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Biochem Flashcards

1
Q

food

A

bread: contains complex carbs. contains starch, the major source of carbohydrates in food consisting of glucose polysaccharides amylose (α1,4 glycosidic bonds) and amylopectin (α1,4 and α1,6 glycosidic bonds)
Honey: contains monosaccharides glucose, fructose
Coffee: contains sucrose disaccharide (depends on roast)
Milk: contains lactose (galactose and glucose disaccharide)
sugar: consists of sucrose (glucose and fructose disaccharide)

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2
Q

complex carbs are disassembled into simple sugars with the help of enzymes

A

an ezyme alpha-amylase and glucose polysaccharide it breaks complex carbs such as starch to dextrins( a glucose oligosaccharide) and maltose (glucose disaccharide).
then enzymes such as dextrinase breaks down dextrin with addition of a water molecule to a glucose a simple monosaccharide. then enzymes such as maltase breaks down maltose with addition of a water molecule to a glucose a simple monosaccharide. then enzymes such as lactase breaks down lactose with addition of a water molecule to a glucose a simple monosaccharide and galalactose. then enzymes such as sucrase breaks down sucrose with addition of a water molecule to a glucose a simple monosaccharide and fructose

  • in our body, we can only distribute monosacchrides
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3
Q

from the digestive system

A

monosaccharides are transported to the cells of the small intestine and then to blood with the help of proteins, glucose transporters. Disaccharides and dextrins cannot be transported

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4
Q

Lactose

A

Lactose intolerance is an example of a condition caused by
inefficient hydrolysis of disaccharides.
Lactose is a disaccharide found in milk, “milk sugar”
Lactose is hydrolyzed to monosaccharides by betagalactosidase, a.k.a. lactase
Mammals are unlikely to encounter lactose after they are
weaned, so the level and activity of lactase are low in adult
Non-hydrolysed lactose moves through the digestive tract to the
colon, fermented and large quantities of CO2, H2 and acids are
produced
Lactose intolerance: normal condition in adult humans.
More common in Asians

how to help people with lactose intolerance: Removal of lactose or hydrolysis of lactose can help people with lactose intolerance

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5
Q

From the blood, glucose enters cells in our body via different
transporters located at the cell surface

A

.

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6
Q

production of ATP

A

glucose is used to recycle ADP to ATP, which is used to drive other processes, e.g. movement of organelles (1 ATP molecule per 8.1 nm)

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7
Q

cells recycle ATP from ADP via

A

glycolysis

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8
Q

Glycolysis is a set of 10 reactions in the cytosol

A

glycolysis can be split in 2 parts: 1 preparatory phase and 2 pay off phase

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9
Q

Preparatory phase

A

The first five steps are regarded as the preparatory (or investment) phase because they consume energy to convert the glucose into two three carbon sugar phosphates. where 2 ATP molecules are lost in this molecule

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10
Q

glucose transporters

A

can transport glucose into and out of the cells with the same efficiency. the purpose of the first reaction of glycolysis is to trap glucose in the cell. the first reaction is catalysed by hexokinase, which phosphorylates glucose to prevent its transport from the cell. The reaction is highly spontaneous and irreversible under cellular conditions. It acts to keep glucose in the cell, because cells can transport glucose across the membranes but lack transporters for D-Glucose-6-phosphate. the hexokinase transports the phosphate of ATP; which converts to ADP, to the monosoccharide to form D-Glucose-6-phosphate

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11
Q

in the second reaction,

A

phosphoglucose isomerase converts
glucose 6-phosphate to fructose 6-phosphate. The reaction is reversible and is necessary to prepare the molecule for the next steps – phosphorylation and cleavage. in this phase an atp is lost

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12
Q

in the third reaction.

A

phosphofructokinase phosphorylates the molecule second time to produce Fructose-1,6-bisphosphate, where also an ATP was lost in the reaction. the reaction is irreversible under cellular conditions.

