Download Unit 4 - Chemistry, DNA transcription, translation & protein synthesis

Get Ready for A & P!
Chemistry, DNA Transcription,
Translation & Protein Synthesis
Elements
 Fundamental
forms of matter
 Can’t
be broken apart by normal
chemical means
 92
occur naturally on Earth
Most Common Elements in
Living Organisms
Oxygen
Hydrogen
Carbon
Nitrogen
Fig. 2-3, p.20
What Are Atoms?
 Smallest
particles that retain properties of
an element
 Made
up of subatomic particles:

Protons (+)

Electrons (-)

Neutrons (no charge)
Atomic Number
 Number
of protons
 All atoms of an element have the same
atomic number
 Atomic number of hydrogen = 1
 Atomic number of carbon = 6
Mass Number
Number of protons
+
Number of neutrons
Isotopes vary in mass number
Isotopes
 Atoms
of an element with different
numbers of neutrons (different mass
numbers)
 Carbon 12 has 6 protons, 6 neutrons
 Carbon 14 has 6 protons, 8 neutrons
Radioisotopes
 Have
an unstable nucleus that
emits energy and particles
 Radioactive decay transforms
radioisotope into a different element
 Decay occurs at a fixed rate
Radioisotopes as Tracers
 Tracer
is substance with a
radioisotope attached to it
 Emissions from the tracer can be
detected with special devices
 Following movement of tracers is
useful in many areas of biology –
Ex.: PET scans
Other Uses of Radioisotopes
 Drive
artificial pacemakers
 Radiation
therapy
Emissions from some radioisotopes can
destroy cells. Some radioisotopes are used to
kill small cancers.
What Determines
Whether Atoms Will
Interact?
The number and arrangement
of their electrons
Electrons
 Carry
a negative charge
 Repel one another
 Are attracted to protons in the nucleus
 Move in orbitals - volumes of space that
surround the nucleus
Electron Orbitals
 First
orbital can hold up to two
electrons
 Atoms differ in the number of
occupied orbitals
 Orbitals closest to nucleus are
lower energy and are filled first
Shell Model

First shell



Lowest
energy
Holds 1 orbital
with up to 2
electrons
SODIUM
11p+ , 11e-
CARBON
6p+ , 6e-
OXYGEN
8p+ , 8e-
HYDROGEN
1p+ , 1e-
HELIUM
2p+ , 2e-
Second shell

4 orbitals
each hold up
to 8 electrons
CHLORINE
17p+ , 17e-
electron
SODIUM
11p+ , 11e-
CHLORINE
17p+ , 17e-
CARBON
6p+ , 6e-
OXYGEN
8p+ , 8e-
HYDROGEN
1p+ , 1e-
HELIUM
2p+ , 2e-
proton
neutron
NEON
10p+ , 10e-
Fig. 2-6, p.23
Electron Vacancies
 Unfilled
shells make atoms likely
to react
 Hydrogen, carbon, oxygen, and
nitrogen all have vacancies in their
outer shells
Chemical Bonds, Molecules,
& Compounds
 Bond
is union between electron structures
of atoms
 Atoms bond to form molecules
 Molecules may contain atoms of only one
element - O2
 Molecules of compounds contain more
than one element - H2O
Chemical Bookkeeping
 Use
symbols for elements when writing
formulas
 Formula
for glucose is C6H12O6

6 carbons

12 hydrogens

6 oxygens
Molecular Mass & Moles
1
mole of a pure substance has a mass
equal to its molecular mass (MM) in grams

