Transcript Unit 2, Module 2 Biochemistry - rev 2012

Reminders:
 Today
you are to be wearing your
ID badges (they can still be picked
up!)
 If you are absent, you have 5 days
to get your work into me…HW was
assigned Friday!
 QUIZ ON MODULE 1 TOMORROW!
Progress Check 2/4




1. The dependent variable of the plant-bulb
experiment (your answer to #4)
2. Water temperature that caused the lowest
rate of respiration (your answer to #15)
3. Difference in the number of seeds
germinated between days 10 and 15 at 10°C
(your answer to #17)
4. STERNGRR life process described in #33.
Agenda 2/4
 Review
variables
 pH demonstration
 Reading
 Biochemistry notes
 Molecules sheets
Review:

Mr. Cudi noticed his jeans aren’t as clean as
they used to be. He called his mom, who told
him to try Clean-O Detergent. So he washed
one pair of jeans with the old soap and one
pair in the new Clean-O soap. After washing
three times, he noticed that both jeans were
equally clean.
CONTROL:
 INDEPENDENT:
 DEPENDENT:


Nicki notices that her shower is covered in a
strange green slime. Her friend Mariah tells her
that coconut juice will get rid of the green slime.
Nicki decides to check this this out by spraying
half of the shower with coconut juice. She sprays
the other half of the shower with water. After 3
days of "treatment" there is no change in the
appearance of the green slime on either side of
the shower.
CONROL:
 INDEPENDENT:
 DEPENDENT:


NoStank Plus is a new brand of deodorant on the
market and swears to last 50% longer than the
original formula NoStank. Researchers at Men’s
Health decide to try it.
 Tester
“A” wears NoStank.
 Tester “B” wears NoStank Plus
 Tester “C” wears nothing.

After 3 weeks, Tester “B” reports the least
amount of sweat and smell on his clothing
 CONTROL:
 INDEPENDENT:
 DEPENDENT:
pH Demonstration
What is an ACID?
•
pH less than 7
• Neutralizes bases
+
• Forms H ions in solution
• Corrosive-reacts with most
metals to form hydrogen gas
• Good conductors of electricity
Common acids and bases

Do we eat more acids or bases?
What is a BASE?
 pH
greater than 7
 Feels slippery
 Dissolves fats and oils
 Usually forms OH ions in
solution
 Neutralizes acids
Acids and Bases
Acids
0
Bases
7
Where can we find the strongest acids? The
strongest bases?
14
Cellular Chemistry
Unit 2, Module 2
Review from Monday
Name an element:
 Where can we find elements?
 What makes up an element?
 What’s the difference between an element
and a compound?

I. Where can I find chemicals in my body?
A. A chemical is a substance that is made up of
elements/molecules and used in a chemical
reaction. Chemicals made up of more than
one type of element are called compounds.
B. Living things are composed of two main types
of chemical compounds:
C
1. Inorganic: compounds that do not contain
carbon, oxygen, and hydrogen. Water (made of
the elements hydrogen and oxygen) is the most
important inorganic compound for life:
Organic vs. Inorganic?
NH3
CaCl2
C6H12O6
CH4
Name the elements you see here!
I. Where can I find chemicals in my body?
i. Water is the most abundant compound
in a cell (and organism). Most
organisms are 60-90% water by weight
ii. Most chemical reactions occur in water
because it provides an optimum
environment
Ex. transport of molecules in the cell
I. Where can I find chemicals in my body?
2.
Organic: compounds that DO contain
carbon, oxygen, and hydrogen
a. Carbohydrates (carbon, hydrogen,
oxygen)
Ex. Provide energy source for
respiration (glucose)
b. Lipids (carbon, hydrogen, oxygen)
Ex. Insulate and protect organs in the
body (fats)
Carbs
Can you think of carbohydrates in your
house?

Burning Gummy Bear
Lipids  Body fat for women and
men
Age
20-40 yrs
41-60 yrs
61-79 yrs
Age
20-40 yrs
41-60 yrs
61-79 yrs
Underfat
Under 8%
Under 11%
Under 13%
Underfat
Under 21%
Under 23%
Under 24%
Healthy Range
8-19%
11-22%
13-25%
Overweight
19-25%
22-27%
25-30%
Healthy Range
21-33%
23-35%
24-36%
Overweight
33-39%
35-40%
36-42%
Obese
Over 25%
Over 27%
Over 30%
Obese
Over 39%
Over 40%
Over 42%
Liposuction –
Fat suction
Lipid = fat!
Nucleic Acids (carbon, hydrogen,
oxygen, nitrogen and phosphorus)
Ex. Allow traits to be passed from
parent to child (DNA)
d. Proteins (carbon, hydrogen,
oxygen, nitrogen, sulfur,
phosphorus)
Ex. Provide specifically shaped
molecules that can carry other
molecules (hemoglobin carries
oxygen)
c.
Reminders:
 Today
you are to be wearing your
ID badges (they can still be picked
up!)
 If you are absent, you have 5 days
to get your work into me…HW was
assigned Friday!
 QUIZ ON MODULE 1 TODAY!
Agenda 2/5
Progress check  Module notes
 Go over Problem Solving for Module 1
 Module 1 quiz
 Review macromolecules
 Finish macromolecules activity

