Biochem Block 1

Front 1

What is the structure of DNA?

Back 1

Polymer of deoxy ribonucleotides linked by phosphodiester bonds

Front 2

What is the formation of nucleoside?

Back 2

DNA--Deoxy ribonucleotides(dATP, dGTP, dCTP, TTP)--> remove phosphate--> Nucleoside(adenosine, guanine, cytosine-->
remove deoxy ribose--> Heterocyclic Organic bases(AGCT)

Front 3

What charge do nucleosides and nucleotides have?

Back 3

Nucleosides--uncharged

Nucleotides-- negatively charged

Front 4

What bond connects the 5'-3'?

Back 4

Phosphodiester bond on 3'end.

Front 5

What is the distance in the minor and major groove?

Back 5

Minor groove-- 2.0nm

Major groove-- 3.4nm

Front 6

How many hydrogen bonds join bases?
How many bases per turn of helix?
What is the degree of rotation per base?

Back 6

A T,---2 hydrogen bnds
G C -- 3 hydrogen bonds

Adjacent bases are separated by 3.4 Å.

There are 10 bases per turn of helix.

There is a rotation of 36 degrees per base (360 degrees per full turn/10 bases per turn –helical twist).

Front 7

What are the factors that stabilize the DNA structure?

Back 7

1. Phosphodiester bond (covalent bond)
2. Because of phosphate in the back bone, there is certain
amount of repulsion, an optimum force to stabilise and
maintain the structure
3. Inter hydrogen bonds
4. Hydrophobic bonds
5. Van der waals forces

Front 8

What is the melting temp of the structure?

Back 8

The melting temperature (Tm) is defined as the temperature at which half the helical structure is lost.

Tm is influenced by
base composition

Front 9

What are the forms of DNA and when are they found?

Back 9

The B-form of DNA  most of chromosomal DNA; 10residues per turn; 6* tilit

A form  by dehydrating B form  DNA-RNA hybrids, RNA-RNA double stranded regions; 11residues per turn, 20* tilt, Mjr groove N&D; minor groove W&S


Regions of the helix that are rich in pCpG dinucleotides can exist in a novel left-handed helical conformation termed Z-DNA.

Front 10

What are plasmids?

Back 10

small extrachromosomal DNA present in most bacteria;
convey antibiotic resistance and
facilitate transfer of genetic information from one bacterium to another

Front 11

Structure of histones?

Back 11

1. ------------charged proteins
2. Rich in lysine and arginine
3. Along with Mg2+, neutralise the
negatively charged DNA phosphate groups
4. Five classes (H1,H2A,H2B,H3 and H4)
5. Highly conserved between species

Linker H1 associated

Front 12

What is an interphase chromosome?

Back 12

Chromatin fibers are organized into loops or domains anchored in a scaffolding(or supporting matrix) within the nucleus

Front 13

What is mitotic chromosome?

Back 13

30 nm chromatin fiber must be compacted in length another 100-fold!!!!!!!!

Front 14

What are examples of Sngl-base alteration?

Back 14

I. Single-base alteration
a. Depurination
b. Deamination of cytosine to uracil
c. Deamination of adenine to hypoxanthine
d. Alkylation of base
e. Insertion or deletion of nucleotides
f. Base-analog incorporation

Front 15

What are the other types of damage and examples of causes?

Back 15

II. Two-base alteration
a. UV light –induced thymine-thymine dimer
b. Bifunctional alkylating agent cross-linkage

III. Chain breaks
a. Ionizing radiation
b. Radioactive disintegration of backbone element
c. Oxidative free radical formation

IV. Cross-linkage
a. Between bases in same or opposite strands (Mitomycin C)
b. Between DNA and protein molecules

Front 16

What is mismatch repair mechanism?

Back 16

- Corrects errors made when DNA is copied
- eg. C in the opposite of A
5’ C 3’
3’ A 5’

-Small loops due to many mismatch pairs

Front 17

What is base excision repair?

Back 17

Base-excision repair
Defect: Depurination of DNA (spontaneous because of thermal lability of the purine N-glycosidic bond at 37C)
Deamination
Cytosine Uracil
Adenine Hypoxanthine
Guanine Xanthine

Front 18

What is nucleotide -excision repair?

Back 18

3. Nucleotide-excision repair
Cause: UV-light
Ionizing radiation
Cancer chemotherapy agents
Smoking
Distortion of normal shape of the DNA locally
Fragment of DNA 30 nucleotides long is excised

Front 19

What is double strand break repair?

Back 19

Double strand break repair
Cause: Ionizing radiation (X ray and gamma)
Anticancer drugs
Oxidative free radicals
Physiologically in immunoglobulin gene arrangement

Severe lesions because incorrect rejoining of double strands of DNA can lead to gross chromosomal rearrangements that can affect the functioning of genes (“hybrid genes”)

Two types
1. Non-homologous end –joining
2. Homologous recombination repair

Front 20

What is non-homologous end joining?

