Micro Chapter 3

Front 1

Thymine: keto-enol tautomerization

Back 1

Normally found in the keto form 99.9% of the time. Make two bond with adenosine

-thymine can be in enol form. Triple bond with b guanine- spontaneous mutation.

Keto-lactam form

Enol-lactim form

Front 2

Keto form of thymine

Back 2

99.9 % of the time, 2 bonds with adenosine

Keto-lactam form

Front 3

Enol form of thymine

Back 3

Triple bond with guanine. Spontaneous mutation. Enol-lactim form

Front 4

Keto

Back 4

Lactam form

Front 5

Enol

Back 5

Lactim form

Front 6

Nucleic acid/polynucleotide

Back 6

-Polymer made up nucleotides

-backbone made out of sugar and phosphate alternating

-nucleotide covalently bonded by phosphate from c3' to c5' of one sugar to another

-phosphate linkage is covalent phosphodiester, one phosphate connect to ester link two separate sugars. 3' 5' phosphodiester linkage.

Front 7

What is the linkage for fatty acid of lipids?

Back 7

Esterify to gycerol - triglyceride

Ester linkage

Front 8

What is the linkage for monosacharide in polysaccharide?

Back 8

Glycosidic bond

Front 9

What is the linkage between nucleotide of nucleic acid/polynucleotide?

Back 9

3' 5' phosphodiester linkage

Front 10

3' 5' phosphodiester linkage

Back 10

* 2 Ester connects between 2 sugars and 1 phosphate

* phosphodiester bond from dehydration

* template is required to specify which nucleotide is next

* enzyme catalyze phosphodiester is polymerase

* synthesize from 5' to 3 ' direction only

Front 11

What is the enzyme catalyze the phosphodiester bond linkage reaction ?

Back 11

Polymerase

Front 12

In which direction does the phosphodiester synthesize?

Back 12

5' to 3 '

Front 13

DNA helix is antiparallel

Back 13

@One strand run 5'-3'

@Another strand runs 3'-5'

@Polymerase replicate DNA only synthesize from 5'-3'

@copying the 3'-5' strand complicates DNA replication

Front 14

DNA vs RNA

Back 14

@deoxyribonucleic acid/DNA carries the genetic blueprint for the cell

@Ribonucleic acid/RNA is an intermediate convert blueprint to Amino acid sequence for proteins

@Central Dogma

DNA (replicate)- transcript RNA- translate proteins.

@RNA more function than DNA

@RNA is mostly single stranded, has 2rd structure.

Front 15

DNA

Back 15

@In cell, DNA is double stranded

@each DNA molecule have 2 strands of DNA

@each strand have several miliions of nucleotide link by phosphodoester bonds

@DNA strand associated by H bond

@Stabilized further by hydrophobic base stacking and phosphate's interaction with water

Front 16

DNA base pairing

Back 16

@most stable H-bonds occurs when guanine bonds with cytosine. Adenine bonds with thymine

@specific base pairing is called complementarity

@if one strand is guanine, the complementary strand is cytosine. If one strand is Adenine, the complementary strand is thymine

Front 17

Melting temperature of DNA

Back 17

@Tm is the melting temperature of DNA

@ temperature require to break H-bond and separate two strands

@temperature required to produce 50% of separated strands. Half way point of melting

@As GC/AT ratio increase the Tm value also increases. Tm increase due to greater stability of DNA as GC has 3 H-bonds, and AT only have 2 H-bonds

Front 18

RNA

Back 18

@with a few a exception, all RNA see single stranded

@may have 2rd structure due H-bonding

@some viruses have dsRNA

@RNA plays three crucial role in the cell:

1. Messenger RNA (mRNA)- complementary to DNA.

2. Transfer RNA (tRNA)-adapter molecule

3. Ribosomal RNA(rRNA)-structural and catalytic components of the ribosome

@also have new discovery role of RNA: enzyme, gene silencing, regulatory RNAs, interference RNA.

Front 19

Amino Acids

Back 19

@Amino acids are the monomeric units of proteins

@most amino acid contains of C,O,N,H

@two amino acid (cysteine, methionine) has sulfur. Only cysteine has a sulfahydryl group.

@all amino acids contain two important functional groups:

1. Carboxylic acid/carboxylic group (-COOH)

2. Amino group (-NH2)

@ the R group gives the amino acid it's characteristic-families

Front 20

R groups of amino acids

Back 20

@there are 4 groups of amino acids

@ionizable acidic: contain carboxylic acid

@ionizable basic: contain a nitrogen base

@nonionizable polar: water soluble

@nonpolar (hydrophobic): insoluble in H2O

Front 21

Introduction to proteins

Back 21

@protein are polymer made out of amino acid covalent bonded by peptide bond.