Therefore, one mole of a compound, say CO (carbon
monoxide) is equal to:
MM of C =
12
MM of O =
16
MM of CO =
28 grams/ mole of CO
So the molecular mass, MM, (molecular weight, MW) of a
compound is the sum of the atomic masses (atomic
weights) of the atomic species as given in the molecular
formula.
Chemical Bookkeeping
 Chemical
equation shows reaction
Reactants ---> Products
 Equation for photosynthesis:
REACTANTS
12H2O
WATER
+
6CO2
CARBON
DIOXIDE
24 hydrogens 6 carbons
12 oxygens 12 oxygens
sunlight
energy
PRODUCTS
6O2
+
OXYGEN
12 oxygens
C6H12O6
GLUCOSE
+
6H2O
WATER
6 carbons 12 hydrogens
12 hydrogens 6 oxygens
6 oxygens
Important Bonds in
Biological Molecules
 Ionic
Bonds
 Covalent Bonds
 Hydrogen Bonds
Ion Formation
 Atom
has equal number of
electrons and protons - no net
charge
 Atom
loses electron(s), becomes
positively charged ion
 Atom
gains electron(s), becomes
negatively charged ion
Ionic Bonding
 One
atom loses electrons,
becomes positively charged ion
 Another atom gains these
electrons, becomes negatively
charged ion
 Charge difference attracts the
two ions to each other
Formation of NaCl
 Sodium

atom (Na)
Outer shell has one electron
 Chlorine

atom (Cl)
Outer shell has seven electrons
transfers electron to Cl forming Na+
and Cl-
 Na
 Ions
remain together as NaCl
Formation of NaCl
electron transfer
sodium
atom
11 p +
sodium
ion
11 p +
10 e-
chlorine
atom
17 p +
17 e-
chlorine
ion
17 p +
18 e-
Covalent Bonding
Atoms share a pair or pairs of electrons
to fill outermost shell
•Single covalent bond
•Double covalent bond
•Triple covalent bond
Covalent Bonding
Two hydrogen atoms,
each with one proton,
share two electrons
in a single nonpolar
covalent bond.
molecular hydrogen (H2)
H—H
Fig. 2-8b(1), p.25
Covalent Bonding
Two oxygen
atoms,
each with eight
protons,
share four
electrons in a
nonpolar double
covalent bond.
molecular oxygen (O2)
O=O
Fig. 2-8b(2), p.25
Nonpolar Covalent Bonds
 Atoms
share electrons equally
 Nuclei
of atoms have same
number of protons
 Example:
Hydrogen gas (H-H)
Covalent Bonding
Oxygen has
vacancies for two
electrons in its
highest energy
level orbitals. Two
hydrogen atoms
can each share
an electron with
an oxygen. The
resulting two
polar covalent
bonds form a
water molecule.
water (H2O)
H—O—H
Fig. 2-8b(3), p.25
Polar Covalent Bonds
 Number
of protons in nuclei of
participating atoms is not equal
 Electrons
spend more time near
nucleus with most protons
 Water
- Electrons more attracted to
O nucleus than to H nuclei
Hydrogen Bonding
 Molecule
held together by polar covalent
bonds has no net charge
 However,
atoms of the molecule carry
different charges
 Atom
in one polar covalent molecule can
be attracted to oppositely charged atom in
another such molecule
Water Is a Polar
Covalent Molecule
 Molecule
has no net
charge
end has a
slight negative charge
O
 Oxygen
 Hydrogen
end has a
slight positive charge
H
+
H
+
Water Is a Good Solvent
 Ions
and polar molecules dissolve easily
in water
 When
solute dissolves, water molecules
cluster around its ions or molecules and
keep them separated
The pH Scale
H+ concentration of fluid
 Change of 1 on scale means 10X change
in H+ concentration
 Measures
Highest H+
Lowest H+
0---------------------7-------------------14
Acidic
Neutral
Basic
Examples of pH
 Pure
water is neutral with pH of 7.0
 Acidic