Review from Tues.
Organic vs. Inorganic?
NH3
CaCl2
C6H12O6
CH4
Review: What is this?
0
7
14
Review:
 Name
a household substance we
tested yesterday that was an acid.
 Name a household substance we
tested yesterday that was a base.
What IS an acid or a base?
Acids:
Hydrogen donor
Bases:
Hydrogen acceptor
H+
H+
H+
H+
OH-
OHOH-
H+
H+
H+
OHOH-
H+
H+
OH-
OHOHH+
OH-
What do we mean by strong
acids and bases?
0
7
pH stands for “Potential Hydrogen”
14
pH ScaleAcid: form H+ ions in a solution
pH range 0-6.9
Base: Form OH- ions in a solution
pH range 8-14
I. Where can I find chemicals in my body?
C.
Scientists can test for the presence of the
different chemicals, such as carbohydrates,
using indicators. For example, iodine
changes to a blue-black color in the
presence of starches.
I. Where can I find chemicals in my body?
D. The six essential elements (CHNOPS)
are essential to life because they help
maintain homeostasis.
a. The elements make up essential organic and
inorganic compounds. Each type of
molecule performs specific jobs in
organisms (see examples above).
I. Where can I find chemicals in my body?

b. Hydrogen is also donated or accepted by weak acidbase pairs to regulate the pH of a system like cells and
blood. These weak acid-base pairs are called buffers.




i. When a cell’s pH drops (becomes more acidic), the buffers in
the cell “accept” the hydrogen ions which reverses the pH
change
ii. When a cell’s pH rises (becomes more basic), the buffers in
the cell “donate” hydrogen ions
iii. In a cell, acid is being produced as the cell respires. To
maintain the pH, a cell must use buffers to counteract the acid
iv. Different cells or areas of the organism need different pH
levels to perform. Buffers help keep that pH level constant
You make acid just by breathing!
Carbonic acid!
Buffer
Buffers can donate
hydrogen
Buffers can accept
hydrogen.
http://chemcollective.org/activities/tutorials/buffers/buffers3
These are examples of
artificial “buffers” we use
Add to margins of notes!

Monomer: molecule that may
chemically bond to other
molecules to form a large chain

Polymer: large molecule
(“macromolecule”) made up of
repeating subunits

monomer animation

Build a Carb animation

Build a nucelotide
Proteins in your body
Repair, maintenance
 Transport
 Enzymes
 Hormones
 Antibodies

THURSDAY
Journal 2/6

In your journal, write a reflection regarding your work and
performance in Module 1. Consider the following:
 Did
you complete all assigned work to the BEST of your
ability?
 Were you in class every day? If you were and your
grades are NOT what you want, why might this be?
 Do you have a good attitude about learning the material
in this class? Are you keeping a positive outlook?
 How do you feel about your quiz grade? Does it reflect
the time/effort you put in to learning this material?
What IS an acid or a base?
Acids:
Hydrogen donor
Bases:
Hydrogen acceptor
H+
H+
H+
H+
OH-
OHOH-
H+
H+
H+
OHOH-
H+
H+
OH-
OHOHH+
OH-
0
7
14
I. Where can I find chemicals in my body?

b. Hydrogen is also donated or accepted by weak acidbase pairs to regulate the pH of a system like cells and
blood. These weak acid-base pairs are called
buffers.




i. When a cell’s pH drops (becomes more acidic), the buffers in
the cell “accept” the hydrogen ions which reverses the pH
change
ii. When a cell’s pH rises (becomes more basic), the buffers in
the cell “donate” hydrogen ions
iii. In a cell, acid is being produced as the cell respires. To
maintain the pH, a cell must use buffers to counteract the acid
iv. Different cells or areas of the organism need different pH
levels to perform. Buffers help keep that pH level constant
Buffer Demonstration

Observe!
Buffer Demonstration 2

1 male and 1 female volunteer
You make acid just by breathing!
Carbonic acid!
Buffer
Buffer Demonstration 3
We’re going to repeat the last
demonstration, and fill out the lab on Pg. 2C
[Data table and #1]

Monomer: molecule that may
chemically bond to other
molecules to form a large chain

