Download Topic 2 Review

Topic 3 Review
Biochemistry
Syllabus Statements
• 3.1.1 – State that the most frequently occurring
chemical elements in living things are carbon,
hydrogen, oxygen and nitrogen
• 3.1.2 – State that a variety of other elements are
needed by living organisms including nitrogen,
calcium, phosphorous, iron and sodium
• 3.1.3 – State one role for each of the elements
mentioned in 3.1.2 in plants animals and
prokaryotes
Kinds of Atoms
4 most common elements
1. H (lightest to form 1 bond)
2. O (lightest to form 2 bonds)
3. N (lightest to form 3 bonds)
4. C (lightest to form 4 bonds)
In earth’s crust 39.2% is Al, Fe, Si
*For each of the 11 know example of use in plant & animal
11 most important elements
1. H – (p + a) electron carrier, part of water,
part of most organic molecules
2. O – (p + a) cellular respiration, terminal
electron acceptor
3. N – (p + a) component of protein &
nucleic acids (DNA, RNA), essential
plant nutrient
4. C - (p + a) backbone of organic
components (18.5% of human body)
5. S - (p + a) component of most proteins
11 most important elements
6. P – (p + a) backbone for nucleic acids, part of
energy storage molecule ATP
7. I – (a) part of thyroid hormone Thyronine
8. K – (a) important to nerve function, (p) regulate
water balance, opening of stomata
9. Ca – (a) part of bones and teeth, triggers
muscle contractions (p) formation of cell walls,
response to stimuli
10. Na – (p + a) acid base balance, (a) nerve
function
11. Fe – (a) hemoglobin component, (p) in
cytochrome, used in electron transport
Syllabus statements
• 3.1.4 – Draw and label a diagram showing the
structure of water molecules to show their
polarity and hydrogen bond formation
• 3.1.5 – Outline the properties of water that are
significant to living organisms including
transparency, cohesion, solvent properties, and
thermal properties. Refer to the polarity of water
molecules and hydrogen bonding where
relevant.
• 3.1.6 – Explain the significance to organisms of
water as a coolant, transport medium and
habitat in terms of its properties
Draw water and show its H bonds
A. Water is a polar
molecule. All of the
properties of water stem
from this fact.
B. This allows water to
interact with one
another and form up to
4 hydrogen bonds with
oxygen atoms of
neighboring molecules
in liquid water.
Hydrogen Bonding
• Bond between molecules: weak bond but
very important
• Forms between hydrogen and adjacent,
more electronegative atom
• Important in life sustaining properties of
water
– Surface tension, thermal properties, capillary
action, viscosity
• Hold complementary strands of DNA
together
Water Properties & significance I
1. Transparency – the ability of light to pass through
water
•
Primary production in aquatic habitats is possible, Light
can pass into plant cells, retinal cells
2. Cohesion – Water molecules stick to each other
due to hydrogen bonding
•
•
Tall trees can transport water to their tops
Surface tension – water surface is a habitat
3. Solvent properties – Many substances dissolve in
water due to its polarity
•
Substances dissolved and carried in blood or sap
Water properties & significance II
4. Thermal properties: heat capacity – large
amounts of energy needed to raise temperature
•
Water temp remains stable, good for aquatic
organisms, blood use for thermoregulation
5. Thermal properties: boiling & freezing points –
boiling and freezing temps are relatively high –
must break H bonds
•
In natural habitats water rarely boils, ice forms on
surface of water so life exists below
6. Thermal properties: cooling by evaporation –
evaporation possible before boiling, resulting
water cools
•
Transpiration in plants, sweat in humans for cooling
Syllabus Statements
• 3.2.1 – Distinguish between organic and inorganic
• 3.2.2 – Identify amino acids glucose, ribose and fatty acids from
diagrams showing their structure
• 3.2.3 – List three examples for each of monosaccharides,
disaccharides and polysaccharides
• 3.2.4 – State one function of glucose, lactose and glycogen in
animals and fructose, sucrose and cellulose in plants
• 3.2.5 – Outline the role of condensation and hydrolysis in the
relationships between monosaccharides, disaccharides and
polysaccharides; fatty acids, glycerol and glycerides; amino
acids, dipeptides, polypeptides
• 3.2.6 – State three functions of lipids
• 3.2.7 – Discuss the use of carbohydrates and lipids in energy
storage
• Organic = compounds containing carbon
and found in living things (except
hydrogencarbonates, carbonates and
oxides of carbon
• Inorganic = the rest of it
What is this Structure?