Stomach acid: pH 1.0 - 3.0

Lemon juice: pH 2.3
 Basic

Seawater: pH 7.8 - 8.3

Baking soda: pH 9.0
Acids & Bases
 Acids

Donate H+ when dissolved in water

Acidic solutions have pH < 7
 Bases

Accept H+ when dissolved in water

Acidic solutions have pH > 7
Salts
 Compounds
that release ions other than
H+ and OH- when dissolved in water
 Example:
 Many
NaCl releases Na+ and Cl–
salts dissolve into ions that play
important biological roles
Organic Compounds
Hydrogen and other elements
covalently bonded to carbon
 Carbohydrates
- C, H and O
 Lipids - C, H, O and sometimes P
 Proteins - C, H, O, N and sometimes S
 Nucleic Acids - C, H, O, N, P
Carbon’s Bonding Behavior
 Outer
shell of carbon
has 4 electrons; can
hold 8
 Each
carbon atom
can form covalent
bonds with up to four
atoms
Carbohydrates
Monosaccharides
(simple sugars)
Oligosaccharides
(short-chain carbohydrates)
Polysaccharides
(complex carbohydrates)
Monosaccharides

Simplest carbohydrates

Most are sweet tasting, water soluble

Most have 5- or 6-carbon backbone
Glucose (6 C)
Fructose (6 C)
Ribose (5 C)
Deoxyribose (5 C)
Two Monosaccharides
glucose
fructose
Fig. 3-7, p.38
Disaccharides
 Type
of
oligosaccharide
 Two
monosaccharides
covalently bonded
 Formed by
condensation reaction
glucose
fructose
+ H2O
sucrose
Fig. 3-7b, p.38
Polysaccharides
 Straight
or branched chains of many sugar
monomers
 Most
common are composed entirely of
glucose

Cellulose

Starch (such as amylose)

Glycogen
Cellulose & Starch
 Differ
in bonding patterns between
monomers
 Cellulose
- tough, indigestible, structural
material in plants
 Starch
plants
- easily digested, storage form in
Glycogen
 Sugar
storage form in animals
 Large
stores in muscle and liver
cells
 When
blood sugar decreases,
liver cells degrade glycogen,
release glucose
Fig. 3-9, p.38
Lipids
 Most



include fatty acids
Fats
Phospholipids
Waxes
 Sterols
and their derivatives have no fatty
acids
 Tend to be insoluble in water
Fats
 Fatty
acid(s)
attached to
glycerol
 Triglycerides
are most
common
Fig. 3-12, p.40
Fatty Acids
 Carboxyl
 Carbon
group (-COOH) at one end
backbone (up to 36 C atoms)

Saturated - Single bonds between carbons

Unsaturated - One or more double bonds
Phospholipids
 Main
components of cell
membranes
Waxes
 Long-chain
fatty acids linked to
long chain alcohols or carbon rings
 Firm
consistency, repel water
 Important
in water-proofing
Sterols and Derivatives
 No
fatty acids
 Rigid
backbone of
four fused-together
carbon rings
 Cholesterol
- most
common type in
animals
Fig. 3-14, p.41
Amino Acid Structure
carboxyl
group
amino
group
R group
Properties of Amino Acids
 Determined
 Amino
by the “R group”
acids may be:

Non-polar

Uncharged, polar

Positively charged, polar

Negatively charged, polar
Protein Synthesis
 Protein
is a chain of amino acids linked
by peptide bonds
 Peptide



bond
Type of covalent bond
Links amino group of one amino acid with
carboxyl group of next
Forms through condensation reaction
Fig. 3-15b, p.42
Primary Structure

Sequence of amino acids

Unique for each protein

Two linked amino acids = dipeptide

Three or more = polypeptide

Backbone of polypeptide has N atoms:
-N-C-C-N-C-C-N-C-C-None
peptide
group
Primary Structure
& Protein Shape
 Primary
structure influences shape in
two main ways:


