role of vitamin B1
thiamine
found in active site of pyruvate dehydrogenase
role of vitamin B6
coenzymes for aminotransferases and neurotransmitters
role of vitamin B12
serves as an enzyme in fatty acid processing
role of vitamin A
contained within the retinas of the eye
role of vitamin B2
riboflavin
precursor of coenzymes for redox reactions
role of vitamin D
involved in calcium absorption - bone health
role of sodium
Main cation in extracellular fluids
Essential for electrical transmission in nerves and muscle
Maintains water content in various compartments of the body
role of calcium
critical component of bones and blood clotting
role of potassium
interacts with Na+ to maintain fluid balance and electrical impulses
role of magnesium
cofactor for hundreds of enzymes
role of iron
embedded in proteins handling oxygen and the electron transport chain
role of copper
is a cofactor for cytochrome, a key component in the electron transport chain
role of zinc
sits in the active site of around 200 enzymes, one of which helping get rid of co2
role of manganese
a cofactor for over 100 enzymes involved in metabolism
role of chloride
main anion of extracellular fluids. it interacts with Na in maintenance of fluid balance and electrical charges across cell membranes
used in production of HCL
role of phosphorus
phosphoryl groups covalently attached to vast array of biological compounds (nucleic acids, high energy phosphates)
what is transcription
DNA becoming mRNA
what is translation
mRNA becoming a protein
how many different types of protein in human body
74,000
what are the 3 parts to an amino acid
amino group
carboxyl group
side chain/ variable group
what gives an amino acid its identity
the side chain/ variable group
how are amino acids joined
covalently through peptide bonds
what is it called when multiple amino acids are joined together
a polypeptide chain
what is primary structure of a protein
the basic amino acid sequence that determines protein shape and function
The simplest structure
what is secondary structure of a protein
peptides fold in complex ways due to hydrogen bonds
alpha helix & beta pleated sheet
what is tertiary structure of a protein
hydrogen bonds
electrostatic bonds
van der Waals interactions
disulphide bonds
what are electrostatic bonds between
positive and negatively charged groups
what are ionic bonds between
positive and negatively charged groups
what are van der Waals interactions between
a non covalent attraction due to movement of ions in atomic or molecular orbitals
what is quaternary structure of a protein
many proteins contain subunits that link together via the same interactions
what causes the denaturation of proteins
environmental factors such as heat/ acidity which can alter/ break forces
what are enzymes
essential catalysts that accelerate metabolic reactions
what are the 3 main features of enzymes
speed up reactions
display high specificity- each enzyme catalyses one reaction
catalytic power is regulated - speed of reaction is subject to a variety of factors
what are the limiting factors affecting rate of enzyme reactions
Substrate availability
Enzyme concentration
Temperature
pH
What are the purines
adenine & guanine
What are the pyrimidines
thymine (uracil in RNA)
cytosine
what are nucleotides joined together by
phosphodiester bonds
is DNA double or single stranded
double helix
is RNA double or single stranded
single stranded
describe DNA replication
- separate strands
DNA helices breaks H bonds to unzip molecule - primer binding
a small strip of RNA primer kickstarts replication - elongation
DNA polymerase adds complimentary base pairs in the 5- to 3- direction - termination
exonuclease removes original primers and then bases are re added to complete a new DNA double helix
what are the 3 types of RNA
mRNA (messenger, which decodes DNA)
rRNA (ribosomal, which decodes mRNA)
tRNA (transfer, which facilitates protein formation)
what are promotors
DNA region next to transcription site that docks RNA polymerase
what are enhancers
DNA regions that attract the transcription factor complex proteins
what is the trasncription factor complex
proteins that regulate the rate of mRNA formation
what are introns
non coding regions
what are exons
coding regions
describe translation
mRNA binds to subunit of rRNA where it is decoded
3 base sequence on mRNA is called a codon
this codon compliments an anticodon on a tRNA molecule
this binds to large subunit of mRNA holding an amino acid
allowing formation of a polypeptide chain via peptide bonds
ribosome moves along mRNA 5- to 3-
peptide bond formed between each amino acid
golgi apparatus modifies proteins & secreted in vesicles
describe how to measure total protein abundance via spectrophotometry
Bradford essay
protein mixed with blue dye called coomassie blue
in acidic conditions this results in a colour change brown-blue
what is the western blot
commonly used to detect a specific protein in a tissue homogenate or protein extract
what does Eliza testing stand for
enzyme linked immunosorbent assay
how does Eliza testing work
capture antibody and bind to well
add sample
wash microplate
add detection antibody
wash microplate
add substrate
read microplane
calculate results
is the myocyte single or multinucleated
multi nucleated due to fusion of myoblasts during development
can muscle fibres spontaneously contract
yes
what are the thick filaments called
myosin
what are thin filaments called
actin, tropomyosin, troponin
what is the m line made from
