What is the effect of arsenate on energy generation in a cell?

Arsenate poisoning. Arsenate (AsO43-) closely resembles Pi in structure and reactivity. In the reaction catalyzed by glyceraldehyde 3-phosphate dehydrogenase, arsenate can replace phosphate in attacking the energy-rich thioester intermediate. The product of this reaction, 1-arseno-3-phosphoglycerate, is unstable. It and other acyl arsenates are rapidly and spontaneously hydrolyzed.
Glycolysis proceeds in the presence of arsenate, but the ATP normally formed in the conversion of 1,3-bisphosphoglycerate into 3-phosphoglycerate is lost. Thus, arsenate uncouples oxidation and phosphorylation by forming a highly labile acyl arsenate

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Steps in GLYCOLYSIS explained!!!!!!!!!!!!!!

Glycolysis literally means “splitting sugars.” In glycolysis, glucose (a six carbon sugar) is split into two molecules of a three-carbon sugar. Glycolysis yields two molecules of ATP (free energy containing molecule), two molecules of pyruvic acid and two “high energy” electron carrying molecules of NADH. Glycolysis can occur with or without oxygen. In the presence of oxygen, glycolysis is the first stage of cellular respiration. Without oxygen, glycolysis allows cells to make small amounts of ATP. This process is called fermentation.

10 Steps of Glycolysis

Step 1
The enzyme hexokinase phosphorylates (adds a phosphate group to) glucose in the cell’s cytoplasm. In the process, a phosphate group from ATP is transferred to glucose producing glucose 6-phosphate.
Glucose (C6H12O6) + hexokinase + ATP →  ADP + Glucose 6-phosphate (C6H11O6P1)
Step 2
The enzyme phosphoglucoisomerase converts glucose 6-phosphate into its isomer fructose 6-phosphate. Isomers have the same molecular formula, but the atoms of each molecule are arranged differently.
Glucose 6-phosphate (C6H11O6P1) + Phosphoglucoisomerase → Fructose 6-phosphate (C6H11O6P1)
Step 3
The enzyme phosphofructokinase uses another ATP molecule to transfer a phosphate group to fructose 6-phosphate to form fructose 1, 6-bisphosphate.
Fructose 6-phosphate (C6H11O6P1) + phosphofructokinase + ATP → ADP + Fructose 1, 6-bisphosphate (C6H10O6P2)
Step 4
The enzyme aldolase splits fructose 1, 6-bisphosphate into two sugars that are isomers of each other. These two sugars are dihydroxyacetone phosphate and glyceraldehyde phosphate.
Fructose 1, 6-bisphosphate (C6H10O6P2) + aldolase → Dihydroxyacetone phosphate (C3H5O3P1) + Glyceraldehyde phosphate (C3H5O3P1)
Step 5
The enzyme triose phosphate isomerase rapidly inter-converts the molecules dihydroxyacetone phosphate and glyceraldehyde phosphate. Glyceraldehyde phosphate is removed as soon as it is formed to be used in the next step of glycolysis.
Dihydroxyacetone phosphate (C3H5O3P1) → Glyceraldehyde phosphate (C3H5O3P1)
Net result for steps 4 and 5: Fructose 1, 6-bisphosphate (C6H10O6P2) ↔ 2 molecules of Glyceraldehyde phosphate (C3H5O3P1)
Step 6
The enzyme triose phosphate dehydrogenase serves two functions in this step. First the enzyme transfers a hydrogen (H) from glyceraldehyde phosphate to the oxidizing agent nicotinamide adenine dinucleotide (NAD+) to form NADH. Next triose phosphate dehydrogenase adds a phosphate (P) from the cytosol to the oxidized glyceraldehyde phosphate to form 1, 3-bisphosphoglycerate. This occurs for both molecules of glyceraldehyde phosphate produced in step 5.
A. Triose phosphate dehydrogenase + 2 H + 2 NAD+ → 2 NADH + 2 H+
B. Triose phosphate dehydrogenase + 2 P + 2 glyceraldehyde phosphate (C3H5O3P1) → 2 molecules of 1,3-bisphosphoglycerate (C3H4O4P2)
Step 7
The enzyme phosphoglycerokinase transfers a P from 1,3-bisphosphoglycerate to a molecule of ADP to form ATP. This happens for each molecule of 1,3-bisphosphoglycerate. The process yields two 3-phosphoglycerate molecules and two ATP molecules.
2 molecules of 1,3-bisphoshoglycerate (C3H4O4P2) + phosphoglycerokinase + 2 ADP → 2 molecules of 3-phosphoglycerate (C3H5O4P1) + 2 ATP
Step 8
The enzyme phosphoglyceromutase relocates the P from 3-phosphoglycerate from the third carbon to the second carbon to form 2-phosphoglycerate.
2 molecules of 3-Phosphoglycerate (C3H5O4P1) + phosphoglyceromutase → 2 molecules of 2-Phosphoglycerate (C3H5O4P1)
Step 9
The enzyme enolase removes a molecule of water from 2-phosphoglycerate to form phosphoenolpyruvic acid (PEP). This happens for each molecule of 2-phosphoglycerate.
2 molecules of 2-Phosphoglycerate (C3H5O4P1) + enolase → 2 molecules of phosphoenolpyruvic acid (PEP) (C3H3O3P1)
Step 10
The enzyme pyruvate kinase transfers a P from PEP to ADP to form pyruvic acid and ATP. This happens for each molecule of PEP. This reaction yields 2 molecules of pyruvic acid and 2 ATP molecules.
2 molecules of PEP (C3H3O3P1) + pyruvate kinase + 2 ADP → 2 molecules of pyruvic acid (C3H4O3) + 2 ATP

