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Biochemistry Flashcards

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Biology 101 flashcards
1
Q

Define biochemistry

A

Chemical reactions within living organisms

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2
Q

Define biomolecules

A

Carbon compounds with different functional groups made of bulk elements

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3
Q

Explain what is meant by bulk and tract elements

A

Bulk- found most in mammalian body

Trace- found in small quantities in the mammalian body

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4
Q

Define macromolecules

A

The major constituents of cells

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5
Q

What are supramolecular complexes?

A

Assembly of macromolecules into large functional units

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6
Q

Define catabolism

A

Breakdown of large molecules into small, releasing energy

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7
Q

Define anabolism

A

Formation of large molecules from small, uses up energy

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8
Q

Explain how ATP is produced from food

A

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

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9
Q

How does ATP release energy?

A

Hydrolysing ATP breaks bond between phosphate groups which store energy to be released

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10
Q

List the roles of water in the body

A

Lubricant
Solvent
Substrate in reactions
Cushion joints

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11
Q

Why is water a polar solvent?

A

It has poles from the negative oxygen and positive hydrogens

Is able to form hydrogen bonds between molecules

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12
Q

Define hydrophobic

A

Repels water

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13
Q

Define hydrophilic

A

Attracted to water

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14
Q

What type of solutes dont dissolve in water?

A

Hydrophobic

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15
Q

Explain the different ways of lipids dissolving in water

A

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

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16
Q

What is a buffering system

A

Where addition of a weak acid or base has minimal effect on pH

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17
Q

What is the purpose of pH buffers?

A

Maintain optimum pH in the body

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18
Q

What are the main biological buffers?

A

Phosphate
Carbonic acid - bicarbonate
Protein

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19
Q

Explain the carbonic acid - bicarbonate buffer system

A

When acid/H+ is added stored bicarbonate is released from sodium bicarbonate to neutralise the acid into carbonic acid then carbon dioxide and water

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20
Q

What is the structure of an amino acid?

A

Central carbon atom surrounded by carboxyl group, hydrogen atom, amino group and variable R group

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21
Q

What are proteins?

A

Polypeptide chains made up of amino acids connected by peptide bonds

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22
Q

What does the peptide bond form beween?

A

Amino group and carboxyl group of amino acids

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23
Q

What is meant by the C and N terminal of proteins?

A

C- end with free carboxyl group

N- end with free amino group

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24
Q

What is the primary structure of proteins?

A

Amino acid sequence determining conformation and function of the protein

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25
Q

Define secondary structure of proteins

A

Local special arrangement of amino acids formed by hydrogen bonds

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26
Q

Explain alpha helix structure of proteins

A

Helical right hand twist arrangement with R groups facing out

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27
Q

Explain beta pleated sheet structure of proteins

A

Extended poly peptide backbone with R groups above and below plane
Organised parallel or anti-parallel

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28
Q

Define tertiary structure of proteins

A

Overall 3D conformation of polypeptide, forming extended fibrous or compact globular structures

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29
Q

Define quaternary structure of proteins

A

3D arrangement of subunits in multi-subunit protein

Held by ionic bonds

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30
Q

What is the precursor to all amino acids and how does it form amino acids?

A

Glucose

Undergoes 3 pathways to form glucose derivative precursors which form certain amino acids

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31
Q

How is biosynthesis of amino acids regulated?

A

Feedback inhibition, product inhibits further production

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32
Q

List the methods of protein testing

A

Callometric assays
Sodium dodecyl sulphate polyacrylamide gel electrophoresis/ SDS-PAGE and western blotting
ELIZA

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33
Q

Explain the process of callometric assays

A

Reactions cause colour change allowing inference of protein presence or activity
Semi quantitative measure

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34
Q

Explain SDS-PAGE and western blotting

A

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

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35
Q

Explain the ELIZA test

A

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

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36
Q

List advantages of protein testing

A

Identify host/pathogen proteins and show location
Quantitative or qualitative
Convenient and rapid

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37
Q

List disadvantages of protein testing

A

Variable sensitivity and stability

Can be expensive

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38
Q

Under what conditions do amino acids undergo oxidative deamination for energy generation?

