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Principles > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

Detail the bond strength of molecules form strongest to weakest

A

covalent, ionic, hydrophobic interaction (non-polar, polar) van der waals forces

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2
Q

What are the oxidation states of carbon?

A

Alkane(fats), alcohol(carbs), aldehyde, carboxylic acid, carbon dioxide (final product)

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3
Q

What do proteins and peptides consist of?

A

Amino acids

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4
Q

what are some lipids?

A

triglycerides, phopholipids and steroids

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5
Q

Nucleic acids?

A

DNA and RNA

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6
Q

What are some carbohydrates?

A

mono, di, and poly saccharides

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7
Q

give an example of a Monosaccarides?

A

glucose but can be present as multiple structures

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8
Q

What is the struture of lactose?

A

disaccharides

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9
Q

Give an example of a polysaccaride

A

cellulose, glycogen

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10
Q

What is the first law of thermodynamics

A

Energy is neither created nor destroyed

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11
Q

What is the second law of thermodynamics?

A

When energy gets converted from one form into another some of that energy is not available to do work

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12
Q

What equals the change in free energy?

A

energy of products - energy of reactants

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13
Q

When does negative free energy occur?

A

exergonic so it occurs spontaneously

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14
Q

When does positive free energy occur?

A

endergonic ( can not occur spontaneously and therefore requires energy)

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15
Q

How is free energy related to point of equilibrium?

A

Delta G (free energy) is nar zero means the reaction is readily reversible

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16
Q

What does entropy equal

A

loss of usable energy

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17
Q

Detail the four different structures of proteins

A

Primary - sequence of amino acids
secondary - formation of backbone (poly peptide)
tertiary - 3d structure
quaternary - spatial arrangement of multiple subunits (disulphide bonds holds proteins together)

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18
Q

Where are collagen triple helixes present?

A

Abundant in connective tissue

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19
Q

What do SMR release?

A

steroid hormones, lipids, phospholipids - involved in testes, ovaries and skin oil glands

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20
Q

rough ER?

A

synthesises polypeptides

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21
Q

What is the mitochondria?

A

powerhouse of the cell

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22
Q

What does the golgi apparatus do?

A

receives material from ER and distributes to cell, it can also modify proteins

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23
Q

ribosomes

A

RNA is translated into proteins

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24
Q

prokaryote

A

microscopic single cell organism that does not have a defined nucleus

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25
Q

eukaryote

A

normal cell with nucleus

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26
Q

What is a nucleoside?

A

base + sugar

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27
Q

nucleotide?

A

nucleoside + phosphate

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28
Q

Purines

A

adenine and guanine

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29
Q

pyrimidines

A

uracil, thymine and cytosine

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30
Q

Where does phosphodiester bonds lie between?

A

3’ OH group and 5’ triphosphate

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31
Q

What is the basic base pairing of DNA

A

guanine - cytosine

adenine - thymine

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32
Q

What are the main points in DNA replication?

A

always in 5’ to 3’ direction

catalysed by DNA polymerase

RNA primer is required for DNA replication

leading strand - always has free 3’ end

lagging strand - replicated in short fragments called okazaki fragments

helicase unwinds the DNA

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33
Q

What does RNA contain?

A

it is only single stranded but contains a stem loop

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34
Q

What are the three types of RNA?

A

tRNA - transfer RNA take amino acids to ribosomes
anticodons consist of 3 nucleotides

rRNA - they are integral parts of the ribosome (combine with protiens)
mRNA - take genetic information to the protein

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35
Q

What are the different types RNA polymerases?

A

prokayote has 1 type

eukaryote has 3 types (1,2 and 3)

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36
Q

What does polymerase 2 synthesise

A

all mRNA

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37
Q

Detail the whole process of transcription

A

RNA polymerase binding - detects initiation sites on DNA (promoters) but requires transcription factors

DNA chain separation - unwinding of DNA

transcription initiation - selection of first nucleotide of growing RNA, requires other general transcription factors

elongation - addition of further nucleotides to RNA chain - RNA synthesised in 5’ to 3’ direction

Termination - release of finished RNA

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38
Q

When is transcription factor 2 D used?