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13
Q

in the fourth reaction

A

aldolase cleaves fructose-1,6-bisphosphate and generates two similar products; Dihydroxyacetone phosphate and Glyceraldehyde-3
phosphate. the reaction is reversible and the products are similar but not identical

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14
Q

in the last preparatory reaction

A

triosephosphate isomerase
converts dihydroxyacetone into glyceraldehyde-3 phosphate. As
a result, the preparatory phase leads to generation of two
identical molecules of glyceraldehyde-3 phosphate (note, that 1
molecule of glyceraldehyde-3 phosphate is produced by
aldolase).

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15
Q

in the payoff phase

A

two identical
cleavage products
are converted into
pyruvate with the
release of energy
using the same set
of reaction

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16
Q

start of pay off phase

A

starts with oxidation of Glyceraldehyde 3-
phosphate to 1,3-Bisphosphoglycerate with the help of
dehydrogenase.NAD+ is converted to NADH+ H+ in the process.
NAD+ - Nicotinamide adenine dinucleotide, a coenzyme found in all living cells

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17
Q

stage 2 of pay off phase

A

3-Phosphoglycerate Transfer from 1,3-Bisphosphoglycerate to ADP by
phosphoglycerate kinase results in generation of ATP

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18
Q

Conversion of 3-Phosphoglycerate to 2-Phosphoglycerate

A

by phosphoglycerate mutase

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19
Q

Dehydration of 2-Phosphoglycerate to Phosphoenolpyruvate

A

by enolase and water is released. the loss of the water molecule from 2-phosphoglycerate causes a redistribution of energy within the molecule

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20
Q

Transfer of the phosphoenolpyruvate with ADP to
ATP and pyruvate by pyruvate kinase hence results in generation of ATP

A
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21
Q

summary

A

glucose +2ATP + 2ADP +2Pi + 2NADH+ —-> 2PYRUVATE + 4ATP + 2 NADH + 2H+ + 2H2O

GLUCOSE + 2ADP + 2Pi + 2NAD+ —-> 2 PYRUVATE + 2ATP + 2NADH + 2H+ + 2H2O

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22
Q

Glycolysis releases only a fraction of energy
stored in glucose

A

glycolysis energy yield = 5%
glycolysis—> 2x pyruvate and 2x acetylcoA —> CO2 + H2O

2x pyruvate and 2x acetylcoA —> CO2 + H2O; TRICARBOXYLIC
ACID CYCLE and full oxidation Energy yield
= 95 %

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23
Q

why is glycolysis important?

A
  • It is anaerobic (can take place in
    the absence of oxygen)
    so can provide ATP for muscle
    during strenuous exercise.
    and

It provides the ATP extremely
rapidly (suitable for muscle
contraction during sprints).

Oxidative phosphorylation occurs in special organelles
called mitochondria. Glycolysis is used as a primary
mechanism for ATP production in cells that don’t have
mitochondria (e.g. in erythrocytes).

Even under aerobic conditions, glycolysis is the major starting
point for carbohydrate metabolism

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24
Q

Energy Supply During Exercise

A

ATP: up to 4 seconds. High jump, power
lift, shot put, tennis serve
* Phosphocreatine: up to 10 seconds.
sprints, American football line play
* Glycolysis: up to 1.5 minutes. 200-400 m
race, 100 m swim. Cancer tissues switch to glycolysis, because the growing tumour has insufficient access to blood vessels and has
to use alternative strategy to obtain energy. Positron Emission Tomography is used to detect cancer
tumours by monitoring the glucose uptake
* Oxidative phosphorylation: race beyond
500 meters

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25
Q

Levels of AMP, ADP and ATP determine the energy state of
the cells

A

Low energy state, a lot of a (3) ADP, low levels of (1) ATP
ADP. In a very low energy state, 2 ADP molecules are converted into 1 ATP molecule and 1 AMP molecule resulting in accumulation of AMP.
High energy state, a lot of a ATP, low levels of ADP

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26
Q

In a low energy state,

A

, the speed of glycolysis is enhanced via an increase in the activity of phosphofructokinase, a rate limiting enzyme.
Phosphofructokinase is activated by ADP and AMP

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27
Q

An increase in fructose 6-phosphate levels leads to generation of
the fructose 2,6 bisphosphate, which allosterically activates
phosphofructokinase

A

The activity of phosphofructokinase 2
is hormonally stimulated when the
blood glucose level is high.

