Che 214 lecture 02

CHE 214: Biochemistry

Lecture Two

TOPICS;•LIPIDS•PROTEINS•NUCLEIC ACIDS

Lecturer: Dr. G. Kattam Maiyoh

February 21, 2013 1GKM/CHE 214/LEC 02/SEM 02/2013

Lipids

• Lipids include the following;– Fatty acids (Polymers of CH2 units)

– Glycerol– Triglycerides– Other subunits (phosphate, choline, etc) may be

attached to yield “phospholipids”• Charged phosphate groups will create a polar molecule

with a hydrophobic (nonpolar) end and a hydrophillic (polar) end



Lipids


Phospholipids



Phospholipid bilayer

Hydrophillic heads

Hydrophobic tails


Steroids


c. Proteins

• Proteins serve many essential roles in the cell– Polymers of amino acids – There are 20 naturally occurring amino acids• A few modified amino acids are also used (rare)• The large number of amino acids allows huge diversity

in amino acid sequence

N = # of amino acids in a protein N20 = # of possible combinations


Protein FunctionSome examples

• Structure- form structural components of the cell including:– Cytoskeleton / nuclear matrix / tissue matrix

• Movement - Coordinate internal and external movement of cells, organelles, tissues, and molecules. – Muscle contraction, chromosome separation, flagella………

• Micro-tubueles, actin, myosin

• Transport-regulate transport of molecules into and out of the cell / nucleus / organelles.

• Channels, receptors, dynin, kinesin

• Communication-serve as communication molecules between different organelles, cells, tissues, organs, organisms.– Hormones


Protein FunctionSome examples

• Chemical Catalyst – serves to make possible all of the chemical reactions that occur within the cell.– Enzymes (thousands of different enzymes)

• Defense-recognize self and non-self, able to destroy foreign entities (bacteria, viruses, tissues).– Antibodies, cellular immune factors

• Regulatory-regulates cell proliferation, cell growth, gene expression, and many other aspects of cell and organism life cycle. – Checkpoint proteins, cyclins, transcription factors


Protein Structure

• Polymers made from 20 different amino acids– All amino acids have a

Common “core” • Amino end (N end)• Acid end (C end, carboxy

end)

– Linked by peptide bond– 20 different side chains


Properties of amino acids• amino acids: acidic basic hydrophobic

• Amino acids all have The same basic structure

• Chemical properties of the amino acids yield properties of the protein!


Properties of amino acids


Protein Structure

• The 3-D shape and properties of the protein determine its function.

• Shape and properties of protein determined by interactions between individual amino acid components.

• Four “levels” of protein structure

– Primary (Io), secondary (IIo), tertiary (IIIo), and quaternary (IVo) (sometimes).


Levels of Protein Structure• I0 (primary) structure

– Linear order of amino acids in a protein:

– 1 A A S X D X S L V E V H X X V F I V P P X I L Q A V V S I A – 31 T T R X D D X D S A A A S I P M V P G W V L K Q V X G S Q A – 61 G S F L A I V M G G G D L E V I L I X L A G Y Q E S S I X A – 91 S R S L A A S M X T T A I P S D L W G N X A X S N A A F S S – 121 X E F S S X A G S V P L G F T F X E A G A K E X V I K G Q I – 151 T X Q A X A F S L A X L X K L I S A M X N A X F P A G D X X – 181 X X V A D I X D S H G I L X X V N Y T D A X I K M G I I F G – 211 S G V N A A Y W C D S T X I A D A A D A G X X G G A G X M X – 241 V C C X Q D S F R K A F P S L P Q I X Y X X T L N X X S P X – 271 A X K T F E K N S X A K N X G Q S L R D V L M X Y K X X G Q – 301 X H X X X A X D F X A A N V E N S S Y P A K I Q K L P H F D – 331 L R X X X D L F X G D Q G I A X K T X M K X V V R R X L F L – 361 I A A Y A F R L V V C X I X A I C Q K K G Y S S G H I A A X – 391 G S X R D Y S G F S X N S A T X N X N I Y G W P Q S A X X S – 421 K P I X I T P A I D G E G A A X X V I X S I A S S Q X X X A– 451 X X S A X X A

Single letter code for amino acids, also a three letter code. Refer to your genetic code handout.


Levels of Protein StructurePrimary Structure

• Amino acids combine to form a chain• Each acid is linked by a peptide bond• Io structure by itself does not provide a lot of

information.


• 20 (secondary) structure– Based on local interactions between amino acids• Common repeating structures found in proteins.

– Two types: alpha-helix and beta-pleated sheet.

• In an alpha-helix the polypeptide main chain makes up the central structure, and the side chains extend out and away from the helix.• The CO group of one amino acid (n) is hydrogen

bonded to the NH group of the amino acid four residues away (n +4). • From amino acid sequence - Can predict regions of

secondary structure


Ribbon Diagram

α-helical regions


Beta sheet

• Two types; – Parallel– anti-parallel


Beta Sheet ribbon diagram

antiparallel parallel


Protein Structure • 30 (tertiary structure)– Complete 3-D structure

of protein (single polypeptide)

Chymotrypsin with inhibitor

hexokinase


Protein Structure

• 40 (quaternary) structure– Not all proteins have 40

structure– Only if they are made of

multiple polypeptide chains


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) February 21, 2013 24GKM/CHE 214/LEC 02/SEM 02/2013


Function

• Nucleic Acids– Information Storage • DNA / mRNA

– Information transfer / Recognition • rRNA / tRNA / snRNA

–Regulatory • microRNA ?


DNA•Information for all proteins stored in DNAin 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 DNAmolecule a negative charge.



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

Strand 1

(Watson strand)

Strand 2 (Crick strand)

5 ‘ end

3 ‘ end

3’ end

5’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.


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


Documents

Che 214 lecture 02