A

Normal protein turnover and amino acid recycling
Surplus protein from protein rich diet
Starvation so no carbohydrates for energy source

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39
Q

Define deamination

A

Breakdown of amino acids into carbon skeleton and ammonia

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40
Q

How is nitrogen excreted in mammals, birds and aquatic species?

A

Mammals- urea cycle
Birds- excreted as uric acid
Aquatic species- excrete ammonia, diluted in water

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41
Q

What are enzymes?

A

Biological catalysts

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42
Q

How do enzymes work?

A

Speed up the rate of reaction without being changed themselves
Lower activation energy

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43
Q

What do cofactors do?

A

Carriers or donors of functional groups

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44
Q

What factors effects rate of reaction?

A

Reaction catalysed and concentration of the substrate

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45
Q

Explain the difference between competitive and non-competitive enzyme inhibitors

A

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

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46
Q

How is enzyme activity controlled?

A

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

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47
Q

What is the michaelis-menten equation?

A

Rate of product formation= (maximal rate of product formation x substrate concentration)/(enzyme affinity + substrate concentration)

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48
Q

How long can carbon chains be in monosaccharides?

A

3-7

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49
Q

What are the two types of monosaccharides?

A

Ketoses- ketone group present

Aldoses- aldehyde group present

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50
Q

What needs to be present for a monosaccharide to become a stereoisomer?

A

Chiral carbon

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51
Q

Define enantiomers

A

Mirrored isomers so have different configuration in space

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52
Q

Define epimers

A

Sugars that are different by configuration around one carbon

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53
Q

When do monosaccharides form cyclical structures?

A

In solution when they have more than 5 carbons in their chain

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54
Q

Why are monosaccharides known as reducing agents?

A

Donate electrons when oxidised by oxidising agents

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55
Q

Describe the test for reducing sugars

A

Benedicts reagent using Cu2+ ions

Colour change from blue to red

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56
Q

What bonds form between monosaccharide molecules to form di- and polysaccharides?

A

Glycosidic

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57
Q

What are the types of polysaccharide?

A

Homopolysaccharide- one type of monomer

Heteropolysaccharide- multiple types of monomers

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58
Q

What are the functions of carbohydrates?

A

Stored fuel
Information carriers
Energy
Structural materials

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59
Q

How can carbohydrates act as information carriers?

A

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

60
Q

What is mean by a glycoconjugate?

A

Informational carbohydrate linked covalently to protein or lipid

61
Q

What are the types of structural materials of carbohydrates?

A

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

62
Q

What are some examples of heteropolysaccharides?

A

Hyaluronic acid- lubricant in joints
Chondroitin sulphate- cartilage and tendons
Keratin suplhate- bone, hair
Heparan sulphate- interacts with growth factors

63
Q

What are the types of glycoconjugates?

A

Proteoglycans
Glycoproteins
Glycolipids

64
Q

Explain the general process of cell signalling

A

Extracellular signalling molecules bind to cell surface protein receptors
Cascade of signalling events triggered in cell to amplify signal
Response produced

65
Q

What is intercellular signalling?

A

Signalling between cells

66
Q

Describe the types of intercellular signalling

A

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

67
Q

How does the same receptor on different cells cause different responses when triggered?

A

Different intracellular cascades and effector proteins cause different response to the same extracellular receptor

68
Q

List the types of extracellular receptors

A

Ion-channel-couple receptors
Enzyme coupled receptors
G protein coupled receptors

69
Q

Describe how ion-channel-couple receptors work

A

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

70
Q

Describe how enzyme coupled receptors work

A

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

71
Q

Describe how G protein couple receptors work

A

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

72
Q

What are the types of intracellular receptors?

A

Secondary receptors bind molecules released by cell surface receptors
Other receptors bind directly to signalling molecules that diffuse/enter into the cell

73
Q

Describe the process of hormones affect on transcription

A

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

74
Q

What is the primary storage lipid?

A

Triglycerol

75
Q

What are types of membrane lipids?

A

Phospholipids

Glycolipids

76
Q

What structures do membrane lipids form?

A

Micelles
Vesicles
Bilayer

77
Q

What are the types of hormones and what are they formed from?

A

Eicosanoids-arachidonate

Steroids- cholesterol

78
Q

Why cant the body synthesise linolate fatty acid?

