M.

01 INTRODUCTION TO BIOCHEMISTRY BIOCHEMISTRY

Dr. Professor || November 5, 2021 LECTURE
Transcribers: Delicano, Alleen Nove
Editors: Delicano, Alleen Nove

. Ove rvie w o f BioINTRODUCTION

mo le c ule s TO BIOCHEMISTRY
A. Definition of BiochemistryProteins
B.▪ Overview
polymers of amino acids joined by peptide bonds
Biomolecules
Pro te ins C. The Cell
▪ polymers of amino
acids joined by of cell: Prokaryotic and Eukaryotic
1. Types
peptide2.bonds
Cell organelles and their Functions

D. Viruses
Learning Outcomes
At the end of this unit, the students are expected to:

1. Define and differentiate biochemistry from other branches

of chemistry
▪ There are 20 different common amino acids, with different DNA
chemical properties. ▪ Bonding between
2. Differentiate a prokaryotic cell from a eukaryotic cell in
terms of its features and the organisms in which these cells bases on opposite
▪ Essential amino acids ▪ Nonessential amino acids ▪ Amino strands follows
are found
Acids are made up of carbon, oxygen, hydrogen, and strict base-pairing
nitrogen. rules:
3. Identify the organelles found in cells
▪ Different combinations of amino acids give proteins ▪ A with T
4. Give the function of each cell organelle
different properties. ▪ G with C
5. Identify a virus in terms of Lipids
its structural features and how it
exists.
▪ hydrophobic
▪ composed mostly of carbon and hydrogen
▪ three important types include
A. Definition of biochemistry
 the scientific discipline that seeks to explain life at
the molecular level”
Org anizatio n o f the
 It uses the tools and terminology of chemistry to Human Bo dy
describe the various attributes of living organisms

 Biochemistry is also a practical science: It

generates powerful techniques that underlie
advances in other fields, such as genetics, cell
biology, and immunology.
B. Overview of Biomolecules
Types of Biomolecules

1. Carbohydrates
Nucleic Acids
2. Proteins
▪ Nucleic acids = polymers of nucleotides
3. Lipids
▪ Nucleotide = a phosphate + sugar backbone+ a
4. Nucleic Acids
nitrogenous base
Carbohydrates
▪ molecules of carbon, oxygen, and hydrogen
▪ Major source of energy for cells
Physical properties of chemicals
Atoms are the smallest units of an element and are
composed of protons, neutrons, and electrons

▪ Protons (positive charge) and neutrons form atomic

nucleus

▪ Electrons (negative charge) are outside the nucleus

Elements: fundamental forms of matter ▪ carbon, hydrogen,

oxygen, nitrogen

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M.01 INTRODUCTION TO BIOCHEMISTRY

• Circular DNA - plasmid

• lack membrane bound organelles
• no histone proteins
• presence of peptidoglycan in cell wall

- Gram-positive
- Gram-negative

Clas s ific atio n o f

Org anis ms

Cell Structure
• basic unit of life
• lowest level with all attributes of life
• organisms composed of one or more cells
• cell structure correlated to function
• all cells are related
Prokaryotic and Eukaryotic cells
▪ This unity of life is best explained by a tree of life, with
modern species having evolved from common ancestors.

1 µm 2 µm 5 µm
(a) S phe ric al (b) Ro d-s hape d (c ) S piral
(c o c c i) (bac illi)
Prokaryotic Reproduction
• Binary Fission
• Genetic Diversity via Horizontal Gene Transfer
• Transformation
• Transduction
• Conjugation

Unive rs al feature s o f living c e lls

Gram- Gram-
po s itive ne g ative
bacte ria bac te ria

20 µm
Cell Surface Structures
Prokaryotes
• Bacteria or Archaea
• Size (0.5 – 10 µm)
• nucleoid - DNA not membrane bound
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 Cell Surface Structures
M.01
HansINTRODUCTION
Christian Gram: Gram Staining TO BIOCHEMISTRY

Carbo hydrate po rtion

of lipo po lys ac c haride
Oute r
me mbrane
Ce ll Pe ptido glyc an Ce ll
w all laye r w all Pe ptido glyc an
laye r
Plas ma me mbrane

Prote in Plas ma me mbrane

Prote in
Gram- po s itive bac te ria Gram-ne g ative bac te ria

(a) Gram-pos itive : pe ptido glyc an traps 20 µm

c rys tal vio le t. (b) Gram-ne gative : c rys tal viole t is e as ily rins e d away,
re ve aling re d dye .