A

required for all pol 2 transcribed genes

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39
Q

What are are exons and introns? How are they separated?

A

exons coding regions, introns - non coding regions

separated by splicing which splices out the introns

40
Q

How many combinations are there if 20 amino acids are present?

A

64 possible combinations

41
Q

What are the components involved in translation?

A

amino acid, tRNA’s, aminoacyl-tRNA synthetases, protein factors, ATP/GTP, ribosomes and mRNA

42
Q

What is the start codon ?

A

AUG

43
Q

Describe the process of initiation of translation

A

initiation - GTP provides energy, ribosomal subunit binds to 5’ end of mRNA, moves along until start codon is found
initiator tRNA pairs to start codon
large subunit joins assembly and initiator tRNA is located in p site

44
Q

elongation

A

elongation factor brings aminoacyl -tNRA to A site, GTP and second elongation factor regenerates the first to pick up next aminoacyl-tRNA

45
Q

When is peptidyl transferase useful?

A

catalyses peptide bond formation between amino acids in P and A sites

46
Q

Describe the process of termination:

A

Occurs when A site of ribosome encounters a stop codon

finished proteins cleaves off tRNA

47
Q

what are the 3 tRNA binding sites?

A

exit, peptidyl and aminoacyl

48
Q

what are post translation ribosomes?

A

free ribosomes in cytosol proteins (nucleus, mitochondria)

49
Q

What are co - translational ribosomes

A

bound ribosomes on the rough endoplasmic reticulum

50
Q

What are the two different types of genetic code?

A

degenerate - many amino acids have more than one code

unambiguous - each codon codes only for one amino acid

51
Q

What is a biological catalyst

A

Speeds up the rate a reaction reaches equilibrium but doesn’t change the position of equilibrium

lowers activation energy and stabilises the transition state

52
Q

What are apo enzymes and what are holoenzymes?

A 
apo = without cofactor 
holo = with co factor
53
Q

What is induced fit?

A

binding of substrate induces a conformational change in the shape of the enzyme resulting in a complementary fit

54
Q

How is phosphorylation carried out?

A

through the use of protein kinases

55
Q

Define Vmax, Km and why lineweaver burk plots are used over hyperboles

A

Vmax = maximal rate of reaction at unlimited substrate concentration

Km = michaelis constant = 50% Vmax

used because it is easier to read Vmax and Km - Vmax s the interation of the straight line with the Y axis

Km is the line’s intersection with the X axis

56
Q

What are the two different types of enzyme inhibition?

A

competitive - binds to active site, Vmax remains the same and Km varies

Non-competitive - bind to site other than active, Km stays the same and Vmax varies

57
Q

What relationship do enzymes have with allosteric control?

A

sigmoidal relationship

58
Q

Why is cholesterol important?

A

present in cell membranes, component of myelin sheath

precursor molecule for - steriod hormones, Vit D and Bile acids

59
Q

Why are triglycerides important?

A

Present in all cell membranes - lipid bilayer

highly concentrated energy stores

60
Q

What is enthalpy?

A

heat content

61
Q

What does metabolism consist of?

A

Anabolism (requires energy - endergonic and reductive) catabolism ( breakdown of molecules to yield energy - exergonic and oxidative)

62
Q

WHy is ATP less stable than ADP

A

negative charges close together in ATP put a strain ( electrostatic repulsion) on the molecule

63
Q

What is a hydrogen bond?

A

polarised bond allow the hydrogen to interact with unshared electrons from another electroneagive atom

64
Q

What are the shape of hydrogen bonds?

A

tend to be linear(in a straight line)

65
Q

what is the structure of a micelle?

A

head group in contact with water and tail group sequestered from water

66
Q

What is the structure of a peptide bond?

A

partial double bond character
planar
peptide bonds are strong and rigid

67
Q

What defines an acid?

A

proton donators

68
Q

What are zwitterions?

A

amino acids without charged side groups

69
Q

What is central dogma?

A

DNA - RNA to protein (transcrption, translocation)

70
Q

What is the product of glucose oxidation?

A

CO2 and water

71
Q

How does glucose get into the cell?