myosin and M protein
what is the Z line made from
a-actinin (alpha actinin)
what happens to the lengths of the filaments when the sarcomere contracts
they DO NOT change length
but the OVERLAP INCREASES
How is contraction caused in the muscle
by thick myosin and thin actin filaments sliding over each other
describe myosin
very large & abundant in muscle
consists of 2 large heavy chains & 2 small light chains
describe actin
main component of thin filaments
exists in 2 forms- G actin (globular) & F actin (fibrous)
tropomyosin and troponin attach to F actin
what happens to actin and myosin at rest
no binding
what part of myosin binds to actin
myosin head binds to actin
where on the the filament does myosin bind to actin
S1
causing a conformational change
creating a lever arm and power stroke happens generating force for contraction
what ion controls muscle contraction
calcium
how does calcium control muscle contraction
it permits the binding of myosin to F actin via troponin and tropomyosin
what is special about the acetylcholine receptor
it is ligand gated
what does ligand gated mean
it only changes its shape when interacting with its ligand (acetylcholine)
anabolic reactions can also be known as
endergonic
catabolic reactions are also known as
exergonic
what does myokinase do
add phosphate groups
is the myokinase reaction aerobic or anaerobic
anaerobic
what does creatine kinase (CK) do
can rapidly reform ATP
Are synthesis reactions anabolic or catabolic
anabolic eg- condensation
are breakdown reactions anabolic or catabolic
catabolic eg- hydrolysis
is glycolysis aerobic or anaerobic
anaerobic
what are the reactants of glycolysis
glucose
what are the products of glycolysis
2x pyruvate & NADH
how many ATP molecules are generated in glycolysis
2 atp molecules
what does exercise do to glycolysis and how
exercise speeds up glycolysis
- substrate availability
- physiological factors
- cellular factors
- molecular factors
what are the reactants of the Krebs cycle
acetyl coA
what are the products if the Krebs cycle
2 ATP
6 NADH
2 FADH2
8 H+
Is the Krebs cycle aerobic or anaerobic
aerobic pathway
where does the Krebs cycle take place
mitochondrial matrix
where does glycolysis take place
cytosol
What happens to Gibbs free energy when electrons are transferred
Gibbs free energy falls as electrons are transferred to FADH and NAD+ during glycolysis and Krebs cycle
what are reactants of oxidative phosphorylation
8 NADH
4 FADH2
what are products of oxidative phosphorylation
26 atp
6Co2
6H20
is oxidative phosphorylation aerobic or anaerobic
aerobic
what is gluconeogenesis
carbon skeletons from other molecules can be used to synthesise glucose for energy provision in a muscle
what helps digest protein in the stomach
pepsin enzyme
Hydrochloric acid
how much of body % is protein in men
16%
how much of body % is protein in women
14%
how many of the 20 amino acids are glucogenic
14
how many of the 20 amino acids are ketogenic
2
how many of the 20 amino acids are glutogenic and ketogenic
4
is transamination reversible
yes
what is transamination
the transfer of one amino group from one molecule to another
catalysed by enzyme aminotransferase
what is deamination and what does it form
the amino acid removal and loss of its amino group
forms ammonia which is toxic (so gets converted into urea in liver and then excreted)
what does FSR stand for
fractional synthetic rate
what are lipids
Diverse biological compounds, characterised by low solubility in water
what makes up a phospholipid
glycerol & 2 fatty acids
what does amphipathic mean in relation to phospholipids
one end is hydrophobic
one end is hydrophilic
what is a triacylglycerol made of
one glycerol unit
3 fatty acids
what are chylomicrons
a class of lipoprotein transport of insoluble triacylglycerol
where does breakdown of triacylglycerol happen
in cytosol
where does synthesis of triacylglycerol happen
in cytosol
what is lipolysis affected by
epinephrine both increases and decreases lipolysis
insulin reduces lipolysis
how are fatty acids degraded
through the pathway of beta oxidation in the mitochondria
how are lipids transported
in lipoproteins
what does exercise do to fatty acid oxidation
speeds it up
what is the energy yield of ATP-PC system
low
what is the energy yield of anaerobic system
medium
what is the energy yield of the aerobic system
high
what is the power of the ATP-PC system
High
what is the power of the anaerobic system
medium
what is the power of the aerobic system
low
how long does the ATP-PC system last
7 seconds
how long does the anaerobic system last
7-60s
how long does the aerobic system last
above 60s
is loosing electrons oxidation or reduction
oxidation
OILRIG
Is gaining electrons oxidation or reduction
redution
OILRIG
what Is the non specific part of the immune system called
innate immune system
what Is the specific part of the immune system called
acquired/ adaptive immune system
what is one of the main functions of the immune system
to be able to recognise self vs non self
what responses come under adaptive/ specific Immune system
cell mediated response (T cells) Humoral response (B cells)
what responses come under innate/ non specific Immune system
blood borne (phagocytes) Physical barriers (skin, saliva, yucas, stomach, tears)
what do T cells do
T cells release cytokine proteins which assist with killing infected cells
what do B cells do
can trigger release of antibodies
can differentiate into plasma cells to produce antibodies
