Topic 3 Review

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Topic 3 Review

• Biochemistry

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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

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Kinds of Atoms

• 4 most common elements
• H (lightest to form 1 bond)
• O (lightest to form 2 bonds)
• N (lightest to form 3 bonds)
• C (lightest to form 4 bonds)
• In earths crust 39.2 is Al, Fe, Si
• For each of the 11 know example of use in plant
  animal

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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

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11 most important elements

1. P (p a) backbone for nucleic acids, part of
   energy storage molecule ATP
2. I (a) part of thyroid hormone Thyronine
3. K (a) important to nerve function, (p) regulate
   water balance, opening of stomata
4. Ca (a) part of bones and teeth, triggers muscle
   contractions (p) formation of cell walls,
   response to stimuli
5. Na (p a) acid base balance, (a) nerve
   function
6. Fe (a) hemoglobin component, (p) in cytochrome,
   used in electron transport

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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

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Draw water and show its H bonds

• 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.

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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

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Water Properties significance I

• Transparency the ability of light to pass
  through water
• Primary production in aquatic habitats is
  possible, Light can pass into plant cells,
  retinal cells
• 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
• Solvent properties Many substances dissolve in
  water due to its polarity
• Substances dissolved and carried in blood or sap

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Water properties significance II

• Thermal properties heat capacity large amounts
  of energy needed to raise temperature
• Water temp remains stable, good for aquatic
  organisms, blood use for thermoregulation
• 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
• Thermal properties cooling by evaporation
  evaporation possible before boiling, resulting
  water cools
• Transpiration in plants, sweat in humans for
  cooling

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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

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• Organic compounds containing carbon and found
  in living things (except hydrogencarbonates,
  carbonates and oxides of carbon
• Inorganic the rest of it

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What is this Structure?
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What is this Structure?
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What is this Structure?
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What is this Structure?
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What is this Structure?
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Which is saturated which is not?
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Which is more common in plants?
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List 3 examples each for 3 sugar levels
Compound Example
Monosaccharide Glucose, Galactose, Fructose
Disaccharide Maltose, Sucrose, Lactose
Polysaccharide Starch, Cellulose, glycogen, chitin
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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

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Outline the process of condensation hydrolysis
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• 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

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What process is shown here?
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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

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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

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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

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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
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What are the complementary base pairs in DNA?
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Draw a double helix explain the bonding
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2.5 DNA Replication

• 2.5.1 State that DNA replication is
  semi-conservative.
• 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.

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What is meant by semi-conservative replication?
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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.

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Recall complementary base pairing conserves
sequence
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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.

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List 3 ways RNA is different from DNA

• RNA nucleotides contain the sugar ribose. Ribose
  has one more hydroxyl than deoxyribose.
• Uracil, a pyrimidine, is unique to RNA and is
  similar to thymine (A, C, G, U).
• RNA is single stranded.

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Outline the process of transcription (Initiation,
Elongation, Termination)

• 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 3end 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.

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Genetic Code codons, triplets of bases
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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

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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.

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2. Elongation amino acids are added one by one
to the initial amino acid.

1. 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.
2. 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.
3. 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.

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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.

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So Heres a DNA Strand

• ATTCGGCCACATTTC
• 1. Write out the complementary strand
• TAAGCCGGTGTAAAG
• Write out the RNA transcript of the original
  strand
• UAAGCCGGUGUAAAG
• Write out the first 3 tRNA anticodons
• AUU CGG CCA

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1 gene 1 polypeptide

• DNA ? transcription to mRNA ? translation to
  polypeptide
• Functional protein may combine multiple
  polypeptides

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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

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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)

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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

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Effects of Substrate concentration on Enzyme
Activity
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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

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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)

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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

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Cell Respiration

• The controlled release of energy, in the form of
  ATP, from organic compounds in cells

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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

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Overview of Cell Respiration
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Glycolysis takes place in the cytoplasm
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Aerobic Cell Respiration in the mitochondria ?
the Krebs Cycle
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Aerobic Cell Respiration in the mitochondria ?
Chemiosmosis
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Anaerobic Respiration Alcoholic Fermentation
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Anaerobic Respiration Lactic Acid Fermentation
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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

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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

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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
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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

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Figure 10.4 An overview of photosynthesis
cooperation of the light reactions and the Calvin
cycle (Layer 3)
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Measuring Rates of Photosynthesis

• Involves production of oxygen, uptake of carbon
  dioxide increase in biomass.
• All can be measured
• Oxygen production
• Aquatic plants release bubbles during
  photosynthesis. Collect measure volume
• Carbon dioxide uptake
• Uptake from air is hard to measure. Uptake from
  water will cause pH to rise measurably
• Biomass increase
• Harvest plants and measure biomass over time

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• 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

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Effects of Carbon Dioxide on Photosynthetic Rate