What is this Structure?
What is this Structure?
What is this Structure?
What is this Structure?
Which is saturated which is not?
Which is more common in plants?
List 3 examples each for 3 sugar
levels
Compound
Example
Monosaccharide
Glucose, Galactose,
Fructose
Disaccharide
Maltose, Sucrose,
Lactose
Polysaccharide
Starch, Cellulose,
glycogen, chitin
Carbohydrate Functions
• Glucose = Simple sugar created by
photosynthesis and used in respiration
• Lactose – mammals produce it as a
disaccharide in milk for infants
• Glycogen – storage polysaccharide in animals –
generally located in the liver
• Fructose – common sugar form in plant fruits
and tubers
• Sucrose = Plants transport carbs from leaves to
roots in this form
• Cellulose = Basic structural unit of the plant cell
wall
Outline the process
of condensation &
hydrolysis
• Condensation Reactions
– 2 Amino Acids  Dipeptide + Water
– Many amino acids  Polypeptide + Water
– Monosaccharides  Di or Polysaccharides +
Water
– Fatty acids + Glycerol  Glycerides + water
• Hydrolysis Reactions
– Polypeptides + Water  Dipeptides or AAs
– Polysaccharides + Water 
Di or monosaccharides
- Glycerides + water  Fatty acids + Glycerol
What process is
shown here?
Functions of Lipids
1. Energy Storage – fat in humans, oils in
plants
2. Building membranes – phospholipids and
cholesterol form membrane structure
3. Heat insulation – layer of fat under the
skin reduces heat losses
4. Bouyancy – lipids less dense than water
so help animals float
Comparison of Lipids and Carbs for
Energy Storage
Carbohydrates
• More easily digested
providing rapid
energy release
• Water soluble so easy
to transport and store
Lipids
• More energy per
gram
• Lighter storage
method
• Insoluble in water so
no osmosis problems
for cells
3.3 DNA Structure
• 3.3.1 – Outline DNA nucleotide structure in terms of
sugar (deoxyribose), base and phosphate
• 3.3.2 – State the names of the four bases in DNA
• 3.3.3 – Outline how the DNA nucleotides are linked
together by covalent bonds into a single strand
• 3.3.4 – Explain how the DNA double helix is formed
using complementary base pairing and hydrogen bonds
• 3.3.5 – Draw a simple diagram of the molecular structure
of DNA
• 3.5.1 – Compare the structure of RNA and DNA
Outline the structure of a DNA
nucleotide
Name the 4 DNA bases
Outline how nucleotides are
linked together by covalent
bonds into a single strand
(phosphodiester bonds)
What is the direction of this strand
What are the complementary base
pairs in DNA?
Draw a double helix & explain the
bonding
2.5 DNA Replication
2.5.1 State that DNA replication is semiconservative.
2.5.2 Explain DNA replication in terms of
unwinding of the double helix and separation of
the strands by helicase, followed by formation of
the new complementary strand by DNA
polymerase.
2.5.3 Explain the significance of complementary
base pairing in the conservation of the base
sequence of DNA.
What is meant by semiconservative replication?
How Does replication happen?
Unwinding
•
Helicase: which unwinds the DNA double helix and separates the
strands by breaking the hydrogen bonds
•
Multiple origins of replication, leading and lagging strands
replicated separately
Base pairing
•
DNA Polymerase which links up the nucleotides to form the new
strand of DNA.
•
the single strands act as templates for the new strands.
•
Free nucleotides are present in large numbers around the
replication fork.
•
The bases of these nucleotides form hydrogen bonds with the
bases of the parent strand.
Rewinding
a)
Daughter DNA molecules each rewind into a double helix.
Recall complementary base pairing
conserves sequence
2.6 Transcription & Translation
2.6.1 Compare the structure of RNA and DNA
2.6.2 Outline DNA transcription in terms of the formation of
an RNA strand complementary to the DNA strand by
RNA polymerase.
2.6.3 Describe the genetic code in terms of codons
composed of triplets of bases.
2.6.4 Explain the process of translation, leading to peptide
linkage formation.
2.6.5 Define the terms degenerate and universal as they
relate to the genetic code.
2.6.6 Explain the relationship between one gene and one
polypeptide.
List 3 ways RNA is different from
DNA
a) RNA nucleotides contain the sugar
ribose. Ribose has one more hydroxyl
than deoxyribose.
b) Uracil, a pyrimidine, is unique to RNA
and is similar to thymine (A, C, G, U).
c) RNA is single stranded.