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28
Q

Glycolysis rates depend on the transport of glucose to the
cytosol. The efficiency of the transport is determined by the
numbers of glucose transporters at the cell surface

A

Glucose transporters are stored in vesicles, which deliver the
transporters to the cell surface when glucose levels increase

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29
Q

Summary of the key enzymes in the regulation of the
glycolysis

A

Hexokinase (step 1):
Glucose + ATP -> glucose-6-phosphate + ADP
is inhibited by glucose-6-phosphate (product inhibition)

Phosphofructokinase (step 3):
Fructose-6-phosphate + ATP -> fructose-1,6-biphosphate + ADP
is activated by ADP and AMP, inhibited by ATP and NADH

Pyruvate kinase (step 10):
Phosphoenolpyruvate + ADP -> pyruvate + ATP
is inhibited by ATP

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30
Q

Liver cells store excess glucose when it is not needed
for other cells by expressing glucokinase instead of
hexokinase

A

Hexokinase is ubiquitous, the same end product: glucose-6-phosphate , high affinity to glucose, and initial step in glycolysis.

glucokinase is in liver cells, low affinity to glucose, traps only excess glucose to store as glycogen

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31
Q

balance sheet of glycolysis

A

glucose + 2ADP 2Pi + 2NAD+ —–> 2 PYRUVATE + 2 ATP + 2NADH + 2H+ + 2H2O

the problems: 1 cells need NAD+ for glycolysis to continue and cells need to prevent accumulation of NADH and pyruvate.
cells solve these problems differently depending on whether they have access to oxygen. we must consider:
1 aerobic conditions (abundant oxygen)
2 anaerobic conditions (limiting oxygen)

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32
Q

in the presence of oxygen

A

pyruvate is transported from the cytosol to the mitochondrial matrix by the pyruvate translocase. in the mitochondrial matrix, pyruvate is converted into the acetyl-CoA by pyruvate dehydrogenase. this process is called pyruvate decarboxylation and is the entry to the TCA cycle.
Pyruvate + CoA + NADH+ —–> acetyl-CoA + CO2 + NADH+ H+
the pyruvate dehydrogenase complex (PDH) is a large, highly integrated complex of three kinds of enzymes,

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33
Q

E1 E2 E3

A

associate with each other to form the pyruvate dehydrogenase complex.

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34
Q

pyruvate dehydrogenase is a multienzyme complex

A

multienzyme complexes are groups of noncovalently associated enzymes that catalyse two or more sequential steps in a metabolic pathway. advantages:
1. enzymatic rates are limited by a frequency with which enzymes collide with their substrates. when a series of reactions occur within a multienzyme complex, the distance that substrates must diffuse between active sites is minimised.
2 the channeling of metabolic intermediates between successive enzymes in a metabolic pathway reduces the opportunity for these intermediates to react with other molecules.
3 the reactions can be co-ordinately controlled

pyruvate dehydrogenase complex deficiency causes diseases: pyruvate dehydrogenase complex deficiency caused by mutations in genes coding for the E1 subunit is a type of metbaolic disease. the signs appear in infancy and include brain abnormalities, low weight, high levels of lactate, extreme tiredness, rapid breathing and other symptoms. people often pass away in the first years of life.

35
Q

regeneration of NAD+ FROM NADH the anaerobic pathway: Fermentation

A

louis Pasteur originally defined fermentation as respiration without air. fermentation is a process which extracts energy as ATP but does not consume oxygen or change the concentrations of NAD+ or NADH.
In yeasts, regeneration of NAD+ from NADH in the absence of oxygen is coupled to formation of ethanol and CO2 ( the anaerobic or fermentation pathway in yeast).

