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Biology 315 > C5 Chemistry of Life > Flashcards

C5 Chemistry of Life Flashcards

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1
Q

organic vs inorganic

A
  • organic: carbon based compounds, larger and more complex
  • inorganic: not carbon based, simpler/smaller
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2
Q

organic chemistry

A

chemistry of carbon compounds within living things
- other important elements include: O2, H, N, P

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3
Q

State the 4 components essential for life.

A
  • water
  • minerals
  • vitamins
  • biomolecules
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4
Q

Describe how water is essential for life.

A
  • water makes up the greatest % of the body
  • universal solvent
  • an important medium for reactions
  • has a low viscosity = a transport medium (can move easily through small spaces/allow small substances to move through)
  • benefits to plants: support/rigour, adhesive + cohesive properties
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5
Q

Briefly outline what vitamins and minerals are, the two types, and how they are essential for life.

A
  • inorganic ions
  • make up many biomolecules
  • aid key biological processes

Macronutrients: elements needed in large quantities
Micronutrients: elements needed in small quantities
- not having enough = deficiencies

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6
Q

What are vitamins?
What are the two types

A

VITAMINS
- around 13 essential for health
- all except VD must be obtained externally (food)

TWO TYPES
- fat soluable (dissolves in fat)
- water soluable (dissolved in water)

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7
Q

polymers vs monomers

A
  • monomers: smaller molecules/building blocks
  • polymers: larger molecules, subcomponents of monomers
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8
Q

State the four categories of bio/macromolecules needed for life, and their corresponding monomer.

A
  • carbs (monosaccharides)
  • lipids (fatty acids + glycerol)
  • proteins (amino acids)
  • nucleic acids (nucleotides)
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9
Q

metabolism

A
  • the sum total of all enzyme-catalysed chemical reactions that occur within the body
  • includes catabolism and anabolism
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10
Q

catabolism vs anabolism

A

Catabolism
- decomposition
- polymers break down to monomers
- releases energy
- includes hydrolysis

Anabolism
- synthesis
- uses energy
- monomers built up to polymers
- includes condensation reactions

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11
Q

CARBS - biomolecule
- consist of… and their ratio
- monomers (…two? multiple?)

MONOMER
- what are they
- main functions (2)
- provide examples (2)

POLYMER
- main functions (2)
- provide examples (3)

A
  • Consist of: C, H, O (1:2:1 ratio)
  • Monomer: monosaccharides (2 = disaccharide)
  • Polymer: polysaccharide

MONOSACCHARIDES (monomer)
- single sugar molecules
Functions: an energy source for cell metabolism, structural component for polysaccharides
- glucose, ribose

POLYSACCHARIDES (polymer)
- Functions: energy storage, structural support for plants
- cellulose, starch, glycogen

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12
Q

glucose

A
  • monosaccharide
  • source of energy for CR (energy released helps ATP production)
  • produced by Phs
  • animals cannot make, must consume it (or break down polysaccharides)
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13
Q

ribose

A
  • monosaccharide
  • drives synthesis of RNA, DNA and ATP
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14
Q

cellulose

A

structural support in plant cells
- polysaccharide
- not easily broken down (humans cannot)

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15
Q

starch

A

glucose storage in plants
- polysaccharide
- found in seeds and plant roots
- easily broken down by enzymes

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16
Q

glycogen

A

SHORT term storage of sugar in animals
- polysaccharide
- if blood glucose levels drop, glycogen is broken down to release glucose for energy
- located in the liver + skeletal muscles

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17
Q

LIPIDS - biomolecule
- consist of… and their ratio
- monomers (2)
- key qualities (2)
- main functions (3)
- types (2)
- what is the polymer, and what does it consist of?

A
  • Consist of: C, H, O (no set ratio, but greater than 2:1 of H:O)
  • Monomers: fatty acids + glycerol
  • Qualities: hydrophobic, relatively insoluble
  • Functions: long term energy store, body insulation, aid micronutrient absorption
  • Two types: fats/waxes (solid room temp) + oils (liquids room temp)

TRIGLYCERIDES (polymer)
- Consist of: 1x glycerol, 3x FAC

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18
Q

saturated vs unsaturated fats

A
  • fats are a type of lipid

Saturated
- the fatty acid chains are saturated with H
- the greatest number of H possible
- no double bonds

Unsaturated
- one or more double bonds (look like bends/kinks in the fatty acid chain)

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19
Q

relative insolubility
- how lipids are important due to this (3)

A

Lipids are insoluble:
- fats are nonpolar (have no + or - regions)
- water is polar (has + and - regions)
- lipids attracted to lipids, H2O attracted to H2O = they never mix

Important role in:
- maintaining osmotic balance
- formation of cell membranes
- providing protective, hydrophobic coating (hair, skin, feathers, leaves)

