Che 214 lecture 03

CHE 214: Biochemistry
Lecture Three
•NUCLEIC ACIDS
•BIOENERGETICS
Lecturer: Dr. G. Kattam Maiyoh

GKM/CHE 214/LEC 03/SEM 02/2013

d. Nucleic Acids
• DNA –deoxyribonucleic acid
– Polymer of deoxyribonucleotide triphosphate (dNTP)
– 4 types of dNTP (ATP, CTP, TTP, GTP)
– All made of a base + sugar + triphosphate

• RNA –ribonucleic acid
– Polymer of ribonucleotide triphosphates (NTP)
– 4 types of NTP (ATP, CTP, UTP, GTP)
– All made of a base + sugar + triphosphate

• So what’s the difference?
– The sugar (ribose vs. deoxyribose) and one base (UTP vs.
TTP)


Deoxyribose (like ribose) is a sugar with 5 carbon atoms in a ring
Oxygen is one of the ring members

In Deoxyribose, one of the OH groups is missing and replaced with hydrogen,
Thus deoxy = - 1 oxygen
Phosphate groups are important because they link the sugar on one nucleotide
onto the phosphate of the next nucleotide to make a polynucleotide.

Base - pairing
• Nitrogenous bases

• In DNA the four bases are:
– Thymine
– Adenine
– Cytosine
– Guanine

• In RNA the four bases are:
– Uracil
– Adenine
– Cytosine
– Guanine


DNA and RNA are polynucleotides
• Both DNA and RNA are polynucleotides.
• They are made up of smaller molecules
called nucleotides. Nucleotide
• DNA is made of two polynucleotide strands:

Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide


• RNA is made of a single polynucleotide strand:



• Nucleic Acids Function
– Information Storage
• DNA / mRNA
– Information transfer / Recognition
• rRNA / tRNA / snRNA
– Regulatory
• microRNA ?


DNA •Information for all proteins stored in DNA
in the form of chromosomes or plasmids.
•Chromosomes (both circular and linear)
consist of two strands of DNA wrapped
together in a left handed helix.(imagine
screwing inwards)

•The strands of the helix are held together
by hydrogen bonds between the individual
bases.
•The “outside” of the helix consists of
sugar and phosphate groups, giving the
DNA
molecule a negative charge.

The Rule: Complimentarity
• Adenine always base pairs with Thymine (or
Uracil if RNA)

• Cytosine always base pairs with Guanine.

• This is because there is only exactly enough
room for one purine and one pyrimidine base
between the two polynucleotide strands of
DNA/RNA. These bases are complimentary to
each other

Complimentary Base Pairs

A-T Base pairing G-C Base Pairing


DNA Structure
• The DNA helix is “anti-parallel”
– Each strand of the helix
has a 5’ (5 prime) end and
a 3’ (3 prime) end.


DNA Structure
3’ end
5 ‘ end

Strand 2 Strand 1
(Crick strand) (Watson strand)

5’end
3 ‘ end

DNA Structure
• 1 atgatgagtg gcacaggaaa cgtttcctcg atgctccaca gctatagcgc caacatacag
• 61 cacaacgatg gctctccgga cttggattta ctagaatcag aattactgga tattgctctg
• 121 ctcaactctg ggtcctctct gcaagaccct ggtttattga gtctgaacca agagaaaatg
• 181 ataacagcag gtactactac accaggtaag gaagatgaag gggagctcag ggatgacatc
• 241 gcatctttgc aaggattgct tgatcgacac gttcaatttg gcagaaagct acctctgagg
• 301 acgccatacg cgaatccact ggattttatc aacattaacc cgcagtccct tccattgtct
• 361 ctagaaatta ttgggttgcc gaaggtttct agggtggaaa ctcagatgaa gctgagtttt
• 421 cggattagaa acgcacatgc aagaaaaaac ttctttattc atctgccctc tgattgtata

Because of the base pairing rules, if we know one
strand we also know what the other strand is.
Convention is to right from 5’ to 3’ with 5’ on the left.


Chromosomes and Plasmids
• Chromosomes are composed of DNA and
proteins.
– Proteins (histone & histone like proteins) serve a
structural role to compact the chromosome.
– Chromosomes can be circular, or linear.
• Both types contain an antiparallel double helix!
– Genes are regions within a chromosome.
• Like words within a sentence.


Region (red box) of
chromosome XI from the
bakers yeast S.
cerevisiae.
Red and Blue colored
boxes are genes
Note that either strand
may encode a gene, but
that all genes start at
the 5’ end and finish at
the 3’ end.

http://www.yeastgenome.org/


RNA
• Almost all single stranded (exception is RNAi).
• In some RNA molecules (tRNA) many of the
bases are modified (e.g. psudouridine).
• Has capacity for enzymatic function
-ribozymes
• One school of thought holds that early
organisms were based on RNA instead of DNA
(RNA world).