Polymer: large molecule
(“macromolecule”) made up of
repeating subunits
II.
A.
How does synthesis provide important organic
macromolecules using six essential elements?
Carbohydrates
1.
Monosaccharides are organic compounds made of
carbon, hydrogen, and oxygen in a 1:2:1 ratio.
Many monosaccharides bond together forming a
larger compound chain called a carbohydrate.
a.
In plants the monosaccharide called glucose
(C6H12O6) bonds with other glucose molecules again and
b.
again to form starch or cellulose. The plant can use starch
as food (like the “white” of a potato) and cellulose to build
the stem and leaves.
In animals excess glucose bond together to form a
compound (similar to starch) called glycogen which is
used for short-term energy storage. Glycogen is found
in the liver and muscles.

Burning Gummy Bear

Would a marathon runner want to load up
on carbs the week before the big race??
hitting the wall

A sugary snack or soft drink quickly raises your
blood sugar level but it's short-lived. Your pancreas
starts to secrete insulin, which triggers cells in your
body to pull glucose out of your bloodstream and
store it for later use.

Soon, the glucose available to your brain has
dropped. Neurons, unable to store glucose,
experience an energy crisis. Hours later, you feel
spaced-out, weak, confused, and/or nervous. Your
ability to focus and think suffers. The name for this
glucose deficiency is hypoglycemia , and it can even
lead to unconsciousness.
MONOSACCHARIDE
DISACCHARIDE
POLYSACCHARIDE
Examples:

Glucose - monosaccharide -simple sugar

Sucrose – disaccharide – table sugar

Starch – polysaccharide - corn
2.
Functions of carbohydrates
Energy is released when carbohydrates are
digested. This is because glucose is used
for cellular respiration.
a.
i.
ii.
Monosaccharides (simple sugars) provide an
immediate energy source
Starch and glycogen are considered short term
energy sources because these chemicals can be
broken down over a period of minutes, hours or
days to provide glucose for energy.
b.
c.
Some carbohydrates are very stable and can
be used for structure and support in the cell
and body (cellulose in the cell wall of plant
cells).
Carbohydrate chains on the surface of cell
membranes are used as identifiers (like name
tags).
How does synthesis provide important organic
macromolecules using six essential elements?
B.
Lipids
1.
There are several types of lipids, but all
contain subunits of glycerol and fatty acids
made of carbon, hydrogen, and oxygen. It is
different from a carbohydrate because of the
ratio and because the smaller units do not link
together to form a chemical chain
a. Fats can be saturated (usually solid at room
temperature) or unsaturated (usually liquid).
b. Phospholipids also contain a
phosphate group and make up most of
the cell membrane.
c. Steroids are lipid rings and help
regulate the organism through cell
communication (act as hormones)

Phospholipid Bilayer
2.
Functions of lipids
a. Because of the numerous bonds and
the way the body stores lipids, they
can be used as very long-term (weeks,
months) energy sources.
Ex. Bears accumulate a layer of fat
before winter
(when food will be less available)
b. Fats stored in the body act as
insulation and protection for internal
organs.
c. Some hormones are composed of
lipids (steroids).
Lipids  Body fat for women and
men
Age
20-40 yrs
41-60 yrs
61-79 yrs
Age
20-40 yrs
41-60 yrs
61-79 yrs
Underfat
Under 8%
Under 11%
Under 13%
Underfat
Under 21%
Under 23%
Under 24%
Healthy Range
8-19%
11-22%
13-25%
Overweight
19-25%
22-27%
25-30%
Healthy Range
21-33%
23-35%
24-36%
Overweight
33-39%
35-40%
36-42%
Obese
Over 25%
Over 27%
Over 30%
Obese
Over 39%
Over 40%
Over 42%
Liposuction –
Fat suction
Lipid = fat!
NUCLEIC ACIDS,
PROTEINS
Reminders:
 ID
badges
 If you are absent, you have 5 days
to get your work into me.
 If you are absent, you need to get
the journal assignment from a
classmate. They are also on my
webpage.
Progress Check 2/7
 1.
List the elements that can be found
in a nucleic acid (found in answer #1)
 2. What is your answer to #5?
 3. What is your answer to #6?
 4. Name the molecule with a longchain carbon backbone (answer to
#2).
Journal 2/7
ORGANIC
COMPOUND
CARBOHYDRATES
LIPIDS
ELEMENTS
SUBUNIT
(BUILDING
BLOCK)
IMPORTANCE/
FUNCTION
Monosaccharide:
glucose
Dissaccharide: sucrose
Polysaccharide: starch
Lipid: Phospholipid
Lipid: Triglyceride
II. How does synthesis provide important
organic macromolecules using six essential
elements?
C. Nucleic Acids
1. Nucleotides are compounds
made up of carbon, hydrogen,
oxygen, nitrogen and
phosphorus. Many nucleotides
bond together to make up a
long chain called a nucleic acid.
II. How does synthesis provide important
organic macromolecules using six essential
elements?
1.
There are two basic types of nucleic
acids:
a. DNA is a double chain of
nucleotides found in all living cells.
b. RNA is a single chain of
nucleotides that provides the
structures needed for the cell to
make proteins.
Nucleotide structure
The sugar is
different in DNA
and RNA
DNA = Deoxyribonucleic acid
 RNA = Ribonucleic acid

