rh

Lecture 1 Slides

My office hours

rh

2130 Pacific HallMon 2:00-3:00Tues 2:00-3:00

Metabolic Biochemistry BIBC 102

hppt://courses.ucsd.edu/rhampton/bibc102

office hours 2130 Pac Hall

exams 1 midterm, 1 finalproblem sets available on web

IAs sections: you each registered

Tues 2:00- 3:00 Mon 2:00- 3:00

How to take this class1) Bring the lecture slides TO CLASS

you can:a) Download the powerpoints

How to take this class1) Bring the lecture slides TO CLASS

you can:b) Download the lec 1-10 PDF

How to take this class1) Bring the lecture slides TO CLASS

you can:

c) buy a packet at Soft reserves

-ready soon

-pages with holes

-2 slides per page (by popular demand)

How to take this class2) Know everything on the study list

3) Know all the terms on the terms list

How to take this class2) Know everything on the study list

3) Know all the terms on the terms list

4) Take advantage of the problem sets

Podcasting… with benefits

C6H12O6

podcasts on web ~24 hrs after class

An ongoing experiment…

iClicker 2 Why?

1) Allows instant feedback and refocusing

3) Facilitates my teaching

4) Provides easy source of points

2) Pleasantly anonymous

iClicker 2

1) Get one. Must be “iClicker brandSold in UCSD bookstore

2) Bring it to class, use it

3) Credit given for participation not correctness

Ask… ortxt: 203 303 4320

In-class text messaging…

make sure you can check yourUCSD email (@ucsd.edu)

Nelson, Cox and Lehninger 6th Ed.

fifth editionsixth edition

Nelson, Cox and Lehninger 5th Ed.

Since last year, NC&L is suggested, but NOT required…

R-generated reading…

familiarbiomolecules

small biomolecules are “non-iterated”

but do have common functional groups

small biomolecules are “non-iterated”

fig1-16

small biomolecules are “non-iterated”

but do have common functional groups

the metabolic pathway

rh

rh

Why study and understand metabolism?

2) Adult onset diabetes: a metabolic disease

1) Obesity: a world-wide problem in health

4) Important in ageing, cancer and many othermaladies

3) Exercise and metabolism

0) Underlies every life process at some level

5) Biofuel strategies for alternative energy

catabolismand anabolism

Many levels of thinking

Many levels of thinking

Many levels of thinking

Many levels of thinking

rh

Metabolism as a system

The Stedman Institute at Duke U. School of Medicine

ChrisNewgard

The Stedman Institute at Duke U. School of Medicine

PROTEINS

an amino acid

an L amino acid

Aminoacids:TheMolecularTool Box

fig3-5

Aminoacids:TheMolecularTool Box

fig3-5

(G) (A) (V)(S) (T) (C)

(L) (M) (I) (P) (N) (Q)

(D) (E)

(K) (R) (H) (F) (Y) (W)

Aminoacids:The secret practice method

The peptide bond

A polypeptide with 5 residues

has distinct ends or termini: N and C

Chemical independence of R groups

A commercial dipeptide

met-enkephalin: a neuropeptide

Tyr-Gly-Gly-Phe-Met

your own morphine

The a helix

fig 4-4

The a helix

fig4-6

The a helix

fig4-19

The b sheet

The b sheet

fig4-6

fig4-19

common b structures

examples of folded proteinswith a and b 2o structures

fig4-21

fig3-23

Levels of protein structure

fig5-1

heme: a cofactor

fig5-1

heme: a cofactor

fig5-3

heme at home…

Cofactors

ions included in protein structure

rh

discrete molecules

molecular entity in addition to the amino acids of the polypeptide

ENZYMES: the key to metabolism

biological catalysts

proteins (for the whopping majority…)

encoded by genes

diseases, alleles, isozymes

rh

rh

rh

How did (and does) metabolism evolve?

A B C D Eessential essential

non-essential intermediates

2) multiple intermediates

1) chicken and egg issue in origin of metabolism

4) regulatory connections and strategies

3) organism-specific metabolism

fig6-4

fig6-4

B.S. degreein 21 min.

enzymes increase the rates of reactions

Energy map of a reaction

DG‡ is the activation energy

altering rate by catalysis

enzymes alter DG‡. period

how enzymes alter reactions: no enzyme

how enzymes alter reactions: plus enzyme

Main Enzymatic Catalytic Mechanisms

entropy reduction

acid-base catalysis

metal ion catalysis

covalent intermediates

other, stranger things…rh

entropy reduction

rh

Main Enzymatic Catalytic Mechanisms

fig6-7

entropy reduction: reaction 1

fig6-7

entropy reduction: reaction 2

about 105 times faster

fig6-7

entropy reduction: reaction 3

about 108 times faster

entropy reduction

acid-base catalysis

Main Enzymatic Catalytic Mechanisms

recall from O-chem...

acids and bases enhancerates of reactions like this

entropy reduction

acid-base catalysis

metal ion catalysis

Main Enzymatic Catalytic Mechanisms

ions as cofactors

entropy reduction

acid-base catalysis

metal ion catalysis

covalent intermediates

rh

Main Enzymatic Catalytic Mechanisms

entropy reduction

acid-base catalysis

metal ion catalysis

covalent intermediates

other, stranger things…rh

Main Enzymatic Catalytic Mechanisms

“UN-REQUIRED” READING

not required, but interesting

READ LIGAND BINDING

andENZYME CATALYSIS