Outline the process of transcription
(Initiation, Elongation, Termination)
a)
b)
a)
b)
c)
a)
b)
RNA polymerase binds to the promoter region of the gene
(TATA…)
RNA polymerase untwists one turn of DNA double helix at a time
exposing about 10 DNA bases for pairing with RNA nucleotides.
Enzymes add RNA nucleotides at the 3’end of the growing RNA
molecule as it continues along the double helix. This forms a
strand of mRNA.
mRNA molecule peels away from DNA template.
A single gene is transcribed simultaneously by several molecules
of RNA polymerase. Allows the production of large amounts of
mRNA and therefore protein.
RNA polymerase continues adding nucleotides until it reaches the
termination site on the DNA.
Termination site signals RNA polymerase to stop adding
nucleotides and to release the RNA molecule.
Genetic Code = codons, triplets of bases
Define
• Degenerate 
– Amino acids are coded for by multiple
different codon sequences. As many as 6
sequences in some cases for one amino acid
• Universal 
– DNA code is the same in all living things. The
gene for a bacterial polypeptide will create the
same polypeptide in any eukaryote
How does translation work?
• Three stages:
1) Initiation: (assume that tRNA has already
combined with specific amino acids)
a) small ribosomal subunit binds to both mRNA
and a special initiator tRNA. Translation begins
at the start or initiation codon. Anticodon of
tRNA is hydrogen bonded to mRNA codon.
b) large ribosomal subunit attaches to form a
functional ribosome.
2. Elongation: amino acids are added one by one
to the initial amino acid.
a)
b)
c)
Codon recognition: H bonds formed between mRNA
codon in the A site with the anticodon of an incoming
molecule of tRNA with its amino acid.
Peptide bond formation: component of large ribosomal
subunit catalyzes the formation of a peptide bond
between the amino acid extending from the P site and
the newly arrived amino acid in the A site. The
polypeptide chain that was in the P site is transferred
to the amino acid carried by the tRNA in the A site.
Translocation: tRNA that was in the P site is exited.
tRNA in the A site is translocated to the P site;
anticodon stays H bonded to codon, so mRNA and
tRNA move as a unit. Next codon to be translated is
brought to the A site.
Termination
d) Elongation continues until a stop codon reaches
the A site of the ribosome.
• A protein called a release factor binds directly
to the termination codon in the A site and
causes ribosome to add a water molecule to
polypeptide chain.
• This hydrolysis frees the polypeptide chain in
the P site. Ribosomes then separate.
So Here’s a DNA Strand
ATTCGGCCACATTTC
1. Write out the complementary strand
TAAGCCGGTGTAAAG
2. Write out the RNA transcript of the
original strand
UAAGCCGGUGUAAAG
3. Write out the first 3 tRNA anticodons
AUU CGG CCA
1 gene = 1 polypeptide
DNA  transcription to mRNA 
translation to polypeptide
Functional protein may combine
multiple polypeptides
2.3 Enzymes
• 2.3.1 - Define Enzyme & Active Site
• 2.3.2 – Explain enzyme – substrate specificity
• 2.3.3 – Explain the effects of temperature, pH &
substrate concentration on enzyme activity
• 2.3.4 – Define denaturation
• 2.3.5 – Explain the use of pectinase in fruit juice
production and one other commercial application
of enzymes
Definitions
1. Organic = compounds containing carbon that are
found in living things (excluding
hydrogencarbonates, carbonates & oxides of
carbon
2. Enzyme – globular proteins which act as catalysts
for chemical reactions
3. Active site – A region on the surface of an
enzyme to which substrates bind and which
catalyzes a chemical reaction involving substrates
4. Denaturation = a structural change in a protein
that results in a loss of its biological properties
(heat & pH cause it)
Enzyme-Substrate Specificity
• Enzymes are specific – catalyze a few
reactions
• Only small # possible substrates
• Substrate binds to active site
• Shape & chemical properties of active site
match the substrate
• Lock & key model
Effects of Substrate concentration
on Enzyme Activity
Commercial Applications of
Enzymes
• Pectinase is used in production of fruit
juice
– Pectin bonds cellulose in forming large
structural fibers in fruit
– Pectinase breaks this bond, producing liquid
or juice ( clear, less viscous, more flavorful)
• Restriction enzymes are used to “cut”
genes from DNA and splice them into
different organisms
– Used in gene transfer, production of GMO
Lactose intolerant?