@dipeptide-tripeptide-polypeptide

@protein consists of one or more polypeptide

@2 types of proteins:

1. Enzyme/catalytic

2. Structural protein: membrane, cell wall, cytoplasmic component.

Front 22

Peptide bond

Back 22

The Carboxyl (-COOH) and amino groups (-NH2) are functionally important because they firm covalent bonds through dehydration between the carbon of the carboxylic group of one amino acid and the nitrogen of the amino group of a second amino acid to form a peptide bond

Front 23

Four levels of proteins structure

Back 23

@primary (1)

-linear sequence of amino acid linked by peptide bond

-non-repetitve heteropolymers that come from a template (mRNA)

@secondary (2)

-interaction between parts that make up the polypeptide backbone, make H-bond

-major element: a helix, B pleated sheet

-amino acid interaction are close to each other

@tertiary (3)

-overall conformation stabled primarily by weak interactions-> folding in 3D space

-amino mini acid interaction may far from each other

@quaternary(4)

-protein consist of multiple polypeptide

-manner in which they associate : non-covalent and covalent bond

Front 24

Protein: primary structure

Back 24

@linear array of amino acid in a polypeptide

@ditate the type of folding it will have

@not the surface for biological function

@Held together by covalent peptide bond

Front 25

Protein: secondary structure

Back 25

@position of the R group On individual amino acids in a polypeptide forces the molecule to twist and fold in a specific way

@H-bond plays an important role in the type of secondary structure that a protein attains. Interaction between the backbone of the amino acids

@2 forms: a hehix. B pleated sheet

@sexondary structure protein: sequence of amino acids linked by H-bonds

@H-bond of backbone is not a covalent bond

Front 26

2rd structure: the a helix

Back 26

In the A helix conformation, O and N from different amino acids come close to twist structure allow for H-bonding between H from the amine (-NH) and carbonyl O from the carboxylic group (-C=O)

Front 27

Protein: Tertiary structure

Back 27

@After secondary structure, the R group are positioned in a certain way . Can interact with weak non-covalent chemical attractive forces (hydrogen bonding, ionic bonding, hydrophobic forces, Van Der Waal force) or a covalent bond (disulfide bridge). More stable than secondary

Front 28

Protein: 3rd structure

Back 28

@Tertiary structure primarily stabled by weak interaction attractive forces: Vander Wal force, ionic bonding, hydrogen bonding, hydrophobic bonding: one of the strongest influences on protein folding is burial of hydrophobic (nonpolar) side chains into core of polypeptide

@only possible covalent bond: disulfide bridge between two cysteine in the same polypeptide.

Front 29

Disulfide bridge

Back 29

@Cys-SH + HS-cys -> Cys-S-S-Cys. The -SH group is known as a sulfahydryl (Thio) group

@if the difulsude bridge is between two cysteines in the same polypeptide > part of 3rd structure (intramolecular)

@difulsife bridge linked 2 different polypeptides > part of 4th structure (intermolecular)

Front 30

Protein: quaternary structure

Back 30

@if a protein has two or more polypeptides, the number and types of polypeptides that form the final protein molecule is quaternary structure. Ex: hemoglobin has 2a and 2b chains

@two of the same polypeptides = homodimer.

@two different polypeptide = heterodimer

Front 31

Insulin

Back 31

@quaternary structure of insulin

@consist of 2 polypeptides: one A and one B

@Held together by attractive forces and difulside bridges S-S-

@fast-acting: insulin lispro, insulin aspart

@Long-acting: insulin glargine, detemir insulin

Front 32

Denaturation of ribonuclease

Back 32

@gentle denaturation = urea. Inactive. Remove urea > protein reactivated

@harsh denaturation = 100 Celsius degree l. Inactive. Remove heat. Remain inactive

Front 33

Denaturation

Back 33

@proteins denaturation cause it change folding when undergo extreme heat, pH, chemicals, metal. Causes the polypeptides to unfold.

@denatured protein can retain it's primary structure because it is held together by covalent bonds but loses its secondary, tertiary and quaternary structure.

@depending on the severity of denaturation induction, protein can refolf itself when denaturant is removed.

@reduction is needed to break the disulfide bridge. Used in labs: B-ME or DTT

Front 34

Secondary structure: The A helix

Back 34

@many amino acid sequence can adopt a helical symmetry

@stabilized by contacts between nearly universal backbone atoms (carbonyl and amino groups). Rarely glycine, tyrosine & serine. Commonly alanine

@Proline is a helix-breaking residue. Cyclical structure, cannot participate as donor in H-bonding

@Side chains project away from the helix. Because the helix is exclusively construct by backbone contacts. Allow for 3D structure to form in 3rd

Front 35

Secondary structure: B sheet

Back 35

@2 types:

@parallel B sheet: c.n. same terminus at the same side. Angle bonding. Weaker.

@antiparallel B sheet: c.n different terminus at the same side. Straight bonding. Stronger.

@in B sheet, the amino acids in polypeptide folds back and fourth upon itself instead of forming a helix