GLYCOLYSIS

summary of Glycolysis

This is a summary of the steps involved in Glycolysis turning this complex process into easy peasy steps LOL 😉
take a read and enjoy (:

<a href="http://” title=”Glycolysis” target=”_blank”>

heyy yall 🙂 Heres a second youtube video, this one is on the topic of glycolysis.
A detailed description of the process/ stages of glycolysis was given. To me this video was very informative and captured my attention by the illustrations that was used in aid of describing this complex process. Follwing this is a summary of what I learnt.
In glycolysis, one molecule of glucose is converted to 3 carbon molecules. Anet gain of energy is captured by ATP and NADH. In eukaryotes, the end product pyruvated is imported into the mitochondria where it feeds into the Citric Acid Cycle and Electron Transport Chain. Glycolysis involves 10 steps. In the 1st 3steps, energy in the form of ATP is invested and in steps 4 and 5 it allows it to be split into 2 small molecules. The last five steps breaks it down ATP and NADH.The 10 steps were then explained one by one and the reactions taking place were seen. Hope you hav fun looking at this as much i did 🙂

Enzymes

Enzymes are Globular proteins that catalyse or speed up a metabolic reaction.

Early Enzyme discoveries
discovery zone

The existence of enzymes has been known for well over a century. Some of the earliest studies were performed in 1835 by the Swedish chemist Jon Jakob Berzelius who termed their chemical action catalytic. It was not until 1926, however, that the first enzyme was obtained in pure form, a feat accomplished by James B. Sumner of Cornell University. Sumner was able to isolate and crystallize the enzyme urease from the jack bean. His work was to earn him the 1947 Nobel Prize.

Chemical properties of enzymes

A coenzyme – a non-protein organic substance which is  loosely attached to the protein part.

A prosthetic group – an organic substance which  is firmly attached to the protein or apoenzyme portion.

Easy way to remember some definitions of some terms.

Easy way to remember some definitions of some terms.

Specificity of Enzymes
One of the properties of enzymes that makes them so important as diagnostic and research tools is the specificity they exhibit relative to the reactions they catalyze. A few enzymes exhibit absolute specificity; that is, they will catalyze only one particular reaction. Other enzymes will be specific for a particular type of chemical bond or functional group. In general, there are four distinct types of specificity:

Absolute specificity – the enzyme will catalyze only one reaction.
Group specificity – the enzyme will act only on molecules that have specific functional groups, such as amino, phosphate and methyl groups.
Linkage specificity – the enzyme will act on a particular type of chemical bond regardless of the rest of the molecular structure.
Stereochemical specificity – the enzyme will act on a particular steric or optical isomer.
Though enzymes exhibit great degrees of specificity, cofactors may serve many apoenzymes.

Most enzymes end in ‘ase’ however,enzymes can be classified by the kind of chemical reaction catalyzed. For example:

  1. Addition or removal of water
    1. Hydrolases – these include carbohydrases, nucleases and proteases
    2. Hydrases such as fumarase and enolase
  2. Transfer of electrons
    1. Oxidases
    2. Dehydrogenases
  3. Transfer of a radical
    1. Transglycosidases – of monosaccharides
    2. Transphosphorylases and phosphomutases – of a phosphate group
    3. Transaminases – of amino group
    4. Transmethylases – of a methyl group
    5. Transacetylases – of an acetyl group
  4. Splitting or forming a C-C bond
    1. Desmolases
  5. Changing geometry or structure of a molecule
    1. Isomerases
  6. Joining two molecules through hydrolysis of pyrophosphate bond in ATP or other tri-phosphate
          1.Ligases

 

Enzyme Kinetics

Remember as previously stated above, enzymes are catalysts and increase the speed of a chemical reaction without themselves undergoing any permanent chemical change. They are neither used up in the reaction nor do they appear as reaction products.