• Lactase is used in the production of lactose free
milk
• The enzyme breaks down lactose into glucose
and galactose
• Used to predigest the lactose because some
people lack this enzyme
• Gene for producing lactase in our bodies reduce
expression after weaning
• Expression may drop by 5-90%, more so in
populations that have less dairy exposure
(usually in individuals of non-European descent)
2.7 Cell Respiration
• 2.7.1 – Define cell respiration
• 2.7.2 – State that in cell respiration glucose in
the cytoplasm is broken down into pyruvate with
a small yield of ATP
• 2.7.3 – Explain that in anaerobic cell respiration
pyruvate is converted into lactate or ethanol and
carbon dioxide in the cytoplasm, with no further
yield of ATP
• 2.7.4 – Explain that in aerobic cell respiration
pyruvate is broken down in the mitochondrion
into carbon dioxide & water with a large yield of
ATP
Cell Respiration
• The controlled release of energy, in the
form of ATP, from organic compounds in
cells
Overall Process
Organic compounds + Oxygen
Carbon dioxide + Water + Energy
For convenience we usually start with
glucose, but can use lipids, proteins and
other carbohydrates.
C6H12O6 + 6 O2
6 CO2 + H2O + Energy
Glucose is oxidized and oxygen is reduced
Overview of Cell Respiration
Glycolysis takes place in the
cytoplasm
Aerobic Cell Respiration in the
mitochondria  the Krebs Cycle
Aerobic Cell Respiration in the
mitochondria  Chemiosmosis
Anaerobic Respiration: Alcoholic
Fermentation
Anaerobic Respiration: Lactic Acid
Fermentation:
2.8 Photosynthesis
• 2.8.1 – State that photosynthesis involves the conversion of light
energy into chemical energy
• 2.8.2 – State that white light from the sun is composed of a range of
wavelengths (colors)
• 2.8.3 – State that chlorophyl is the main photosynthetic pigment
• 2.8.4 – Outline the differences in absorbtion of red, blue and green
light by chlorophyl
• 2.8.5 – State that light energy is used to split water molecules
(photolysis) to give oxygen & hydrogen and produce ATP
• 2.8.6 – State that ATP and hydrogen (derived from the photolysis of
water) are used to fix carbon dioxide to make organic molecules
• 2.8.7 – Explain that the rate of photosynthesis can be measured
directly by the production of oxygen of the uptake of carbon dioxide
or indirectly by the increase in biomass
• 2.8.8 – Outline the effects of temperature, light intensity & carbon
dioxide concentration on the rate of photosynthesis
Photosynthesis basics
• Photosynthesis involves the conversion of
energy. Light energy usually sunlight is
converted into chemical energy
• Sunlight is called white light, but actually it
is composed of a wide range of
wavelengths, including red, green, & blue
• Substances call pigments can absorb light.
The main photosynthetic pigment is
chlorophyl
Figure 10.8 Evidence that chloroplast pigments participate in photosynthesis:
absorption and action spectra for photosynthesis in an alga
Absorbance
Peaks in:
Red & Blue
Minimum in
Green
Process of Photosynthesis
• Some of the light energy absorbed by chlorophyl is
used to produce ATP
• Some of the energy absorbed by chlorophyl is used
to split water molecules (photolysis)
• Photolysis of water results in production of
hydrogen and oxygen, oxygen is released as a
waste product
• Carbon dioxide is absorbed for use in
photosynthesis. Carbon is used to create a wide
range of organic substances.
• Conversion of carbon into solid substances is
called Carbon fixation.
• Carbon fixation involves the use of hydrogen from
photolysis and energy from ATP
Figure 10.4 An overview of photosynthesis: cooperation of the light reactions and the
Calvin cycle (Layer 3)
Measuring Rates of Photosynthesis
•
Involves production of oxygen, uptake of
carbon dioxide & increase in biomass.
• All can be measured
1. Oxygen production
•
Aquatic plants release bubbles during
photosynthesis. Collect & measure volume
2. Carbon dioxide uptake
•
Uptake from air is hard to measure. Uptake
from water will cause pH to rise measurably
3. Biomass increase
•
Harvest plants and measure biomass over time
•A = at low light intensities light is a limiting
factor and temperature has no effect
• B = at higher light intensities, temperature is
a limiting factor, warmer  higher rate of
photosynthesis
Effects of Carbon Dioxide on
Photosynthetic Rate