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20
Q

essential fatty acids
- functions (3)
- example

A
  • essential to body, but we must ingest (cannot produce)
  • Functions: cell membrane structure, gene transcription, energy sources
  • e.g. omega-3
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21
Q

phospholipids
- what?
- consist of?
- qualities (2)
- main function

A
  • a specialised type of lipid (not true fats)
  • 1x glycerol, 2x FAC, 1x phosphate group
  • are amphipathic (hydrophilic head + hydrophobic tail)
22
Q

PROTEINS - biomolecule
- consist of?
- monomer
- polymer

MONOMER
- how many types?
- describe the structure
- describe how polymer is formed

PROTEIN STRUCTURE (4)
- describe

PROTEIN TYPES (2)
- describe
- functions
- examples

A
  • Consist of: C, H, O, N
  • Monomer: amino acids
  • Polymer: polypeptide chains

AMINO ACIDS
- 20 different types
Structure
- central C atom, attached to:
- R group
- carboxyl group (COOH)
- amino group (NH2)
- hydrogen atom (H)

  • AAs join together to form a dipeptide + H2O
  • this bond is called a peptide bond
  • multiple AAs binding together form a polypeptide chain (polymer)
  • these fold up to form proteins

PROTEIN STRUCTURE
- Primary: a linear sequence of AAs (a PP chain)
- Secondary: the PP chain twists into a repetitive structure (double helix)
- Tertiary: PP chain folds into a more complex, 3D shape
- Quaternary: multiple PP chains join together to form a protein

PROTEIN TYPES
Fibrous
- long narrow strands
- secondary structure
- Functions: support, structure, movement
- they ARE something (keratin in hair/nails, elastin in skin)

Globular
- compact + rounded
- tertiary structure
- Functions: controls/assists biological functions
- they DO something (haemoglobin, enzymes, antibodies)

23
Q

denaturing

A

a structural change in a protein that results in the loss of its biological properties
- AS of enzyme changes shape
- no longer compatible to specific substrate(s)
- reaction doesn’t occur

  • can be reversible or permanent
  • Caused by: temp, pH change, chemicals
24
Q

NUCLEIC ACIDS - biomolecule
- consist of?
- monomer
- polymers (2)

MONOMER
- made up of?
- describe structure

POLYMERS
- functions of each

A
  • Consist of: C, H, O, N, P
  • Monomer: nucelotides
  • Polymers: DNA + RNA

NUCLEOTIDES (monomer)
- Made up of: 5 carbon-pentose sugar (ribose/deoxyribose), phosphate group, nitrogenous base (A/G/C/T/U)
- sugar in middle, base + phosphate attached to either side

DNA/RNA (polymers)
- DNA function: carry/contain all genetic information in all cells
- RNA function: transfer specific genes outside the nucleus to synthesise proteins

25
Q

Describe the 3 differences between DNA + RNA.

A

DNA
- deoxyribose sugar
- adenine, guanine, cytosine, thymine
- double stranded

RNA
- ribose sugar
- adenine, guanine, cytosine, uracil
- single stranded

26
Q

enzymes
- what
- structure

A
  • biological catalyst (lower the activation energy for the body’s chemical reactions
  • they facilitate, speed up + control reactions
  • not a reactant: are unchanged after reaction and can be used again

STRUCTURE
- globular proteins
- many unique enzymes, each with a specific active site (AS)
- AS of an enzyme has a specific complementary shape to a specific substrate (reactant)

27
Q

Describe the model that best describes how enzymes bind to a substrate.

A

INDUCED FIT MODEL
- can be either anabolic reactions or catabolic reactions
1. The substrate bonds to the enzyme’s active site.
2. AS changes to become more complementary to the substrate, forming the enzyme-substrate complex (ESC)
3. The reaction occurs (anabolic/catabolic), products are released

28
Q

Describe the two types of reaction that enzymes facilitate.

A
  • Catabolic: polymers to monomers
  • Anabolic: monomers to polymers
29
Q

Describe the factor affecting the rate of an enzyme-facilitated reaction.

A

TEMP
- each enzyme has an optimum (37°C for humans)
- Lower: slower ROR = less KE = less reactions
- Higher: enzyme denatures (AS changes shape)
- graph will increase to optimum, then rapidly decrease (denaturing)

pH
- each enzyme has an optimum pH depending on where it functions in the body (e.g. stomach = pH 2)
- graph will increase to optimum, then rapidly decrease (denaturing)

Substrate
- substrate conc increases = ROR increases
- limited by enzyme conc
- graph will increase then plateau

Enzyme
- enzyme conc increases = ROR increases
- limited by substrate conc
- graph will increase then plateau

30
Q

Describe the factors that assist or inhibit enzyme activity.