A

Hepatocytes can’t induce double bonds at carbon 10 onwards

79
Q

Explain the process of desaturation of fatty acids

A

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

80
Q

How are eicosanoids manufactured?

A

Cycloxygenase reduces arachidonate to prostaglandin G2 then H2

81
Q

What roles do lipids have in the body?

A

Membranes- lipid bilayer
Energy
Hormones
Vitamins

82
Q

How are lipids digested and stored?

A

Absorbed in small intestine

Fatty acids released by TAGs are packaged and delivered to muscle and adipose

83
Q

How do fatty acids get released for energy?

A

Lipolysis via lipases releases 3 fatty acids and a glycerol into the blood

84
Q

How do fatty acids enter the mitochondrial matrix for oxidation

A

Some enter directly others need to undergo enzymatic reactions before entry

85
Q

Name examples of each type of hormones

A

Eicosanoids- prostaglandins, leukotrienes, paracrine hormones
Steroids- endocrine hormones, glucocorticoids, sex hormones, mineralocorticoids

86
Q

What is the purpose of vitamins A, D3, E, K?

A

A- retinol, pigment
D3- cholecalciferol, calcium phosphate homeostasis
E- tocopherols, antioxidant
K- blood clotting

87
Q

What is the structure of nucleotides?

A

Nitrogenous base
Pentose sugar
Phosphate group

88
Q

What are the types of nitrogenous base?

A

Purines- adenine and guanine

Pyrimidines- cytosine, thymine, uracil

89
Q

Describe how chromosomes form

A

Condensed DNA strands wrapped around histones to form nucleosome units
Nucleosomes form chromatin which further condenses into chromosomes

90
Q

Describe the structure of chromosomes

A

2 sister chromatids joined at centromere

Telomeres are non coding buffers at the end of the arms to prevent shortening of chromosome

91
Q

What are the P and Q arms of chromosomes?

A

P- short arm

Q- long arm

92
Q

Compare the structure of DNA and RNA

A

DNA- double stranded, complementary strands running anti-parallel
RNA- single stranded

93
Q

Explain the general structure of DNA and RNA

A

Nucleotides linked by phosphodiester bonds to form a sugar phosphate backbone

94
Q

How many hydrogen bonds form between A-T and C-G?

A

A-T- 2

C-G- 3

95
Q

What codes for amino acids on DNA?

A

Codons

96
Q

What is meant by DNA code being degenerate?

A

Some amino acids are coded by more than one codon

97
Q

What are the start and stop codons in DNA?

A

Start- AUG

Stop- UAA, UAG, UGA

98
Q

What are genes?

A

Sequences of DNA coding for RNA so proteins

99
Q

List what makes up genes

A

Introns- non-coding
Exons- coding
Promoter- before start codon

100
Q

What are genomes structure?

A

Strands of DNA containing genes and non-coding DNA

101
Q

What is meant by semi-conservative DNA replication?

A

2 new DNA molecules produced have one parent strand from the original molecule and one new strand from free nucleotides

102
Q

What is the main synthesis pathway for new nucleotides?

A

De novo synthesis

103
Q

What are the metabolic precursors for de novo synthesis?

A 
Adenosine triphosphate
Guanosine triphosphate
Cytidine triphosphate
Uridine triphosphate
Deoxythymidine triphosphate
104
Q

What is the precursor for purines?

A

Inosinate

105
Q

What are the precursors for pyramidines?

A

Carbamoyl phosphate and aspartate

106
Q

What is the salvage pathways?

A

Recycling of free bases and nucleotides released from nucleic acid breakdown

107
Q

Name drugs that can affect nucleotide biosynthesis

A 
Azaserine and acivicin
Fluorouracil 
Methotrexate
Trimethoprim
Allopurinol
108
Q

List advantages and disadvantages of DNA testing

A

Advantages- identify DNA mutations, identify pathogens, high sensitivity
Disadvantages- samples need to be sent to a lab, more expensive than protein tests

109
Q

What is meant by genetically modified organisms and name some examples?

A

Organisms with modified genes for a specific function
GM bacteria- produce insulin
GM food- increase nutritional value and pest resistance

110
Q

What is mean by cytogenetics?

