Biochemistry Flashcards
Define biochemistry
Chemical reactions within living organisms
Define biomolecules
Carbon compounds with different functional groups made of bulk elements
Explain what is meant by bulk and tract elements
Bulk- found most in mammalian body
Trace- found in small quantities in the mammalian body
Define macromolecules
The major constituents of cells
What are supramolecular complexes?
Assembly of macromolecules into large functional units
Define catabolism
Breakdown of large molecules into small, releasing energy
Define anabolism
Formation of large molecules from small, uses up energy
Explain how ATP is produced from food
Food is broken down into metabolic intermediates and CO2, releases energy
Energy converts NAD+ to NADH and H+ which then get converted back to NAD+ releasing energy to convert H+ and O2 into water which creates ATP
How does ATP release energy?
Hydrolysing ATP breaks bond between phosphate groups which store energy to be released
List the roles of water in the body
Lubricant
Solvent
Substrate in reactions
Cushion joints
Why is water a polar solvent?
It has poles from the negative oxygen and positive hydrogens
Is able to form hydrogen bonds between molecules
Define hydrophobic
Repels water
Define hydrophilic
Attracted to water
What type of solutes dont dissolve in water?
Hydrophobic
Explain the different ways of lipids dissolving in water
Each lipid molecule gets surrounded by highly ordered water molecules
Clusters of lipids push water out of between molecules so water only is around edge of cluster
Micelles form from clusters so only the hydrophilic head of lipids is exposed to water
What is a buffering system
Where addition of a weak acid or base has minimal effect on pH
What is the purpose of pH buffers?
Maintain optimum pH in the body
What are the main biological buffers?
Phosphate
Carbonic acid - bicarbonate
Protein
Explain the carbonic acid - bicarbonate buffer system
When acid/H+ is added stored bicarbonate is released from sodium bicarbonate to neutralise the acid into carbonic acid then carbon dioxide and water
What is the structure of an amino acid?
Central carbon atom surrounded by carboxyl group, hydrogen atom, amino group and variable R group
What are proteins?
Polypeptide chains made up of amino acids connected by peptide bonds
What does the peptide bond form beween?
Amino group and carboxyl group of amino acids
What is meant by the C and N terminal of proteins?
C- end with free carboxyl group
N- end with free amino group
What is the primary structure of proteins?
Amino acid sequence determining conformation and function of the protein
Define secondary structure of proteins
Local special arrangement of amino acids formed by hydrogen bonds
Explain alpha helix structure of proteins
Helical right hand twist arrangement with R groups facing out
Explain beta pleated sheet structure of proteins
Extended poly peptide backbone with R groups above and below plane
Organised parallel or anti-parallel
Define tertiary structure of proteins
Overall 3D conformation of polypeptide, forming extended fibrous or compact globular structures
Define quaternary structure of proteins
3D arrangement of subunits in multi-subunit protein
Held by ionic bonds
What is the precursor to all amino acids and how does it form amino acids?
Glucose
Undergoes 3 pathways to form glucose derivative precursors which form certain amino acids
How is biosynthesis of amino acids regulated?
Feedback inhibition, product inhibits further production
List the methods of protein testing
Callometric assays
Sodium dodecyl sulphate polyacrylamide gel electrophoresis/ SDS-PAGE and western blotting
ELIZA
Explain the process of callometric assays
Reactions cause colour change allowing inference of protein presence or activity
Semi quantitative measure
Explain SDS-PAGE and western blotting
Separates proteins by size, gel forms pores for proteins to pass with larger proteins being less able to pass
Electrical current is applied causing proteins to become negatively charged and follow the current
When separated proteins get transferred to membrane and get detected by antibodies binding
Secondary antibodies bind for visualisation
Explain the ELIZA test
Antibodies detect certain proteins inside the cells
Cells get fixed and primary antibody is added to bind to protein
Labelled secondary antibody binds to primary antibody allowing protein visualisation
List advantages of protein testing
Identify host/pathogen proteins and show location
Quantitative or qualitative
Convenient and rapid
List disadvantages of protein testing
Variable sensitivity and stability
Can be expensive
Under what conditions do amino acids undergo oxidative deamination for energy generation?
Normal protein turnover and amino acid recycling
Surplus protein from protein rich diet
Starvation so no carbohydrates for energy source
Define deamination
Breakdown of amino acids into carbon skeleton and ammonia
How is nitrogen excreted in mammals, birds and aquatic species?
Mammals- urea cycle
Birds- excreted as uric acid
Aquatic species- excrete ammonia, diluted in water
What are enzymes?
Biological catalysts
How do enzymes work?
Speed up the rate of reaction without being changed themselves
Lower activation energy
What do cofactors do?
