BIOC 2070 WK. 5

Chargaff's Rules

A=T and G=C

Watson-Crick base pairs

A-T and G-C pairs linked by hydrogen bonds

Double Helix Geometry

Consists of two antiparallel right-handed helices with base pairs stacked 3.4 Å apart

Major and Minor Grooves

Gaps in the Double Helix structure important for protein interactions

Central Dogma

Describes the flow of genetic information from DNA to RNA to protein synthesis

DNA Replication

Process where DNA serves as a template for the synthesis of new DNA molecules

Transcription

DNA-templated synthesis of mRNA molecules in the cell

Translation

Process where ribosomes read mRNA codons to incorporate amino acids into polypeptide chains

Each DNA strand encodes the same _______ _______, in a ________ fashion

biological information, complementary

How many H-bonds form between C and G?

3

How many H-bonds form between A and T?

2

The two strands (helices) of a double helix run?

antiparallel

Are the two helices of a double helix left-handed or right-handed?

right-handed

Each complete turn of the helix contains how many base pairs?

~ 10

10 base pairs are how long?

34 Å

The two strands of the Double Helix are?

plectonemically coiled

Plectonemically coiled

wrapped around one another, so you can’t pull the two strands apart

How do you separate plectonomically coiled strands?

unwind them from one end

major groove

large angle

minor grove

small angle

DNA secondary structure is largely independent of?

sequence

Is the sugar-phosphate backbone hydrophobic or hydrophilic or polar?

polar

Are the bases hydrophobic or hydrophilic or polar?

hydrophobic

mRNA

messenger RNA

glycosylic bonds

C-N

glycosydic bonds

C-O

Each groove is lined by potential?

hydrogen-bond donor and acceptor atoms

ATP

Adenosine Triphosphate

ATP is the cell’s most important reservoir of?

Free energy available for immediate use

ATP is a type of?

nucleotide

ATP is comprised of?

Adenosine, ribose, and three phosphate groups

ATP is a link between?

catabolism and anabolism

ATP is earned/produced in?

exergonic reactions

ATP is spent/consumed in?

endergonic reactions

Catabolism

Cells breakdown nutrient (large) molecules

Anabolism

synthesis of metabolic intermediates and macromolecules

The typical lifetime of an ATP molecule is measured in?

seconds to minutes

The free energy change for hydrolysis of ATP is?

- 50 kJ/mol

The free energy change for amides, esters, and phosphoesters is?

15-20 kJ/mol

What are 3 reasons to choose ATP as energy currency?

1. It is metabolically available

2. It is kinetically stable

3. It is chemically versatile

Hydrolysis of the link between gamma and beta phosphate in ATP yields?

ADP and Pi

Hydrolysis of the alpha-beta linkage in ATP yields?

AMP and PPi

PPi

pyrophosphate

Hydrolysis of the alpha-beta linkage in ATP is done via a?

nucleophilic attack of the alpha phosphate

Hydrolysis of the link between gamma and beta phosphate is done via a?

nucleophilic attack of the gamma
phosphate

Glutamine synthetase

the cell drives the synthesis of glutamine forward by coupling the reaction to ATP hydrolysis

Glutamine Synthetase: Step 1

ATP reacts with glutamate to produce a covalent intermediate

What is the covalent intermediate produced in step 1 of Glutamine Synthetase?

mixed anhydride of phosphate and glutamate

Glutamine Synthetase: Step 2

ammonia reacts with the carbonyl carbon atom

In step 2 of Glutamine Synthetase what is the leaving group?

Pi

The carbonyl carbon always acts as the?

electrophile

Phosphorylated compounds are?

Chemically versatile

What’s an example of a phosphorylated compound?

ATP

chemically versatile means that the phosphate group can?

participate in a variety of chemical reactions with common organic functional groups

ATP provides energy through?

group transfer

ATP can also transfer a PPi or an AMP moiety to a?

substrate or amino acid residue of an enzyme

PPi

pyrophosphoryl

AMP

adenylate

Metabolism can be divided into?

anabolism and catabolism

Anabolism

process of building up larger and more complex molecules from simple precursors

Catabolism

breakdown of large molecules and foodstuffs into simpler products

Catabolic processes _____ ATP energy

supply

Anabolic processes _____ ATP energy

require

Catabolic pathways?

converge

Anabolic pathways?

diverge

Metabolic pathways are?

irreversible

Metabolic pathways always occur in?

one direction

All metabolic pathways are

regulated

Regulation takes place near which part of the pathway?

beginning

The carbon “skeletons” of most sugars, fats, and amino acids are converted into which single centrally-important metabolite?

Acetyl CoA

Acetyl CoA

Acetyl Coenzyme A

Acetyl CoA is composed of?

two-carbon (acetate) units

Activity of enzymes are regulated through?

1. transcriptional control of the level of enzyme

2. inhibition and activation of the activity of the enzyme

Precursor-product relationship?

product of one step is the precursor for the next

Elucidation of complex metabolic pathways?

identification of a series of linked precursor-product relationships

What are the 3 experimental approaches to the study of metabolic pathways?

1. use of metabolic inhibitors

2. biochemical Genetics

3. use of radioactively labeled substrates

Metabolic inhibitors

block pathways at specific points leading to a buildup of preceding
intermediates

2 Types of Biochemical Genetics

1. Genetic Diseases

2. Auxotrophic mutants

Genetic Diseases

deficiency of a specific enzyme of a metabolic pathway leads to the
accumulation of intermediates preceding the point of deficiency

Radioactively labeled substrates

If you synthesize a compound from 14C, then the compound, and any products derived from the carbon atoms in it, will be radioactive

Why can the radioisotope be traced so easily?

when it decays, it releases a little flash of energy

14C is an example of a?

radioisotope

Oxidation and reduction reactions must?

occur together

Reducing agent

electron donating molecule

Oxidizing agent

electron accepting molecule

Standard hydrogen electrode has a reduction potential of?

0

The reaction will proceed spontaneously if?

ΔE0′ > 0

2 Categories of cofactors are?

1. Inorganic ions

2. Coenzymes

Many of coenzymes are derivatives of?

adenosine

ATP ‘phosphate’ definition:

metabolic carrier/donor of phosphate groups

Coenzyme A (CoA/CoASH):

carrier of acyl (acid) groups

Fe2+, Mg2+, Mn2+, Zn2+, Cu2+

inorganic ions

What are the inorganic ions?

• Fe2+

• Mg2+

• Mn2+

• Zn2+

• Cu2+

Coenzymes

complex organic or metalloorganic compounds that act as transient
carriers of specific functional groups

CoASH has which group?

thiol (-SH) group

CoASH forms _____ derivatives with organic acids

thioester

Universal electron carriers

• NAD+

• NADP+

• FAD

• FMN

NAD+

nicotinamide adenine dinucleotide

NADP+

nicotinamide adenine dinucleotide phosphate

FAD

flavin adenine dinucleotide