The basic enzymatic reaction can be represented as follows

where;
E represents the enzyme catalyzing the reaction
S the substrate, the substance being changed
P the product of the reaction.

  • Energy levels
Activation energy

Activation energy

 

Lock and key Hypothesis or Induced fit Model

This compares the active site (place where the chemical reactions occur) to represent the keyhole and the substrate being the key. When the right substrate entered the active site, catalysis occurred because the substrate was perfectly complementary to the active site. This model described some enzymes, but not all. For others, binding leads to conformational, or shape changes, in the enzyme active site to enhance the bond breakage and formation required to reach the transition state. In both models, the active site provides the tightest fit for the transition state, and the substrate is drawn into the transition state configuration as a result.

lock n keey

Several factors affect the rate at which enzymatic reactions proceed. These are:
Temperature
pH
Enzyme concentration
Substrate concentration
The presence of any inhibitors or activators

  • Temperature

Enzymes have an optimum temperature – this is the temperature at which they work most rapidly. Below the optimum temperature, increasing temperature will increase the rate of the reaction. This is because temperature increases the kinetic energy of the system, effectively increasing  the number of collisions between the substrate and the enzyme’s active site. Temperatures above the optimum will lead to denaturation This occurs because the hydrogen bonds and disulphide bridges which maintain the shape of the active site are broken. Thus, enzyme substrate complexes can no longer be formed.

temp

  • pH

As with temperature, similarly if pH increases or decreases much beyond this optimum, the ionisation of groups at the active site and on the substrate may change, effectively slowing or preventing the formation of the enzyme substrate complex. At extreme pH, the bonds which maintain the tertiary structure are disrupted and hence the enzyme is irreversibly denatured.

Graph showing the effect of pH on enzyme.

Graph showing the effect of pH on enzyme.

  • Enzyme concentration

Normally reactions are catalysed by enzyme concentrations which are much lower than substrate concentrations. Thus as the rate of the enzyme concentration is increased , so will the rate of the enzyme reaction. If the substrate concentrations is at a high level and other conditions are optimum then the rate of reaction is proportional to the enzyme concentration.

  • Substrate concentration

At low substrate concentration the reaction proceeds slowly. This is because there are not enough substrate molecules to occupy all of the active sites on the enzyme. As substrate concentration increases, the rate increases because there are more enzyme substrate complexes formed. At point x, however, increasing the substrate concentration will have no further effect on the rate of reaction. This is because all of the enzyme’s active sites are now occupied by substrate molecules – increasing the substrate concentration further will have no effect, because no more enzyme substrate complexes can form. The rate of reaction now depends on the turnover rate of the enzyme, i.e. the number of substrate molecules transformed by one molecule of enzyme per second.

MM equation saturation curve

 

  • Inhibitors

Inhibitors slow down the rate of reaction. As such, they are an essential form of cellular control, allowing enzyme reaction rate to be slowed when necessary. Some enzymes are inhibited by the end product of the reaction they catalyse.

there are two types of reversible inhibitors:

  1. competitive reversible inhibitors 
  2. non-competitive inhibitors

reversible inhibition

types

Irreversible inhibitors bind covalently and permanently to the enzyme, preventing normal enzyme function.

So that’s it for enzymes, I’m not sure if i forgot anything but i really enjoyed doing this topic.
this is definitely one of the interesting topics in biochemistry that caught my attention like no other!

Until Next time xo Stefi M

 

Amino acids Humour!!!!!!!!!!!!!

Image

ImageImage

Amino Acids and Proteins

<a href="” title=”Amino Acids and Proteins”>Amino Acids and Proteins

In this video the topic of amino acids and proteins was discussed. It was said that Proteins are very important since its what we are made up of. Amino acids are considered the building blocks of protein. We get protein from our diet.You are what you eat lol………….literally

There are five(5) basic amino acids:

  • Aspartic acid
  • Alanine
  • lysine
  • Threonine
  • Glutamine

They all have a common C-H and N-H2(amino group) bond. That carbon is called the alpha carbon. The only difference is the R-group. Theses amino acids when placed together form a polypeptide chain that eventually form a protein.