Carriers or donors of functional groups
What factors effects rate of reaction?
Reaction catalysed and concentration of the substrate
Explain the difference between competitive and non-competitive enzyme inhibitors
Competitive- inhibitor binds to active site of enzyme
Non-competitive- inhibitor binds in place not active site but changes active sites shape so enzyme cant bind
How is enzyme activity controlled?
Supply of substrate- storing in vacuoles
Amount of enzyme
Allosteric control- allosteric regulators bind to enzyme to change its active sites shape altering its activity
Proteolytic cleavage- enzymes produced as zymogen then later activated
Covalent modification- phosphorylation or dephosphorylation in increase or decrease activity
What is the michaelis-menten equation?
Rate of product formation= (maximal rate of product formation x substrate concentration)/(enzyme affinity + substrate concentration)
How long can carbon chains be in monosaccharides?
3-7
What are the two types of monosaccharides?
Ketoses- ketone group present
Aldoses- aldehyde group present
What needs to be present for a monosaccharide to become a stereoisomer?
Chiral carbon
Define enantiomers
Mirrored isomers so have different configuration in space
Define epimers
Sugars that are different by configuration around one carbon
When do monosaccharides form cyclical structures?
In solution when they have more than 5 carbons in their chain
Why are monosaccharides known as reducing agents?
Donate electrons when oxidised by oxidising agents
Describe the test for reducing sugars
Benedicts reagent using Cu2+ ions
Colour change from blue to red
What bonds form between monosaccharide molecules to form di- and polysaccharides?
Glycosidic
What are the types of polysaccharide?
Homopolysaccharide- one type of monomer
Heteropolysaccharide- multiple types of monomers
What are the functions of carbohydrates?
Stored fuel
Information carriers
Energy
Structural materials
How can carbohydrates act as information carriers?
Communication between cells and extracellular surroundings
Label proteins for transport or destruction
Recognition sites for extracellular molecules
Form glycocalyx layer or eukaryotic cells for recognition and binding
What is mean by a glycoconjugate?
Informational carbohydrate linked covalently to protein or lipid
What are the types of structural materials of carbohydrates?
Cellulose- homopolysaccharide, unbranched glucose chain forming tough insoluble plant cell walls
Chitin- similar to cellulose, important in exoskeletons
Peptidoglycans- heteropolysaccharide in bacterial and algal cell walls
Glycosaminoglycans- heteropolysaccharide making extrcellular matrix to provide elasticity and adhesiveness
What are some examples of heteropolysaccharides?
Hyaluronic acid- lubricant in joints
Chondroitin sulphate- cartilage and tendons
Keratin suplhate- bone, hair
Heparan sulphate- interacts with growth factors
What are the types of glycoconjugates?
Proteoglycans
Glycoproteins
Glycolipids
Explain the general process of cell signalling
Extracellular signalling molecules bind to cell surface protein receptors
Cascade of signalling events triggered in cell to amplify signal
Response produced
What is intercellular signalling?
Signalling between cells
Describe the types of intercellular signalling
Endocrine- molecules travel between cells in the blood
Paracrine- signalling molecules act on cells in immediate area
Neuronal- Signalling molecules travel from neuronal cell to target cell across a synapse
Contact dependent- signal molecules expressed on cell surface of one cell bind to another cells receptor when make contact
How does the same receptor on different cells cause different responses when triggered?
Different intracellular cascades and effector proteins cause different response to the same extracellular receptor
List the types of extracellular receptors
Ion-channel-couple receptors
Enzyme coupled receptors
G protein coupled receptors
Describe how ion-channel-couple receptors work
In electrically excitable cells, convert chemical signals into electrical signals
Signal molecule binds to receptor causing channel to open allowing ions to move across plasma membrane
Causes membrane potential to change producing electrical current
Describe how enzyme coupled receptors work
Binding of signal molecules induces binding of two receptors
Activates intracellular protein kinase domain which phosphorylates the receptor and target proteins on tyrosine residues
Signal gets relayed by activated signalling proteins
Describe how G protein couple receptors work
Linked to cell surface receptors that are activated by signal molecule which in turn activates the G protein
Activated G protein activates enzymes to amplify the signal by producing lots of secondary messenger molecules
What are the types of intracellular receptors?
Secondary receptors bind molecules released by cell surface receptors
Other receptors bind directly to signalling molecules that diffuse/enter into the cell
Describe the process of hormones affect on transcription
Hormone diffuses into cell carried on serum binding protein
Hormone binds to intracellular receptor in nucleus causing dimerization with hormone receptor complexes
This binds to regulatory regions adjacent to specific genes
Attracts co activator or co repressor protein to regulate transcription
What is the primary storage lipid?
