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Principles (Y1) > Biochem > Flashcards

Biochem Flashcards

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1
Q

What are the bond strengths strongest to weakest

A

covalent–>ionic–>hydrogen–>hydrophobic interactions–>vanderwaals

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2
Q

Redox reations

A

OILRIG- one molecule is reduced and one is oxidised

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3
Q

what is electronegativity

A

the attractive force that an atomic nucleus exerts on electrons

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4
Q

talk about the electronegativity of carbon and hydrogen

A

carbon>hydrogen.. carbon has a greater attractive force for electrons, so it gains electrons, therefore it is reduced and hydrogen is oxidised

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5
Q

Carbohyrates

A

monosaccharides- glucose
disaccharides- lactose
polysaccharides-cellulose, glycogen (alpha 1-4 occationally alpha 1-6)

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6
Q

1st law of thermodynamics

A

energy neither created nor destroyed

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7
Q

2nd law of thermodynamics

A

energy converted from one form to another, some of that energy become unavailable to do the work (ie energ is lost and never 100% effective)

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8
Q

Change in free energy (Kj/mol) DeltaG

A

DeltaG = (energy of products {delta H}) - (energy of reactants {T delta S} )

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9
Q

if free energy is negative

A

exergonic (can occur spontaneously) ie products have less fre energy than reactants

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10
Q

if free energy is positive

A

endergonic (cannot occur spontaneously - requires energy e.g. walking upstairs) ie products have more free energy than the reactants

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11
Q

at equlibrium delta G=0 what does this mean

A

readily reversible reactions

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12
Q

Ka=

A

acid dissociation constant

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13
Q

pH=

A

measurement of how many H+ ions in a solution

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14
Q

Reaction spontaneity can be achieved by

A
  • change in conc of a reactant
  • coupling with highly favourable processes
  • both of the above help delta G become neg
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15
Q

protein structures

A

Primary - sequence of amino acids

Secondary - formation of backbone (polypeptide)

Tertiary - 3d structure

Quaternary - Spatial arrangement of multiple subunits (disulphide bonds hold proteins together)

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16
Q

The N terminal of a peptide chain is +ve due to NH3

A

…

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17
Q

The C terminal of a peptide chain is -ve

A

..