The structure of a protein can be classified as :

  • Primary structure
  • Secondary structure
  • Tertiary structure
  • Quaternary structure

Proteins are special, in that their structure suits their function. If this is not present and their structure for some reason is different ,this is known as denaturation.

 

Wordle

Wordle

Here’s my wordle that was done on both cells and carbohydrates ^_^

CARBOHYDRATES

Heyy guys ,its week2 and we just started carbohydrates. Honestly I don’t really like this topic, never did :/ I always got confused when it comes to identifying and drawing the structures some of these compounds. However so far based on how our lecturer Mr.Matthew  is teaching, I think I’ve understood most of it. So here’s the thing loll I’m going to try to explain what I’ve learnt sooo far and hopefully this will be of some benefit to us both.

Carbohydrates are:1)      The single most abundant class of organic compounds

  1. Metabolism and energy sources (glucose, glycogen)
  2. Structure and coverings (cellulose, chitin)
  3. Precursors in the formation of other essential substances
  4. Various other biological functions: cellular recognition, etc.

2)      Polyfunctional molecules

  1. Either polyhydroxyaldehydes or polyhydroxyketones
  2. Most naturally occurring monosaccharides do not have free carbonyl groups but exist instead as polyhydroxy acetals or ketals

3)      General categorizations of carbohydrates

  1. Monosaccharides
  2. Disaccharides
  3. Oligosaccharides: as many as 10-20 monosaccharides, but often fewer
  4. Polysaccharides: generally consist of a single or two alternating monosaccharides
    carbohydrate

4)      Nomenclature: most carbohydrates end in “ose”

5)      General

  1. Empirical formula (CH2O)n
  2. 3 – 7 carbon atoms in backbone
  3. The carbon backbone is unbranched
  4. All of the carbons but the carbonyl carbon are bonded to a hydroxyl group
  5. White crystalline solids at room temperature, (relatively) high M.P., highly soluble in water, insoluble in nonpolar solvents, sweet to taste

6)      Categorization based on the nature of the carbonyl group and on numbers of carbons in backbone

  1. Aldoses and ketoses
  2. Trioses, tetroses, pentoses, hexoses, heptoses
  3. Group names combine carbonyl name then backbone number: ketopentoses, aldohexoses, ketohexoses, etc.

7)      Stereoisomerism
num7

  1. There are 2n possible stereoisomers in a compound with n tetrahedral stereocenters
  2. D- and L-glyceraldehyde are the reference compounds for assigning the absolute configuration of all optically active compounds
  3. For monosaccharides having two or more chiral carbons, D- and L- assignments are based on the chiral carbon located furthest away from the carbonyl carbon
  4. Nearly all biologically important monosaccharides are of D- configuration; L- forms are possible but generally not synthesized
  5. Epimers: stereoisomers with multiple chiral carbons that vary only in the configuration around one of the chiral carbons

8)      Aldoses
aldoses

9)      Ketoses

  1. ketoses
  2. The common names of some ketoses were derived from adding an “ul” to the name of the corresponding aldose e.g., ribose and ribulose

10)  Deoxy sugars – replace one or more hydroxyl groups with a hydrogen atom, e.g., ribose and 2-deoxyribose

11)  Aldohexoses (actually aldoses with five or more carbons) tend to form pyran-like structures – pyranoses – by forming cyclic hemiacetals through the reaction of the carbonyl group and the hydroxyl group on one of the backbone carbons (usually C-5)

  1. Anomers: isomeric forms of monosaccharides that differ only in their configuration around the carbonyl carbon
  2. The carbonyl carbon is referred to as the anomeric carbon
  3. All aldoses (and ketoses) with five or more carbons form stable pyranose rings and can exist as various anomers

12)  Ketoses with five or more carbons tend to form furan-like structures – furanoses – by forming cyclic hemiacetals (hemiketals) through the reaction of the carbonyl group and the hydroxyl group on one of the backbone carbons (usually C-5)

13)  Haworth projections (Haworth structures) – used to convey the 3-dimensionality of cyclic hemiacetals

Chemical and physical properties of monosaccharides

14)  Mutarotation

15)  Acetal formation and the production of glycosides

  1. The anomeric carbon loses its hydroxyl group, the alcohol loses its hydroxyl proton
  2. The ether linkage between between the anomeric carbon and the alkoxy group is called an O-glycosidic bond (as compared to a N-glycosidic bond)
  3. The bond will be an a- or b-glycosidic linkage depending on the configurations of the anomeric carbon involved in the bond
  4. These bonds can be referred to briefly as (e.g.) b(1->4) glycosidic linkages, which means that a b-anomer shares a glycosidic linkage between its C-1 and the C-4 of another anomer which may be either a- or b-
  5. The bonds between the monosaccharides in disaccharides and polysaccharides are glycosidic bonds
  6. Can also form N-glycosidic bonds between anomeric carbons and the nitrogen atoms of amines