36
Q

in skeletal muscle during exercise

A

regeneration of NAD+ from NADH is coupled to the anaerobic fermentation of lactate.

37
Q

The primary role of enzymes

A

is to enhance rates of reactions, so that they are compatible with the needs of an organism.

38
Q

What is Enzyme Kinetics?

A

The rate at which an enzyme works.

39
Q

Why Study Enzyme Kinetics?

A
  • to understand enzyme catalytic power
  • when and why it works best
  • factors that affect activity (inhibitors)
  • these are important for biology
  • are of economic importance for industry* are central to pharmaceutical design
40
Q

Enzyme Reaction Velocity is AffectedBy

A

Substrate Concentration

41
Q

The Michaelis-Menten Constant - KM

A

KM
the substrate concentration at which the enzyme reaction
velocity is half its maximal rate

42
Q

Enzymes have Different KM Values*

A

enzyme lysozyme has the substrate Hexa-N-acetylglucosamine. a KM of 6 and turnover/sec of 0.5
enzyme Penicillinase has the substrate Benzylpenicillin a KM of 50 and aturn over/sec of 2000
enzyme carbonic anhydrase has the substrate CO2 a KM of 8000 and a turnover/sec of 600,000

turnover represents the number of molecules of substrate converted to a product per second and is directly related to Vmax

43
Q

What is the Meaning of KM?

A

1) The substrate concentration required for significant
catalysis to occur
2) A value related to the rate constants of the steps of
catalysis

44
Q

When does KM allow estimation of binding strength?

A

Km= k-1+ k2/k1
If the rate k-1&raquo_space; the rate of k2 ES dissociates rapidly to E and S and product (P) is not formed.

  • low KM indicates strong binding (greater affinity)- high KM indicates weak binding (lesser affinity). The value of KM is inversely related to the affinity of
    the enzyme for its substrate.

V0 = Vmax [S]/ ([S] + KM)
Case 1:
when [S] is very low and smaller than KM, V0
is proportional to [S]
Case 2:
when [S] is very large and greater than KM, V0
is equal to Vmax

45
Q

Problems with the Michaelis-Menten Equation:

A

Vmax is approached asymptotically, which is difficult to measure.As KM is Vmax/2, KM is difficult to measure.

46
Q

Perfect Kinetics in Enzymes:

A

A kinetically perfect enzyme is one for which:
- its catalytic rate is limited only by the rate at which it
encounters substrate
- in these cases, catalysis rates reflect those of diffusion.
Enzymes such as superoxide dismutase, acetylcholine
esterase, triosephosphate isomerase have achieved ‘kinetic perfection’. Why is acetylcholine esterase no surprise?

If we can measure the efficiency of enzymes, we can
engineer them to become more efficient

47
Q

Competitive Inhibition

A

Inhibitor molecules bind the active site of enzyme.
Inhibitor competes with binding of substrate, thus reducing rate of catalysis.
Degree of inhibition depends on concentration of substrate and inhibitor.

48
Q

Non-Competitive Inhibition

A

Inhibitor molecules bind at another site of the enzyme.
This alters the structure of the active site, affecting the capacity of the
enzyme to convert substrate to product (affects transition state?)
It does not compete with binding of substrate.

49
Q

Allosteric Enzymes - inhibition

A

Allosteric enzymes contain regulatory and active sites
- Small molecules can bind to regulatory sites.
These cause conformational changes that reduce catalysis at active site.
- Allosteric enzymes exist in two conformations.

Some BUT NOT ALL enzymes show feedback inhibition, where the
products formed are their own inhibitors.
Where feedback inhibition is found, the inhibition is often to the first enzyme in a pathway.

Allosteric Enzymes Can Show Cooperativity
Allosteric enzymes also have multiple active sites that display
cooperativity. Activity at one active site increases the activity at others

Allosteric Enzymes do not show Michaelis-Menten Kinetics. Allosteric enzymes show sigmoidal kinetics (resembles an S).