Outs ide o f c e ll
TEM o f a plas ma membrane
• Phospholipid bilayer
• Cholesterol
• Proteins
• Carbohydrates

Ins ide o f ce ll
0.1 mm
Carbo hydrate s ide c hains
Endo me mbrane Sys tem
cholesterol
Hydro philic
re g io n

Hydro pho bic 8 hm

reg io n
Hydro philic
reg io n Pho s pho lipid Pro te ins
Inside cell

(b) S truc ture o f the plas ma membrane

Plant and Animal Ce lls

Nuc le us
Nuc le olus
• Nucleus
• genetic control Chromatin
• DNA synthesis
• RNA synthesis
• Nuclear pores
• Nuclear envelope
• Inner membrane
• Outer membrane

Po re Roug h ER
c o mple x
Ribo s o me

Clo s e -up
o f nuc le ar Chromatin
e nve lo pe

Chromatin
DNA + histone proteins =
nucleosome

Nucleolus

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M.01 INTRODUCTION TO BIOCHEMISTRY

– ribosomes
•– protein
Roughsynthesis
Endoplasmic
Reticulum (RER)
– ribosomes
Nucleolus – protein synthesis

Nuc lear
po re s
Nucleo lus
Nuclear
Nuc le ar membrane
membrane

A trans mis s io n e le ctro n microg raph (X 6,000)

Ribosomes
Ribosomes
Free or bound Golgi
Protein synthesis apparatus/body/complex
• Golgi apparatus/body/complex
• receives
• modifies
0.25 mm
• stores
• ships
Fre e ribosomFigure 6es.10in cytos ol c is fac e
(“re ce iving ” s ide o f 0.1 mm
Endo plas mic re tic ulum (ER) Ribo s o me s bo und to ER Go lg i apparatus )
Cis te rnae
Larg e
s ubunit

S mall
s ubunit
TEM s howing ER and
trans fac e
ribo s ome s Diag ram o f a ribo s o me (“s hipping” s ide o f TEM o f Golg i apparatus
Golg i apparatus )

Lysosome
Endoplasmic Reticulum Ves ic le co ntaining
two damag ed 1 mm
organe lles

Smooth ER Nucle ar
envelo pe • Lysosome
Ro ug h ER
• intracellular frag me nt
digestion of
Endoplasmic nutrients/dead
organelles Peroxis ome

Reticulum ER lume n
• programmed cell
destruction
frag ment

Cis ternae Trans itio nal ER

Ribo s o me s
Trans po rt ve s icle
Smo o th ER Ro ug h ER 200 nm Lys os ome

Pe roxis o me

• Rough ER
Mito c hondrion Dig e s tio n
• Smooth ER Ve s ic le

(b) Autophagy

Rough Endoplasmic Endomembrane System

Nuc le us
Reticulum (RER)

Rough ER
Smoo th ER

Plas ma
me mbrane

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M.01 INTRODUCTION TO BIOCHEMISTRY

Endomembrane System
Nuc leus

Ce ntral vac uo le
Roug h ER Cyto s o l
S mo oth ER

Ce ntral
Nuc le us vac uole
Ce ll wall
Plas ma
me mbrane
Chloro plas t
trans Go lgi

5 mm

Endomembrane System Types of Vesicles

• Storage &
Types of Vesicles Nuc le us

Harmle s s
• Storage & shipping was te
Alc ohol
vesicles
Ro ug h ER
• Secretory vesicles Pe ro xis ome
S mo o th ER
• Endocytic vesicles Go lg i Ce ll to xic
c is Go lg i was te
– vacuoles apparatus

– food
Lys o s o me
– contractile shipping
• expels waste vesicles Re s idual
• Peroxisomes • Secretory body

– contain enzymes that vesicles Bac te rium

Plas ma
detoxify me mbrane •
trans Go lg i

Plas ma
me mbrane

Mitochondrion/mitochondria
• Double membrane Mitochondrion/mitochondria Endocytic vesicles
Double
• Inner membrane
membrane – vacuoles
• Inner
• Cristae membrane
- energy production – food
• Cristae
• Matrix - energy - energy production
production – contractile
• Matrix - energy production • expels waste
• DNA
DNA • Peroxisomes
• binary
binaryfission
fission – contain enzymes that detoxify
• found
foundininall
allaerobic
aerobiceukaryotes
eukaryotes Peroxisome Peroxisome
10 mm
1 mm
Inte rme mbrane s pac e
Oute r • single Mito
membrane
c ho ndria Chloroplas t
me mbrane
• plants and animals Pe ro xis ome •
• detoxifies cells Mito c ho ndrio n
DNA • H2O2
Inne r
Fre e me mbrane Mito c ho ndrial
ribo s o me s DNA
in the Cris tae
mito c ho ndrial Nuc le ar DNA
Matrix
matrix
0.1 mm
(a) Diag ram and TEM o f mito c ho ndrion (b) Ne two rk of mito c ho ndria in a pro tis t
c e ll (LM)