Some important monosaccharides

16)  Glucose: the most important simple carbohydrate in human metabolism

17)  Galactose: commonly found in plant gums and resins, a component of the disaccharide lactose (milk sugar)

18)  Fructose: found in honey and many different fruits; also known as fruit sugar

19)  Ribose and 2-deoxyribose: found in nucleic acids

Disaccharides

20)  Maltose: two glucose molecules, a(1->4) glycosidic linkage: (glucose-a(1->4)-glucose)
maltose

21)  Cellobiose: two glucose molecules, b(1->4) glycosidic linkage: (glucose-b(1->4)-glucose)
cellobiose

22)  Lactose: galactose and glucose, b(1->4) glycosidic linkage: (galactose-b(1->4)-glucose)

23)  Sucrose: between the hemiacetal groups of a-D-glucose and a-D-fructose: (glucose-a(1->2)-fructose)

Polysaccharides

24)  Starch and glycogen: based on glucose

Most starches are 10-30% amylose and 70-90% amylopectin

Amylose is linear and unbranched with a backbone of a(1->4) glycosidic linkages
amylopectin

Amylopectin is linear with a backbone of a(1->4) glycosidic linkages and highly branched with a(1->6) glycosidic linkages

Glycogen is similar to amylopectin but more extensively branched

Cellulose is based on glucose and is linear and unbranched with b(1->4) glycosidic linkages.


So we all know that nothing is perfect and in every good , there must a little bad 😛
Until next time ……
Take a look at this 😉
good-carbs-bad-carbs

 

CELLS

During the 1st week of biochem lectures we discussed the cell , its organelles such as Golgi apparatus, chloroplast, lysosomes, peroxisomes, glyoxysomes, mitochondria, nucleus the proteasome and endoplasmic reticulum. The structure and function of these organelles were also described . Here’s a summary of what i learnt 🙂

The Cell is the fundamental unit of life and every living organism is composed of them. Modern cell Theory states that :

  • all living matter is composed of cells;
  • all new cells arise from other cells;
  • all metabolic reactions of an organism takes place in the cell;

cells contain hereditay information of organisms of which they are a part and this is passed from parent to daughter cell

Their Cell size is restricted by :

  • the surface area to volume ratio, which must be as large as possible to allow exchange of metabolic substances.
  • the capacity of the nucleus to excercise control over the rest of the cell.

Capture

   

Eukaryotic Cell Prokaryotic Cell
Nucleus: Present Absent

 

Number of chromosomes: More than one One–but not true chromosome: Plasmids
Cell Type: Usually multicellular  

Usually unicellular

 

True Membrane bound Nucleus: Present Absent
Example: Animals and Plants Bacteria and Archaea

 

Genetic Recombination: Meiosis and fusion of gametes Partial, undirectional transfers DNA
Lysosomes and peroxisomes: Present Absent
Microtubules: Present Absent or rare

 

Endoplasmic reticulum: Present Absent

 

Mitochondria: Present Absent

 

Cytoskeleton: Present May be absent

 

DNA wrapping on proteins.: Eukaryotes wrap their DNA aroundproteins called histones. Multiple proteins act together to fold and condense prokaryotic DNA. Folded DNA is then organized into a variety of conformations that are supercoiled and wound around tetramers of the HU protein.

 

Ribosomes: larger smaller

 

Vesicles: Present Present

 

Golgi apparatus: Present Absent

 

Chloroplasts: Present (in plants) Absent; chlorophyll scattered in the cytoplasm
Flagella: Microscopic in size; membrane bound; usually arranged as nine doublets surrounding two singlets Submicroscopic in size, composed of only one fiber
Permeability of Nuclear Membrane: Selective not present
Plasma membrane with steriod: Yes Usually no
Cell wall: Only in plant cells and fungi (chemically simpler)

 

Usually chemically complexed
Vacuoles: Present

 

Present
Cell size: 10-100um 1-10um

 

The Endosymbiosis Theory  

 The theory of Endosymbiosis explains the origin of chloroplasts and mitochondria and their double membranes.This concept postulates that chloroplasts and mitochondria  are the result of years of evolution initiated by the endocytosis of bacteria and blue-green algae.

According to this theory, blue green algae and bacteria were not digested; they became symbiotic instead.  Endocytosis is when a substance gains entry  into a cell without passing through its cell membrane.

lysosomes2.gif (3319 bytes)