A

Using karyotype to determine sex by looking at sex chromosomes

111
Q

What is the polymerase chain reaction?

A

Method of replicating a fragment of DNA millions of times

112
Q

What are advantages of the polymerase chain reaction?

A

Allows detection of DNA from tiny amount

Rapid, simple and inexpensive

113
Q

What is the purpose of gene therapy?

A

Replacing a defective gene with a functional copy

114
Q

What is meant by qPCR and RT-PCR?

A

qPCR- quantitative polymerase chain reaction

RT-PCR- quantitative reverse transcriptase polymerase chain reaction

115
Q

How does qPCR work?

A

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

116
Q

What is the purpose of RT-PCR?

A

Determine mRNA levels by reverse transcriptase to convert RNA to DNA
Is then amplified by PCR

117
Q

Explain the different categories of hormones and how they travel and bind to their target cell

A

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

118
Q

Describe glucose homeostasis after eating

A

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

119
Q

Where are fuel reserves in the body?

A

Glycogen in the liver and some in muscles
TAGs in adipose
Tissue proteins when needed

120
Q

How are fuel reserves managed?

A

Hormones to keep blood glucose constant

121
Q

Describe the effect of insulin

A

Signals blood glucose too high so causes cells to take up excess glucose from blood and convert it to glycogen and TAGs for storage

122
Q

Describe the effect of glucagon

A

Signals blood glucose is too low causing tissues to produce glucose by glycolysis, liver also produces glucose by gluconeogenesis

123
Q

Explain the affect of adrenaline on metabolism

A

Signals impending activity from tissues causing metabolic change- increases heart rate, glucose production, glycolysis and fatty acid metabolism

124
Q

What is the role of glucocorticoids on glucose homeostasis?

A

Mediate long term response to stress and starvation stimulating breakdown of non-essential muscle proteins and promotes gluconeogenesis

125
Q

What is the function of the pancreas?

A

Produce digestive enzymes and hormones to control blood glucose

126
Q

What do the different islets of Langerhans produce?

A

beta- insulin
alpha- glucagon
delta- somatostatin

127
Q

What are the different types of diabetes?

A

Type 1- failure of pancreas to produce or secrete insulin

Type 2- failure of body to respond to insulin

128
Q

How is diabetes diagnosed?

A

Glucose tolerance test after overnight fast

129
Q

What are metabolic disturbances associated with diabetes for carbohydrates and triglycerides?

A

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

130
Q

What happens in obesity?

A

Taking in more calories than used as fuel so excess is stored as fat or wasted in heat production

131
Q

What is the purpose of adipokine hormones in regulation of body mass?

A

Regulate fuel intake and energy use to maintain suitable levels of adipose tissue

132
Q

What are the examples of adipokines?

A

Leptin and adiponectin

133
Q

Explain the role of adiponectin

A

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

134
Q

Explain the role of leptin

A

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

135
Q

What happens if there are defects involving leptin?

A

Not signalling adequate fat reserves

Causes high cortisol, unable to stay warm, unrestrained appetite, abnormal growth, infertility, insulin resistance

136
Q

Low leptin levels effects

A

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

137
Q

How are short term eating behaviors regulated?

A

Ghrelin- appetite stimulant

PYY3-36- respond to food entering the stomach causing hunger to be reduced

138
Q

What are the precursors for TAGs?

A

Fatty acyl CoA and glycerol 3 phosphate

139
Q

What regulates TAG production?

A

Insulin by promoting conversion of carbohydrates and proteins to TAGs

140
Q

What different RNA is involved in translation?

A

mRNA- encodes amino acid sequences of protiens
tRNA- reads mRNA and carries correct amino acid
rRNA- part of ribosomes

141
Q

How does translation occur?

A

In ribosomes mRNA directs joining of amino acids

mRNA read 5’ to 3’ direction in codons

142
Q

Define glycolysis

A

Glucose to pyruvate for energy generation

143
Q

Define gluconeogenesis

A

Process of creating glucose

144
Q

Define glycogenolysis

A

Glycogen to glucose

145
Q

Define glycogenesis

A

Glucose to glycogen

146
Q

What is needed for DNA polymerase to bind to leading strand in DNA replication

A

RNA primers

Pre-Clinical Science (5 decks)

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