A

Glucose transporters (GLUT) by facilitated diffusion

72
Q

What is the initial pathway of conversion of glucose to pyruvate? -

A

glycolysis

73
Q

What is the net gain of ATP in glycolysis?

A

Net gain of 2 ATP (uses 2 ATP but creates 4 ATP)

74
Q

Describe glycolysis

A

Glucose is converted into fructose 1-6-bisphosphate (using 2 ATP)

then it turns inot 2 triose phosphates then into 2 pyruvate generating 4 ATP and 2 NADH + 2H+

75
Q

What does hexokinase do?

A

phosphorylates glucose

76
Q

What does phosphofructokinase do?

A

phosphorylates fructose 6 phosphate

77
Q

How is NAD+ regenerated?

A

oxiadtive metaboism of pyruvate

78
Q

What are the two outcomes of pyruvate?

A

anaerobic - lactic acid, alcoholic fermentation

aerobic - further oxidised in TCA

79
Q

What is the structure of a mitochondira?

A

contain inner membrane proteins, outer membranes, central matrix and contain crisae folds

80
Q

Detail the aerobic metabolism of pyruvate

A

Enters mitochondrial matrix, converted to acetyl CoA (catalysed by PDC)

condenses with 4C compound to form 6C compound

6C compound decarboxylated twice - yields CO2

4 oxidation reactions, ( yields NADH + H+ and FADH2

GTP formed

4C compound recreated

81
Q

Where are the enzymes found int he TCA cycle?

A

matrix, apart from succinate dehydrogenase ( integrated into mitochondrial membrane)

82
Q

What are the products of the TCA cycle

A

3 NADH + H+
1 FADH2
1 GTP
2 CO2

83
Q

What is phosphoryl transfer potential

A

Free energy change for ATP hydrolysis

84
Q

How is electron transfer potential measured?

A

redox potential of a compound

85
Q

What is the standard redox potential - negative and positive

A

A measure of how readily it donates an electron

negative - reduced form og X has lower affinity for electrons than hydrogen

positive - reduced form of X has higher affinity for electrons than hydrogen

86
Q

What are the 2 stages of oxidative phosphorylation

A

coupling of respiration to ATP synthesis

electron transport and ATP synthesis:

87
Q

What happens during the electron transport chain?

A

respiratory chain, Electrons from NADH enter at complex 1, elections from FADH2 enter at complex 2 (TCA cycle)

electrons are handed down from higher to lower redox potentials - transferred onto O2 from H2O

Transfer of electrons through resp chain is coupled to H+ transport from mito matrix to intermembrane space

electochemical gradient - more protons in inter-membranous space than matrix, matrix side more negative, protons attracted to matrix - coupled to ATP synthesis

88
Q

How is oxidative phosphylation inhibited?

A

Cyanide, axzide, adn CO inhibit electrons to O2

no proton gradient formed therefore no ATP generated

89
Q

Why is oxidative phosphorylation important?

A

electrons form NADH and FADH2 used to reduce O2 and H20

energy used to pump protons from mitochondiral matrix to intermembrane space

protons flow back across membrane
energy of proton flow is used to phosphorylate ADP to ATP

90
Q

What is the final balance of this whole cycle?

A 
glycolysis = 2 ATP 
TCA (2 GTP) = 2 ATP 
10 NADH + H+ = 25 ATP 
TCA cycle (2FADH2) - 3 ATP 
1 glucose molecule yields = 30-32ATP molecules
91
Q

What are isozymes?

A

Isozymes are like isomers – they catalyse the same reaction but have
different structures and chemical properties.

92
Q

What is a zymogen?

A

A zymogen is an inert substance

which can be chemically converted into an enzyme.

93
Q

What does negative enthalpy equal?

A

exothermic reaction

94
Q

What does negative gibbs energy equal?

A

The reaction is carried out spontaneously

95
Q

What is an accurate description of hydrogen bonds?

A

They usually lie in a straight line

96
Q

Production of ATP is required to produce the basic currency of energy for all cellular processes - why do rapidly contracting human muscle cells start producing lactic acid?

A

The cells have to convert NADH into NAD+

Principles (10 decks)

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