RNA
• Several different “types” which
reflect different functions
– mRNA (messenger RNA)
– tRNA (transfer RNA)
– rRNA (ribosomal RNA)
– snRNA (small nuclear RNA)
– RNAi (RNA interference)


RNA function
• mRNA – transfers information from DNA to
ribosome (site where proteins are made)
• tRNA – “decodes” genetic code in mRNA, inserts
correct A.A. in response to genetic code.
• rRNA-structural component of ribosome
• snRNA-involved in processing of mRNA
• RNAi-double stranded RNA, may be component of
antiviral defense mechanism.


RNA

A - hairpin loop
B- internal loop
C- bulge loop
D- multibranched loop
E- stem
F- pseudoknot

Complex secondary structures can form in linear molecule


mRNA
• Produced by RNA polymerase as product of transcription

– Provides a copy of gene sequence for use in translation
(protein synthesis).
– Transcriptional regulation is major regulatory point
– Processing of RNA transcripts occurs in eukaryotes
• Splicing, capping, poly A addition
– In prokaryotes coupled transcription and translation can
occur


The Central Dogma of molecular
Biology


Bioenergetics


What is Bioenergetics ?
•It is the study of the energy relationships and energy
conversions in biological systems.
•All organisms need free energy to keep themselves alive
and functioning.
•The source of energy is just one; solar energy.
•Only plants use that energy directly.
•What the other organisms use is the chemical energy in
the form of foods.
•The very first conversion of solar energy into a chemical
energy is the sugar molecule.


Respiration
• Respiration is important for bioenergetics
as it stores the energy to form a molecule
ATP; adenosine triphosphate.
• This molecule is a link between catabolism
and anabolism.
• The process of photosynthesis is helpful in
understanding the principles of energy
conversion i.e. bioenergetics.


• Metabolism refers to all the chemical reactions
of the body
– some reactions produce the energy stored in
ATP that other reactions consume
– all biological molecules will eventually be
broken down and recycled or excreted from
the body


Catabolism and Anabolism
• Catabolic reactions breakdown complex
organic compounds
– providing energy (exergonic)
– glycolysis, Krebs cycle and electron transport
• Anabolic reactions synthesize complex
molecules from small molecules
– requiring energy (endergonic)
• Exchange of energy requires use of ATP
(adenosine triphosphate) molecule.
GKM/CHE 214/LEC 03/SEM 02/2013 25-27

ATP Molecule & Energy
a

b
• Each cell has about 1 billion ATP molecules that last for less than
one minute
• Over half of the energy released from ATP is converted to heat
02/2013
25-28

Mechanisms of ATP Generation

• Phosphorylation is the addition of phospahate
group.
– bond attaching 3rd phosphate group contains stored
energy
• Mechanisms of phosphorylation
– within animals
• substrate-level phosphorylation in cytosol
• oxidative phosphorylation in mitochondria
– in chlorophyll-containing plants or bacteria
• photophosphorylation.

25-29

Phosphorylation in Animal Cells
• In cytoplasm (1)
• In mitochondria (2, 3 & 4)

GKM/CHE 214/LEC 03/SEM 02/2011 25-30

Carbohydrate Metabolism--In Review
• In GI tract
– polysaccharides broken down into simple sugars
– absorption of simple sugars (glucose, fructose &
galactose)
• In liver
– fructose & galactose transformed into glucose
– storage of glycogen (also in muscle)
• In body cells --functions of glucose
– oxidized to produce energy
– conversion into something else
– storage energy as triglyceride in fat
25-31

Fate of Glucose
i. ATP production during cell respiration
– uses glucose preferentially
i. Converted to one of several amino acids in many
different cells throughout the body
ii. Glycogenesis
– hundreds of glucose molecules combined to form
glycogen for storage in liver & skeletal muscles
i. Lipogenesis (triglyceride synthesis)
– converted to glycerol & fatty acids within liver & sent to
fat cells

25-32

Glucose Movement into Cells
• In GI tract and kidney tubules,
Na+/glucose symporters
• Most other cells, GluT facilitated
diffusion transporters move glucose
into cells
– insulin increases number of GluT
transporters in the membrane of most
cells
– in liver & brain, always lots of GluT
transporters
• Glucose 6-phosphate forms
immediately inside cell (requires
ATP) thus, glucose hidden in cell
• Concentration gradient favorable for
more glucose to enter
02/2013
25-33

Glucose Catabolism
• Cellular respiration
– 4 steps are involved
– glucose + O2 produces
H2O + energy + CO2
• Anaerobic respiration
– called glycolysis (1)
– Results in formation of acetyl CoA (2)
is transitional step to Krebs cycle
• Aerobic respiration
– Krebs cycle (3) and electron transport chain (4)

02/2013
25-34

Historical Perspective
Glycolysis was the very first biochemistry or oldest biochemistry studied.
It is the first metabolic pathway discovered.

Louis Pasture 1854-1864: Fermentation is caused by microorganism. Pastuer’s
effect: Aerobic growth requires less glucose than anaerobic condition.

Buchner; 1897: Reactions of glycolysis can be carried out in cell-free yeast
extract.

Harden and Young 1905: 1: inorganic phosphate is required for fermentation.
2: yeast extract could be separated in small molecular weight essential
coenzymes or what they called Co-zymase and bigger molecules called
enzymes or zymase.