Back 20

Non-homologous end-joining
- Rejoining the non-homologous ends of 2 DNA
molecules
- The DNA ends usually from the same chromosome locus
- Loss of several base pairs
- error-prone and mutagenic

Front 21

What is homologous recombination repair?

Back 21

2. Homologous Recombination Repair
- Uses enzymes that normally perform genetic recombination between homologous chromosomes during meiosis
- Less error prone

Front 22

What disease is caused by failure of mismatch repair?

Back 22

Hereditary nonpolyposis colon cancer (HNPCC)
Faulty mismatch repair
Loss of function of MSH2 (50-60% cases), MLH1 (other cases)--->

Inability to remove small loops of unpaired DNA--->

Increase in microsatellite size -->

Affects the expression or the function of a protein critical in surveillance of cell cycle in these colon cells

Front 23

What disease is caused by failure nucleotide-excision repair?

Back 23

Xeroderma pigmentosum
UV-light--> thymine-thymine dimer--> XP-A through XP-G

Front 24

What is mRNA?

Back 24

Messenger RNAs (mRNAs)
Used by the translational machinery in the process of translation.

Front 25

What is tRNA?

Back 25

Transfer RNAs (tRNAs)
Form covalent attachments to individual amino acids and recognize the encoded sequences of the mRNAs to allow correct insertion of amino acids into the elongating polypeptide chain

Front 26

What is rRna?

Back 26

Ribosomal RNAs (rRNAs):[28S, 18S, 5.8S, 5S]
Assembled, together with numerous ribosomal proteins, to form the ribosomes

Front 27

What is the principal enzyme for RNA synthesis? Function?

Back 27

Principal enzyme for RNA synthesis is RNA polymerase
Catalyzes the polymerization of ribonucleoside 5 -triphosphates (NTPs) as directed by a DNA template

Front 28

What does the holoenzyme consist of? Core enzyme?

Back 28

holoenzyme, is α2ββ’σ

RNA polymerase without this σ subunit (α2ββ’) is called the core enzyme

Front 29

What is the function of core enzyme?

Back 29

The core enzyme contains the catalytic site
The α2ββ’ core of RNA polymerase is unable to start transcription at promoter sites.
Role of σ is to direct the polymerase to promoters, leading to the initiation of transcription at the beginning of a gene

Front 30

What is an α-amino acids ?

Back 30

An α-amino acid consists of
A central carbon atom, called the α-carbon, linked to
An amino group,
A carboxylic acid group,
A hydrogen atom, and
A distinctive R group.
The R group is often referred to as the side chain.

Front 31

What are the nonessential amino acids?

Back 31

Alanine
Asparagine
Aspartate
Cysteine
Glutamate
Glutamine
Glycine
Proline
Serine
Tyrosine

Front 32

What are the essential amino acids?

Back 32

Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine
Arginine
Histidine

Front 33

What is an example of aliphatic?

Back 33

methyl group of alanine

Front 34

What is an example of aromatic?

Back 34

phenyl group of phenylalanine

Front 35

What are the hydrophobic aa?

Back 35

Glycine
Alanine
Valine
Leucine
Isoleucine
Methionine
Proline
Phenylalanine
Tryptophan

Front 36

What are the hydroxy aa?

Back 36

Serine'
Threonine

Front 37

What aa contain sulfur?

Back 37

Cysteine
Methionine

Front 38

What aa are acidic with amide group?

Back 38

Aspartic Acid
Asparagine
Glutamic acid
Glutamine

Front 39

What are the basic aa?

Back 39

Arginine-- guanido group
Lysine-- e amino group
Histidine-- imidazole group

Front 40

What are the aromatic aa?

Back 40

Phenylalanine
Tyrosine
Tryptophan
Proline(indole ring)

Front 41

What is the primary function of Histidine?

Back 41

pKa of its Imidazole group  acid or base at neutral pH

Front 42

What aa are termed nucleophiles?

Back 42

Serine (-OH) & cysteine (-SH)

Front 43

What aa regulate the enzyme activity?

Back 43

-OH of Serine, Tyrosine, & Threonine

Front 44

What are α-COOH & -NH3+ considered?

Back 44

weak acid groups

Front 45

What are -COO- & -NH2 considered?

Back 45

weak basic

Front 46

What are zwitterions?
?

Back 46

Molecules that contain equal no. of ionisable groups of opposite charge & therefore bear no net charge are termed zwitterions

Front 47

What is a conjugate base, & conjugate acid?

Back 47

isonization of acid--conjugate base

protonation of a base--conjugate acid

Front 48

How is the pH of solution measured? What is the equation?

Back 48

The pH of a solution is a measure of its concentration of H+. The pH is defined as
pH=log10(1/[Ht])= -log10[H+]

Front 49

What is the pKa?

Back 49

pKa of an acid is the pH at which it is half dissociated, when [A-]=[HA].

Front 50

What is a buffer?

Back 50

An acid-base conjugate pair (such as acetic acid and acetate ion) has an important property: it resists changes in the pH of a solution

Front 51

What is isoelectric species?

Back 51

Isoelectric species is the form of the molecule that has an equal number of positive and negative charges and thus is electrically neutral