Triglycerol
What are types of membrane lipids?
Phospholipids
Glycolipids
What structures do membrane lipids form?
Micelles
Vesicles
Bilayer
What are the types of hormones and what are they formed from?
Eicosanoids-arachidonate
Steroids- cholesterol
Why cant the body synthesise linolate fatty acid?
Hepatocytes can’t induce double bonds at carbon 10 onwards
Explain the process of desaturation of fatty acids
Double bond is introduced in oxidative reaction catalysed by fatty acetyl CoA desaturase
NADPH is oxidised via intermediates causing desaturation and 2 water produced as a by product
How are eicosanoids manufactured?
Cycloxygenase reduces arachidonate to prostaglandin G2 then H2
What roles do lipids have in the body?
Membranes- lipid bilayer
Energy
Hormones
Vitamins
How are lipids digested and stored?
Absorbed in small intestine
Fatty acids released by TAGs are packaged and delivered to muscle and adipose
How do fatty acids get released for energy?
Lipolysis via lipases releases 3 fatty acids and a glycerol into the blood
How do fatty acids enter the mitochondrial matrix for oxidation
Some enter directly others need to undergo enzymatic reactions before entry
Name examples of each type of hormones
Eicosanoids- prostaglandins, leukotrienes, paracrine hormones
Steroids- endocrine hormones, glucocorticoids, sex hormones, mineralocorticoids
What is the purpose of vitamins A, D3, E, K?
A- retinol, pigment
D3- cholecalciferol, calcium phosphate homeostasis
E- tocopherols, antioxidant
K- blood clotting
What is the structure of nucleotides?
Nitrogenous base
Pentose sugar
Phosphate group
What are the types of nitrogenous base?
Purines- adenine and guanine
Pyrimidines- cytosine, thymine, uracil
Describe how chromosomes form
Condensed DNA strands wrapped around histones to form nucleosome units
Nucleosomes form chromatin which further condenses into chromosomes
Describe the structure of chromosomes
2 sister chromatids joined at centromere
Telomeres are non coding buffers at the end of the arms to prevent shortening of chromosome
What are the P and Q arms of chromosomes?
P- short arm
Q- long arm
Compare the structure of DNA and RNA
DNA- double stranded, complementary strands running anti-parallel
RNA- single stranded
Explain the general structure of DNA and RNA
Nucleotides linked by phosphodiester bonds to form a sugar phosphate backbone
How many hydrogen bonds form between A-T and C-G?
A-T- 2
C-G- 3
What codes for amino acids on DNA?
Codons
What is meant by DNA code being degenerate?
Some amino acids are coded by more than one codon
What are the start and stop codons in DNA?
Start- AUG
Stop- UAA, UAG, UGA
What are genes?
Sequences of DNA coding for RNA so proteins
List what makes up genes
Introns- non-coding
Exons- coding
Promoter- before start codon
What are genomes structure?
Strands of DNA containing genes and non-coding DNA
What is meant by semi-conservative DNA replication?
2 new DNA molecules produced have one parent strand from the original molecule and one new strand from free nucleotides
What is the main synthesis pathway for new nucleotides?
De novo synthesis
What are the metabolic precursors for de novo synthesis?
Adenosine triphosphate Guanosine triphosphate Cytidine triphosphate Uridine triphosphate Deoxythymidine triphosphate
What is the precursor for purines?
Inosinate
What are the precursors for pyramidines?
Carbamoyl phosphate and aspartate
What is the salvage pathways?
Recycling of free bases and nucleotides released from nucleic acid breakdown
Name drugs that can affect nucleotide biosynthesis
Azaserine and acivicin Fluorouracil Methotrexate Trimethoprim Allopurinol
List advantages and disadvantages of DNA testing
Advantages- identify DNA mutations, identify pathogens, high sensitivity
Disadvantages- samples need to be sent to a lab, more expensive than protein tests
What is meant by genetically modified organisms and name some examples?
Organisms with modified genes for a specific function
GM bacteria- produce insulin
GM food- increase nutritional value and pest resistance
What is mean by cytogenetics?
Using karyotype to determine sex by looking at sex chromosomes
What is the polymerase chain reaction?
Method of replicating a fragment of DNA millions of times
What are advantages of the polymerase chain reaction?
Allows detection of DNA from tiny amount
Rapid, simple and inexpensive
What is the purpose of gene therapy?
Replacing a defective gene with a functional copy
What is meant by qPCR and RT-PCR?
qPCR- quantitative polymerase chain reaction
RT-PCR- quantitative reverse transcriptase polymerase chain reaction
How does qPCR work?