Allows hydrogen bonds to form between
different amino acids along length of chain
Puts R groups in positions that allow them
to interact
Secondary Structure
 Hydrogen
bonds form between different
parts of polypeptide chain
 These
bonds give rise to coiled or
extended pattern
 Helix
or pleated sheet
Examples of Secondary
Structure
Tertiary Structure
heme group
Folding as a
result
of interactions
between R
groups
coiled and twisted polypeptide
chain of one globin molecule
Quaternary Structure
Some proteins
are made up of
more than one
polypeptide
chain
Hemoglobin
heme
alpha globin
beta globin
alpha globin
beta globin
Fig. 3-17, p.44
Denaturation
 Disruption
of three-dimensional shape
 Breakage
of weak bonds
 Causes
of denaturation:

pH

Temperature
 Destroying
function
protein shape disrupts
Nucleotide Structure
 Sugar

 At
Ribose or deoxyribose
least one phosphate group
 Base

Nitrogen-containing

Single or double ring structure
Nucleic Acids
Cytosine
 Composed
Adenine
of nucleotides
 Single- or double-stranded
 Sugar-phosphate backbone
Structure of Nucleotides
in DNA
 Each
nucleotide consists of

Deoxyribose (5-carbon sugar)

Phosphate group

A nitrogen-containing base
 Four

bases
Adenine, Guanine, Thymine, Cytosine
DNA
 Double-stranded
 Consists
of four
types of nucleotides
 A bound to T
 C bound to G
RNA
 Usually
 Four
single strands
types of nucleotides
 Unlike
DNA, contains the base uracil in
place of thymine
 Three
types are key players in protein
synthesis
Base Pairing
during
Transcription
DNA
base pairing
during
transcription
RNA
DNA
base pairing
during DNA
replication
DNA
Fig. 14-2c, p.220
Gene Transcription
newly forming
RNA transcript
DNA template winding up
DNA template
at selected
transcription site
DNA template unwinding
b All through transcription, the DNA double helix becomes unwound in front
of the RNA polymerase. Short lengths of the newly forming RNA strand
briefly wind up with its DNA template strand. New stretches of RNA unwind
from the template (and the two DNA strands wind up again).
Fig. 14-3b, p.220
Adding Nucleotides
3´
direction of transcription
5´
5´
3´
growing RNA transcript
c What happened at the assembly site? RNA polymerase catalyzed the
assembly of ribonucleotides, one after another, into an RNA strand, using
exposed bases on the DNA as a template. Many other proteins assist this
process.
Fig. 14-3c, p.221
Three Classes of RNAs
 Messenger

Carries protein-building instruction
 Ribosomal

RNA
Major component of ribosomes
 Transfer

RNA
RNA
Delivers amino acids to ribosomes
tRNA Structure
codon in mRNA
anticodon
amino-acid
attachment site
amino
acid
OH
Figure 14.7
Page 223
Ribosomes
funnel
small ribosomal
subunit
+ large ribosomal
subunit
intact ribosome
Fig. 14-8, p.223
Genetic Code
 Set
of 64 base
triplets
 Codons
 61
specify amino
acids
3
stop translation
Fig. 14-6, p.222
Genetic Code
DNA
mRNA
mRNA
codons
amino
acids
threonine
proline
glutamate
glutamate
lysine
Fig. 14-5, p.222
Three Stages of Translation
Initiation
Elongation
Termination
Initiation

Initiator tRNA binds to small
ribosomal subunit
 Small subunit/tRNA
complex attaches to mRNA
and moves along it to an
AUG “start” codon
 Large ribosomal subunit
joins complex
Elongation
 mRNA
passes through ribosomal subunits
 tRNAs
deliver amino acids to the
ribosomal binding site in the order
specified by the mRNA
 Peptide
bonds form between the amino
acids and the polypeptide chain grows
Elongation
Termination
 Stop
codon into place
 No tRNA with anticodon
 Release factors bind to
the ribosome
 mRNA and polypeptide
are released
mRNA
new
polypeptide
chain
Transcription
Overview
mRNA
Mature mRNA
transcripts
Translation
rRNA
ribosomal
subunits
tRNA
mature
tRNA