50
Q

Allosteric Feedback Inhibition of ATCase

A

Aspartate transcarbomoylase (ATCase) catalyses the first step in pyrimidine
biosynthesis.
ATCase is inhibited by cytidine triphosphate, the final product in the pathway.
ATCase has separate catalytic (C) and regulatory (R) subunits:
they form the protein complex: C6R6

51
Q

Zymogens – inactive precursors of enzymes

A

Many enzymes are active after folding to their 3-D shape.
Other enzymes are made as inactive precursors, or zymogens.
A once-off cleavage event will activate the enzyme

52
Q

Enantiomers

A

are mirror images of each other

53
Q

Two sugars that differ only in the configuration around
one carbon atom are called

A

epimers

54
Q

Anomers

A

are epimers which differ in the position of H and OH
groups around the C1 atom in the cyclic forms of the
monosaccharides. In solution, glucose predominantly exists as α
and β anomers and each molecule of glucose continuously
converts from one form to another via mutarotation

55
Q

Amylose

A

s a linear polymer of glucose
glucose units are linked in a linear way with α(1→4) glycosidic bonds;
* water insoluble, non-sweet
* hydrolyzed slowly
* dense

Amylopectin is a branched polymer of glucose
formed by plants store energy
-contains 2,000 to 200,000 glucose
units!
- not soluble in water.
- Glucose units are linked in a linear
way with α(1→4) glycosidic bonds.
Branching takes place with α(1→6)
bonds occurring every 24 to 30
glucose units.

Linear amylose and branched amylopectin form starch
Depending on the plant, starch generally contains 20 to 25% amylose and
75 to 80% amylopectin (higher in medium-grain rice till 100% in waxy rice).
Plants store starch within specialized organelles called amyloplasts. Plants also form polymers of glucose, cellulose, providing
structural support. Cellulose
* is formed by glucose units linked in a
linear way via β(1→4) glycosidic
bonds
* has no taste
* cannot be digested by animals
* can be broken down by some
bacteria, fungi
* component of dietary fiber

56
Q

Glucose and glycogen

A

is the major form of sugar transported to different parts
of the body in animals
Glycogen is the polymer of glucose used by animal cells to store
energy
* is similar to amylopectin
* formed when excess glucose is
eaten
* branching occurs every 8 to 12
glucose units
* is stored in the liver and muscle
tissue as an “instant” source of
energy

57
Q

Polysacharides

A

1 Heteropolysaccharides
* contain two or more
different monosaccharide
units;
* most naturally occurring
contain only two different
ones and are closely
associated with lipid or
protein;
* examples: pectin, lignin,
glycoproteins, glycolipids,
and mucopolysaccharides

2 Homopolysacharides
* formed by at least six
identical monosaccharides;
* have a well-defined
chemical structure
* examples: glycogen,
starch, cellulose

58
Q

thioredoxin (below), all polar amino acid side chains are shown as ball-and-stick models. The spatial arrangement of these amino acids illustrates a common feature of

A

globular proteins.

thioredoxin is an antioxidant protein

59
Q

The general structure of an amino acid includes:

A

carboxyl group

60
Q

You are given an amino acid in solution at pH 13. What are the most likely ionisation states of its amino and carboxyl groups?

A

NH2 and COO-

61
Q

An enzyme substrate:

A

must interact with the active site for catalysis to take place

62
Q

The difference in free energy between the substrates and products of a reaction:

A

indicates whether a reaction is likely to occur spontaneously.
If the difference in the free energy of substrates and products of a reaction is negative (i.e. the free energy of products is lower than that of substrates), then the reaction is favourable and can occur ‘spontaneously’. However, recall that without an enzyme present, even favourable/spontaneous reactions may take a very long time to occur!

63
Q

‘Enzyme kinetics’ is the study of:

A

the catalytic properties of enzymes.

64
Q

The Michaelis-Menten constant of an enzyme:

A

is high when an enzyme-substrate complex dissociates easily to form free enzyme and substrate.