Inhibitor studies: Iodoacetate treatment resulted in the accumulation of
fructose 1,6biphosphate. Similarly fluoride caused accumulation of 2-
phosphoglycerate and 3-phosphoglycerate.

1940: with the efforts of many workers, complete pathways for glycolysis was
established.

6 CH OPO 2−
2 3
5 O
H H
H
4 H 1
OH
OH OH
3 2
H OH
glucose-6-phosphate

Glycolysis takes place in the cytosol of cells.
Glucose enters the Glycolysis pathway by conversion
to glucose-6-phosphate.
Initially there is energy input corresponding to
cleavage of two ~P bonds of ATP.

6 CH2OH 6 CH OPO 2−
2 3
ATP ADP
5 O 5 O
H H H H
H H
4 1 4 H 1
OH H OH
Mg2+
OH OH OH OH
3 2 3 2
H OH Hexokinase H OH
glucose glucose-6-phosphate

1. Hexokinase catalyzes:
Glucose + ATP  glucose-6-P + ADP
The reaction involves nucleophilic attack of the C6
hydroxyl O of glucose on P of the terminal phosphate
of ATP.
ATP binds to the enzyme as a complex with Mg++.

Glycolysis of Glucose & Fate of Pyruvic Acid
• Breakdown of six-carbon glucose molecule into
2 three-carbon molecules of pyruvic acid
– 10 step process occurring in cell cytosol
– produces 4 molecules of ATP after input of
2 ATP
– utilizes 2 NAD+ molecules as hydrogen
acceptors
• If O2 shortage in a cell
– pyruvic acid is reduced to lactic acid so that
NAD+ will be still available for further
glycolysis
– Lactic acid rapidly diffuses out of cell to
blood
– Liver cells remove it from blood & convert
it back to pyruvic acid

02/2013
25-39

10 Steps of Glycolysis

GKM/CHE 214/LEC 03/SEM 02/2011 25-40

Formation of Acetyl Coenzyme A
• Pyruvic acid enters the
mitochondria with help of
transporter protein
• Decarboxylation
– pyruvate dehydrogenase converts 3
carbon pyruvic acid to 2 carbon
fragment (CO2 produced)
– pyruvic acid is oxidized so that NAD+
becomes NADH
• 2 carbon fragment (acetyl group) is
attached to Coenzyme A to form
Acetyl coenzyme A which enter
Krebs cycle
– coenzyme A is derived from
pantothenic acid (B vitamin).

25-42

Krebs Cycle (Citric Acid Cycle)
• Series of oxidation-
reduction &
decarboxylation reactions
occurring in matrix of
mitochondria
• It finishes the same as it
starts (4C)
– acetyl CoA (2C) enters at
top & combines with a 4C
compound
– 2 decarboxylation
reactions peel 2 carbons
off again when CO2 is
formed

THE TCA
The names of the various enzymes in
the previous slide are indicated in the
figure below


Products of the Krebs Cycle
• Energy stored in bonds is released step by step to form several
reduced coenzymes (NADH & FADH2) that store the energy
• In summary: each Acetyl CoA
molecule that enters the Krebs
cycle produces yields;
– 2 molecules of CO2
• one reason O2 is needed
– 3 molecules of NADH + H+
– one molecule of ATP
– one molecule of FADH2
• Remember, each glucose
produced 2 acetyl CoA molecules

02/2013

The Electron Transport Chain
• Involves a series of integral
membrane proteins in the
inner mitochondrial
membrane capable of
oxidation/reduction
• Each electron carrier is
reduced as it picks up
electrons and is oxidized as it
gives up electrons
• Small amounts of energy is
released in small steps
• Energy used to form ATP by
chemiosmosis

Chemiosmosis
• Small amounts of energy
released as substances are
passed along inner
membrane
• Energy used to pump H+ ions
from matrix into space
between inner & outer
membrane
• High concentration of H+ is
maintained outside of inner
membrane
• ATP synthesis occurs as H+
diffuses through a special H+
channel in inner membrane

Steps in Electron Transport

• Carriers of electron transport chain are clustered into 3 complexes
that each act as proton pump (expel H+)
• Mobile shuttles pass electrons between complexes
• Last complex passes its electrons (2H+) to a half of O2 molecule to
form a water molecule (H2O)

Proton Motive Force & Chemiosmosis

• Buildup of H+ outside the inner membrane creates + charge
– electrochemical gradient potential energy is called proton motive force
• ATP synthase enzyme within H+ channel uses proton motive force to synthesize
ATP from ADP and P


Summary of Cellular Respiration
• Glucose + O2 is broken down into CO2
+ H2O + energy used to form 36 to 38
ATPs
– 2 ATP are formed during glycolysis
– 2 ATP are formed by phosphorylation
during Krebs cycle
– electron transfers in transport chain
generate 32 or 34 ATPs from one glucose
molecule
• Points to remember
– ATP must be transported out of
mitochondria in exchange for ADP
• uses up some of proton motive force
– Oxygen is required or many of these
steps can not occur

Che 214 lecture 03

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