Dye uses fluoresces when bound to DNA double strand so level of fluorescence relates to quantity of DNA present
Lower the Ct value the more starting DNA as fluorescence level is reached after fewer cycles
What is the purpose of RT-PCR?
Determine mRNA levels by reverse transcriptase to convert RNA to DNA
Is then amplified by PCR
Explain the different categories of hormones and how they travel and bind to their target cell
Autocrine- bind to cell releasing the hormone
Paracrine- released into extracellular space and act on neighbouring cells
Endocrine- released into blood and carried to cells throughout the body
Describe glucose homeostasis after eating
Initially after eating- high blood glucose, all tissues use glucose as energy source
4-16 hours after meal- low blood glucose, counterbalanced by conversion of glycogen to glucose and gluconeogenesis in the liver
16-30 hours after meal- gluconeogenesis is main glucose source due to low glycogen, some tissues reduce glucose consumption
2-24 days after meal- glycogen stored depleted and gluconeogenesis is only glucose source, brain begins to use ketone bodies for energy
24 days after meal- brain uses ketone bodies for main energy source, glucose very scarce
Where are fuel reserves in the body?
Glycogen in the liver and some in muscles
TAGs in adipose
Tissue proteins when needed
How are fuel reserves managed?
Hormones to keep blood glucose constant
Describe the effect of insulin
Signals blood glucose too high so causes cells to take up excess glucose from blood and convert it to glycogen and TAGs for storage
Describe the effect of glucagon
Signals blood glucose is too low causing tissues to produce glucose by glycolysis, liver also produces glucose by gluconeogenesis
Explain the affect of adrenaline on metabolism
Signals impending activity from tissues causing metabolic change- increases heart rate, glucose production, glycolysis and fatty acid metabolism
What is the role of glucocorticoids on glucose homeostasis?
Mediate long term response to stress and starvation stimulating breakdown of non-essential muscle proteins and promotes gluconeogenesis
What is the function of the pancreas?
Produce digestive enzymes and hormones to control blood glucose
What do the different islets of Langerhans produce?
beta- insulin
alpha- glucagon
delta- somatostatin
What are the different types of diabetes?
Type 1- failure of pancreas to produce or secrete insulin
Type 2- failure of body to respond to insulin
How is diabetes diagnosed?
Glucose tolerance test after overnight fast
What are metabolic disturbances associated with diabetes for carbohydrates and triglycerides?
Carbohydrate- low glucose uptake to muscles and adipose, increased glycogen breakdown and gluconeogenesis causing hyperglycaemia
Triglyceride- increased lipolysis, fatty acid oxidation and ketone body production causing ketoacidosis
What happens in obesity?
Taking in more calories than used as fuel so excess is stored as fat or wasted in heat production
What is the purpose of adipokine hormones in regulation of body mass?
Regulate fuel intake and energy use to maintain suitable levels of adipose tissue
What are the examples of adipokines?
Leptin and adiponectin
Explain the role of adiponectin
Affects metabolism of fatty acids and carbohydrates in liver and muscle
Sensitises organs to insulin
Increases fatty acid uptake by myocytes and beta oxidation of fatty acids in the muscle
Blocks fatty acid synthesis and gluconeogenesis in hepatocytes
Stimulates glucose uptake and catabolism in muscle and liver
Explain the role of leptin
Acts on hypothalamus to reduce appetite as carries message that fat reserves are adequate
Increases energy use
Stimulates production of hormones which decrease appetite and inhibit hormones that increase appetite
What happens if there are defects involving leptin?
Not signalling adequate fat reserves
Causes high cortisol, unable to stay warm, unrestrained appetite, abnormal growth, infertility, insulin resistance
Low leptin levels effects
Maintain fat reserves
Reduces thermogenesis for fuel consumption as less fuel diverted for heat production
Less thyroid hormone produced so slows basal metabolic rate
Less sex hormones produced
How are short term eating behaviors regulated?
Ghrelin- appetite stimulant
PYY3-36- respond to food entering the stomach causing hunger to be reduced
What are the precursors for TAGs?
Fatty acyl CoA and glycerol 3 phosphate
What regulates TAG production?
Insulin by promoting conversion of carbohydrates and proteins to TAGs
What different RNA is involved in translation?
mRNA- encodes amino acid sequences of protiens
tRNA- reads mRNA and carries correct amino acid
rRNA- part of ribosomes
How does translation occur?
In ribosomes mRNA directs joining of amino acids
mRNA read 5’ to 3’ direction in codons
Define glycolysis
Glucose to pyruvate for energy generation
Define gluconeogenesis
Process of creating glucose
Define glycogenolysis
Glycogen to glucose
Define glycogenesis
Glucose to glycogen
What is needed for DNA polymerase to bind to leading strand in DNA replication
RNA primers