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18
Q

what is a prokaryote

A

microscopic single cell organism that does not have a defined nucleus

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19
Q

what is a eukaryote

A

normal cell with nucleus

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20
Q

nucleoside

A

base+sugar

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21
Q

nucleotide

A

nucleoside+ phosphate

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22
Q

Purines

A

adenine and guanine

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23
Q

Pyrimidines

A

uracil, thymine and cytosine

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24
Q

what are phosphodiester bonds

A

bonds between 3’ OH groups and 5’ triphosphate

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25
base pairing
a-t | c-g
26
DNA polymerase
can only add to existing nucleic acids, cannot start sythesis on its own, requires RNA primer to start replicatoin
27
rRNA (ribosomal)
combines with proteins to form ribosomes where protein synthesis takes place
28
tRNA (transfer)
carries amino acids to be incorporated into proteins, anticodons consist of 3 nucleotides
29
mRNA (messanger)
stable RNA, carries genetic information for protein synthesis
30
poll II
synthesises all mRNA
31
transcription
RNA polymerase binding oDetects initiation sites on DNA (promoters) oRequires transcription factors DNA chain separation oUnwinding of DNA Transcription initiation oSelection of first nucleotide of growing RNA oRequired additional general transcription factors Elongation oAddition of further nucleotides to RNA chain oRNA synthesised in 5' - 3' direction Termination oRelease of finished RNA
32
what is TFIID
general transcription factor required for all Pol II transcribed genes
33
exons
coding regions
34
introns
non-coding regions
35
Translation
- Anticodons of tRNA form base pairs with codons of mRNA - AUG is the start codon Initiation oGTP provides energy oRibosomal subunit binds to 5' end of mRNA, moves along until start codon found oInitiator tRNA pairs to start codon oLarge subunit joins assembly and initiator tRNA is located in P site Elongation oElongation factor brings aminoacyl-tRNA to A site oGTP oSecond elongation factor regenerates the first to pick up next aminoacyl-tRNA Peptidyl transferase catalyses peptide bond formation between amino acids in P and A sites Termination oOccurs when A site of ribosome encounters a stop codon (UAA, UAG, UGA oFinished proteins cleaves off tRNA
36
Ribosomes
- 3 tRNA binding sites - Exit, Peptidyl, Aminoacyl - Free ribosomes in cytosol proteins for - cytosol, nucleus, mitochondria - Post translational - Bound ribosomes on rough ER - plasma membrane, ER, Golgi, secretion - Co-translational
37
enzymes
- biological catalysts - speeds up the rate at which a reaction reaches equilibrium doesnt affect the position of equilibrium - lower the activation energy and stablise the transition state and provides alternatice reaction pathways
38
apoenzymes
Enzymes without a cofactor
39
holoenzymes
enzymes with a cofactor
40
Induced fit
binding of the substrate induces a conformational change in the shape of the enzyme, resulting in a complementary fit
41
what carries out phosphorylation
protein kinases
42
Trypsin and chymotrypsin
work in the small intestine at an optimum pH of 7
43
Trypsinogen and Chymotrypsinogen
produced in the pancreas and are produced in an inactive form so that they dont digest the pancreas. Enteropeptidase activates the trypsinogen in the small intestine.
44
CK is an isozyme. The M form is produced in the skeletal muscle and the B form is produced in the brain. The MB form is produced in the heart.
..
45
Vmax=
maximal rate at unlimited substrate conc
46
Km=
Michaelis constant = 50% Vmax
47
low Km=
an enzyme only needs a little substrate to work at 0.5Vmax (it has a high affinity)
48
oVmax is the intersection of the straight line with the Y axis oKm is the line's intersection with the X axis
..
49
``` Competitive o Binds to active site o Vmax remains the same o Km increased (where both lines cross the y axis at same point) ```
..
50
myoglobin
Michaelis Menten regulation | hyperbolic
51
Haemoglobin
allosteric regulation | sigmoidal
52
GLUT3
BRAIN
53
GLUT5
GUT
54
anabolism
required energy- endergonic and reductive
55
catabolism
breakdown of molecules to yield energy-exergonic and oxidative
56
glucose is oxidised to form what
co2 and h2o
57
Glucose gets into cell via Glucose Transporters (GLUT) by facilitated diffusion
..
58
glycolysis
the initial pathway for the conversion of glucose to pyruvate (net gain of 2 ATP ie uses 2 ATP but gains 4 ATP)
59
hexokinase
phosphorylates glucose
60
Phosphofructokinase
phosphorylates fructose-6-phosphate
61
The 1st, 3rd and final reactions in glycolysis are control points and are irreversible and very exergonic.
..
62
what are the 3 enzymes in the glycolysis control points
Hexokinase, phosphofructokinase, pyruvate kinase
63
after glycolysis NADH must what?
by reoxidised to form NAD+ in order to continue ATP synthesis
64
Pyruvate is converted into lactate when there is low oxygen- muscle cells work v hard to allow glycolysis to continue
which forms lactic acid (anaerobic)
65
NAD
- Only limited amounts of NAD+ are present in cell - NAD+ reduced to NADH + H+ in glycolysis - NAD+ is regenerated through the oxidative metabolism of pyruvate
66
pyruvate
- Anaerobic - alcoholic fermentation, lactic acid formation in humans - Aerobic - further oxidised in the Citric Acid Cycle
67
aerobic metabolism of pyruvate
- Enters mitochondria matrix - Converted to acetyl-coA (catalysed by Pyruvate Dehydrogenase Complex PDC) - Condenses with 4C compound to form 6C compound - 6C compound decarboxylated twice - yields CO2 - 4 oxidation reactions - yield NADH + H+ and FADH2 - GTP formed - 4C compound recreated
68
for each Acetyl CoA the TCA cycle generates...
- 3 NADH + H+ - 1 FADH2 - 1 GTP - 2 CO2
69
TCA facts:
substrate= Acetyl CoA - occurs in the mitochondria - Oxaloacetate+ acetyl-CoA= citric acid - 3xNAD+ and 1x FAD+ are reduced in the cycle - Lipids are converted into fatty acids and then Acetyl- CoA which enters the TCA cycle
70
Electrons from NADH and FADH2 reduce O2 to H2O. Electron energy is used to pump protons from the matrix to the intermembrane space, causing matrix pH to increase. Protons follow their conc and flow across the membrane- this energy is used to phosphorylate ADP-ATP
..
71
what does negative electron transfer mean
substance more likely to donate electons than ydrogen
72
Phosphoryl transfer potential
free energy change for ATP hydrolysis
73
Electron transfer potential
measured by redox potential of a compound
74
The standard redox potential of a substance is a measure of how readily it donates an electron
Negative = reduced form of X has lower affinity for electrons than hydrogen Positive = reduced form of X has higher affinity for electrons than hydrogen
75
oxidative phosphorylation
electron transport and ATP synthesis
76
what occurs in the electron transport phase:
electrons from NADH enter complex 1, electrons fromFADH2 enter at complex 2 (TCA), electrons are handed down from high to lower redox potentials, and transferred onto O2 to form H2O Transfer of electrons through respiratory chain is coupled to H+ transport from mitochondrial matrix to intermembrane space 3/4 complexes pump H+
77
what is the electrochemical gradient
more protons in intermembranous space than matrix, matrix side more negative, protons attracted to matrix - coupled to ATP synthesis
78
inhibition of oxidative phosphorylation
- Cyanide, azide and CO inhibit transfer of electrons to O2 | - No proton gradient formed, no ATP synthesised
79
basic Oxidative phosphorylation
- Electrons from NADH and FADH2 used to reduce O2 to H2O - Their energy used to pump protons from mitochondrial matrix to intermembrane space - Protons flow back across membrane - Energy of proton flow used to phosphorylate ADP to ATP
80
- Glycolysis - 2 ATP - TCA cycle (2 GTP) - 2 ATP - Glycolysis, PDH, TCA cycle (10 NADH + H+) - 25 ATP - TCA cycle (2 FADH2) - 3 ATP - 1 glucose molecule yields 30-32 ATP molecules - Transfer of electrons through the respiratory chain is coupled to transport of H+ from the mitochondrial matrix to the intermembrane space
..

Principles (Y1) (9 decks)

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