Chloroplasts Chloroplasts
• Thylakoid (granum/grana)
••photosynthetic
Thylako id (granum/grana)
pigments • S tro ma single membrane
• photosynthetic pigments
• Stroma • Uses chemical energy • plants and animals
• Uses chemical energy • Sugar production • detoxifies cells
• Sugar production • H2O2
Ribo s ome s
S tro ma

Inner and o uter

membranes
Granum

DNA
Thylako id Inte rme mbrane s pac e
1 mm
(a) Diag ram and TEM o f c hlo ro plas t Cytoskeleton

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 M.01 INTRODUCTION TO BIOCHEMISTRY

Dire ction o f s wimming

Ves ic le
ATP
Re c e pto r fo r
motor pro te in
skeleton
Flagella
Mo to r pro te in Mic rotubule and cilia
(a) Motion o f flag e llum 5 mm
(ATP po we re d) o f c ytos ke le to n
Dire c tion o f o rganis m’s mo ve me nt
(a)

Mic ro tubule Ve s ic le s 0.25 mm Po we r s troke Re co very s troke

(b) Mo tio n o f c ilia Figure 6.23

15 mm

0.1 mm Outer micro tubule Plas ma me mbrane

doublet
Dynein pro teins
Ce ntral
mic rotubule
Radial
s po ke

Microtubules Cro s s -linking

(b) pro teins be tween
o uter do ublets
(b) Cro s s s e ctio n o f
Plas ma mo tile c ilium
membrane
Bas al bo dy

0.5 mm 0.1 mm
(a) Lo ng itudinal s e ctio n Triplet
o f mo tile cilium

(c) Cro s s s ec tio n o f

bas al body

Contractile proteins

Mus c le c e ll
0.5 mm
Ac tin
filame nt
Myo s in
filame nt
Myo s in
he ad
(a) Myo s in moto rs in mus cle c ell c ontrac tion
Centros ome Mic ro tubule

Ce ntrio le s
0.25 mm

Lo ng itudinal
s e c tio n of Corte x (o ute r c yto plas m):
o ne c e ntrio le ge l with ac tin ne two rk
100 mm
Inne r c yto plas m: s ol
with ac tin s ubunits

Mic ro tubules Cro s s s e c tio n

of the o the r c e ntrio le

Exte nding
ps e udo po dium

(b) Amo e boid mo ve me nt

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M.01 INTRODUCTION TO BIOCHEMISTRY

Summary
Prokaryotes
Eukaryotes

Locomotory organelles
Cytoskeleton

Viruses
• nonliving
Ebola Polio virions
• obligate intracellular parasites
– only demonstrate
characteristics of life while
“inside” a host cell: bacterium,
animal cell, or plant cell

• are inert outside a host cell

(no enzyme or other activity)

• inside a host cell – viral

nucleic acid (DNA or RNA)
takes over the cell and directs
the cell to produce new virus
particles (replication)
• Basic virus particle is called a
“virion” – intact and infective
virus particle
Influenza A: Enveloped, with
• Components: Nucleic Acid spikes, RNA, multisegmented
(DNA or RNA), Protein coat genome (8 separate pieces
(capsid) made of individual of RNA)
protein subunits called
capsomeres.
Bacteriophage:
• Some may have and outer
envelope or a membrane
derived from the host cell.

• The envelope can have

specific spikes of protein (H and
N spikes of Influenza) that aid in
attachment and makes them
sensitive to chemical actions of
disinfectants.
Viral replication
Morphology of viruses
1. Helical (like TMV or Ebola)
2. Polyhedral (adenovirus and
polio virus)
3. Enveloped (flu)
4. Complex (bacteriophage)

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M.01 INTRODUCTION TO BIOCHEMISTRY

Cultivation of viruses
need living cells, living hosts
Tissue cultures, embryonated
eggs, bacterial cultures, live
animals

Prions
Prions are infectious proteins,
which cause scrappie in sheep,
Kuru in humans, BSE in cattle,
and CJD in people (mad cow in
humans).

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