2. Functions of nucleic acids
a. DNA makes up the genes.
Genes are used to pass
traits from parent to
offspring. Genes determine
traits.
b. DNA controls cellular
activities by controlling the
production of proteins in
response to hormones and
other cellular signals.
c. RNA is used in the
production of proteins.
II.
How does synthesis provide important
organic
macromolecules using six essential
elements?
D.
Proteins
1. All six essential elements may be used in the
production of small subunits called amino acids.
There are 20 different amino acids, each with a
specific side chain of chemicals. Amino acids bond
to other amino acids to form a long chain called a
protein. These chains of amino acids fold into a
particular shape. The shape of a protein will
determine its function. If a protein denatures
(loses its shape) it can no longer function.
II.
How does synthesis provide important
organic
macromolecules using six essential
elements?
a.
b.
Hemoglobin is a protein shaped to
hold oxygen for transport through
the bloodstream.
A group of proteins called
enzymes are shaped to fit and
react with specific molecules.
Hemoglobin
Binds oxygen in
blood
 Sickle-cell anemia

 Inherit
2 bad copies
from parents
 Pain, tiredness
2.
Functions of proteins
a. Some proteins, called pigments, absorb and
reflect light. They also create color by reflecting
light.
 Ex. Chlorophyll absorbs light to gather energy for
photosynthesis, and reflects the color green
b. Some proteins are constructed by cells to bind
with and inactivate foreign particles in the body.
These are called antibodies.
c. Proteins may form structures in an organism –
such as keratin (a protein) in hair and nails.
Pigments
Antibodies
Dietary Protein

1/3 gram per pound of body weight
d.
e.
f.
Some proteins are used for
transport through the cell
membrane or in the bloodstream
(ex. hemoglobin)
Some proteins are used for
communication between cells.
These may be hormones (insulin)
or neurotransmitters. Insulin is
secreted by the pancreas and is
required by the cells of the body in
order for them to remove and use
glucose from the blood. Insulin
can be used to treat diabetes.
Enzymes (a special class of
protein) act to speed up chemical
reactions.
Insulin

It causes cells in
the liver, skeletal
muscles, and fat
tissue to absorb
glucose from the
blood.
Enzymes
Enzymes
III. Why are enzymes necessary
for life?
Enzymes- a fun introduction - YouTube
A. Enzymes help maintain homeostasis
1.
2.
Metabolism (chemical reactions) requires certain conditions
to occur. Enzymes regulate metabolism, allowing life to
continue. Enzymes speed up reactions, making an enzyme
a biological catalyst.
Metabolism (each reaction) has a small range of
temperature and pH at which it can proceed. Each
reaction also needs some energy to begin. This is called
activation energy. Enzymes allow reactions to occur at
lower activation energy (body temperature).
Graph of a reaction with and
without an enzyme
B. The structure of an enzyme determines its function
1.
Enzymes are usually proteins. Proteins have a definite
3-D structure based on how the amino acid chains fold.
a.
b.
On the enzyme, there is a place where the target
molecule can attach. This place is called the active site.
The target molecule/chemical is the substrate.
If the enzyme’s active site changes shape too much, the
substrate will not fit. An enzyme may change shape if it
is denatured by a change in temperature, pH, or salinity.
This means the enzyme will not be able to speed up the
reaction.
2.
Enzymes mediate (help) chemical reactions using
a specific chemical pathway (series of steps).
The enzyme collides with the substrate.
b. The enzyme and substrate fit together at the active site
like a lock and key.
c.
The enzyme changes the substrate in some way
i. It may help break the substrate apart by stressing
bonds.
ii. It may hold two (or more) substrates together
closely so the two parts interact.
d. The enzyme and the substrate (now product) separate.
Enzyme - YouTube
a.
Enzyme-Mediated Pathway
C. Enzymes have distinguishing characteristics
1.
2.
Enzymes are specific. This means enzymes will catalyze
only one specific reaction because only certain substrates
fit due to the shape of the active site.
Enzymes are reusable. Notice in the diagram above that
the enzyme did not change shape or split. This means it
can now fit with another substrate or set of substrates and
repeat its role in speeding up the reaction.