topic 3 review biochemistry. syllabus statements 3.1.1 – state that the most frequently occurring...

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 elements6. P – (p + a) backbone for nucleic acids, part of

energy storage molecule ATP7. I – (a) part of thyroid hormone Thyronine8. K – (a) important to nerve function, (p) regulate

water balance, opening of stomata9. 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 II4. 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 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.

What is meant by semi-conservative 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 separatelyBase 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. Rewindinga) 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 DNA2.6.2 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) RNA polymerase binds to the promoter region of the gene (TATA…)

b) RNA polymerase untwists one turn of DNA double helix at a time exposing about 10 DNA bases for pairing with RNA nucleotides.

a) 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.

b) mRNA molecule peels away from DNA template.c) A single gene is transcribed simultaneously by several molecules

of RNA polymerase. Allows the production of large amounts of mRNA and therefore protein.

a) RNA polymerase continues adding nucleotides until it reaches the termination site on the DNA.

b) 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) 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.

b) 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.

c) 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.

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.

Termination

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

AbsorbancePeaks 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 measured1. 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