The Michaelis-Menten constant, KM, of a reaction can estimate the dissociation constant of the enzyme-substrate complex. A high KM indicates weak binding of the enzyme to its substrate, whereas a low KM indicates strong binding of the the enzyme to its substrate.

65
Q

When studying an enzyme-catalysed reaction, you add equal concentrations of enzyme, substrate, a competitive inhibitor, and a non-competitive inhibitor. In theory, what do you think will happen?

A

The non-competitive inhibitor will inhibit the reaction to a greater extent.

In theory, the non-competitive inhibitor will have a greater effect on slowing the rate of the reaction because it binds to a site on the enzyme that is separate from the active site, whereas the competitive inhibitor will need to compete with the substrate in order to exert its inhibitory effects on the enzyme.

66
Q

The ‘cooperativity’ exhibited by some allosteric enzymes is a useful property for:

A

regulating biochemical pathways.

This is true because allosteric enzymes often have multiple active sites and the property of cooperativity means that the activity at one active site can readily increase or decrease the activity at other active sites of the same enzyme. This is useful for the measured control of biochemical pathways that involve regulatory enzymes with multiple active sites because cooperativity helps the enzyme to become more (or less) effective more quickly.

67
Q

C4H8O4 is:

A

a tetrose monosaccharide

68
Q

Which one of the following carbohydrates is less related to the others?

Question 12Select one:

a.
Cellulose

b.
Amylopectin

c.
Glucose

d.
Glycogen

e.
Amylose

A

Glucose is a 6-carbon monosaccharide whereas all other molecules listed here are large branched or non-branched polymers of many glucose units (i.e. polysaccharides).

69
Q

Glycolysis

A

utilises and generates ATP.

70
Q

Why is glycolysis important?

A

Primary means of energy production in cells with no mitochondria

There are several reasons that glycolysis is a very important pathway. One of them is that glycolysis provides essential energy to cells that do not have mitochondria, such as red blood cells. (Recall that mitochondria are important for producing large quantities of energy via oxidative phosphorylation). Without glycolysis, such cells would not survive.

71
Q

When energy levels in the cell are low:

A

AMP and ADP levels activate phosphofructokinase.
When ATP levels are low, higher AMP and ADP levels in contrast can act to allosterically activate phosphofructokinase (the key regulatory enzyme of glycolysis), to ultimately enhance the rate of glycolysis so that more energy can be produced via catabolism.

72
Q

When lactate is generated from pyruvate in skeletal muscle cells undergoing intense exercise:

A

it can be converted back to glucose via the liver.

As part of the Cori Cycle, skeletal muscle cells can release lactate into the bloodstream which can then be recycled back to glucose via gluconeogenesis in the liver.

73
Q

the conversion of one molecule of fructose 1,6 biphosphate into 2 molecules of pyruvate result in the net synthesis of

A

2 NADH and 4 ATP

74
Q

the conversion of 1 molecule of glucose to 2 lactate

A

results in net synthesis of 2 NADH AND 2 ATP

75
Q

the 10 reactions of glycolysis take splace in the

A

cytoplasm

76
Q

in stage 1 of glycolysis two atp molecules

A

are consumed per molecule of glucose

77
Q

glyceraldehyde 3 phosphate is

A

oxidised and phosphorylated to form 1,3-biphosphoglycerate

78
Q

phosphofructokinase

A

the most importaant control element in glycolysis is inhibited by ATP and citrate and it is activated by AMP and fructose 2,6-biophosphate

79
Q

how much atp is generated from glucose 6 phosphate

A

3

80
Q

how much atp is generated from digydroxyacetone phosphate in the process of glycolysis to lactate

A

2

81
Q

how much atp is generated from glyceradehyde 3 phhosphate in the process of glycolysis to lactate

A

2

82
Q

how much atp is generated from fructose in the process of glycolysis to lactate

A

2

83
Q

how much atp is generated from sucrose in the process of glycolysis to lactate

A

4

physiology (3 decks)

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