A

ASSISTING
Cofactors
- inorganic molecules that bond with the allosteric site of an enzyme
- changes shape of the AS to be more complementary to the substrate

Co-enzymes/co-substrates
- organic molecules that bond with the AS
- help substrate bond faster to enzyme

INHIBITING
Competitive
- molecule bonds to the AS, preventing the substrate from bonding
- reaction cannot occur

Non-competitive
- molecule bonds to the allosteric site, changing the shape of the AS
- substrate cannot bond, reaction cannot occur

31
Q

allosteric site

A

another site on an enzyme, seperate from the active site, that molecules are able to bond to
- can be used for assisting or inhibiting enzyme activity

32
Q

cellular respiration
- what
- word equation

A

the controlled release of energy from organic compounds (glucose, usually) in cells to form ATP
- glucose + oxygen = carbon dioxide + water + ATP

33
Q

ATP
- what
- structure
- how does it work

A

Adenosine Triphosphate
- type of nucleic acid: adenine base, ribose sugar, 3 phosphate groups
- is a high energy molecule and an immediate power source for cell processes

HOW
- ATP releases energy via being hydrolysed (a cycle)
- the third phosphate is held by an unstable bond, when it is released, it releases energy
- results in ADP (Di) and Pi (the released phosphate)
- ADP = low battery, energy used
- can then be regenerated by adding Pi to form ATP again
- ATP = full battery, energy ready to be released

34
Q

anaerobic vs aerobic respiration
- what
- where
- which occurs when?

A

ANAEROBIC
- absence of O2
- partial breakdown of glucose
- in the cytosol
- small yield of ATP (2) from glycolysis

AEROBIC
- presence of O2
- complete breakdown of glucose
- in the mitochondria
- large yield of ATP (30-38)

  • aerobic is far more efficient
  • anaerobic is essential when the body is not able to get enough O2 to all cells (e.g. heavy exercise)
35
Q

Outline/summarise the stages of cellular respiration (like a flow chart):
- what occurs
- where it occurs
- net ATP yield

A

GLUCOSE
|
Glycolysis (cytoplasm)
- 2 ATP
|
PYRUVATE
|
If O2 not present:
Anaerobic CR (cytoplasm)
- no more ATP produced
- fermentation
TOTAL: 2 ATP
|
If O2 present:
Aerobic CR (mitochondria)
- 30-34 ATP
TOTAL: 30-38 ATP

36
Q

CELLULAR RESPIRATION
Describe the process of glycolysis:
- where it occurs
- when it occurs
- total yield (products + ATP)

A

GLYCOLYSIS
- in cytoplasm
- starting process of both AN + AE resp

Glucose is broken down into:
- 2x pyruvate
- 2x NADH (a co-enzyme needed for AE resp)
- 2x ATP

37
Q

CELLULAR RESPIRATION
Describe the process of AE resp:
- where it occurs
- when it occurs
- process steps
- total yield (products + ATP)

A

AE RESP
- in mitochondria
- when O2 is present

Process:
- link reaction
- Krebs cycle
- electron transport chain

Pyruvate converted to:
- CO2
- H2O
- (ideally) 34-36 ATP
NET YIELD: 30-38 ATP (glycolysis + AE resp)

38
Q

CELLULAR RESPIRATION
Describe the process of AN resp:
- where it occurs
- when it occurs
- fermentation (purpose, products and cycle process)
- total yield (ATP)

A

AN RESP
- in cytoplasm
- when O2 is absent (body cannot get to cells fast enough)

FERMENTATION

Why
- body cannot get O2 to cells fast enough, all stored ATP is used up, but energy is needed
- AN resp restores NAD+ (needed in glycolysis reaction to convert to NADH)
- the fermentation cycle allows glycolysis to continue to produce ATP in a low O2 environment

Pyruvate (from glycolysis) converted to:
- Animals: lactic acid (lactate)
- Bacteria/yeast: ethanol + CO2

Process
- is a reversible cycle
- once O2 is present, lactic acid/ethanol is converted back to pyruvate
- AE then continues as normal

TOTAL YIELD: 2 ATP (glycolysis)

39
Q

PHOTOSYNTHESIS
- state equation
- describe 2 stages: name, process, equation

A
  • carbon dioxide + water = glucose + oxygen

STAGE 1: Light Dependent
- Process: photolysis
- chlorophyll absorbs photon (light E) from the sun, excites H2O electrons, they become delocalised
- chlorophyll takes an electron from H2O molecule, SPLITTING it into H2 (used in Stage 2), O2 (waste), + producing ATP
- photon - chlorophyll - ATP + H2 (+ O2 waste)

STAGE 2: Light Independent
- Process: carbon fixation
- H2 + ATP (from S1) + CO2 (from air) react to produce glucose

40
Q

Describe the structure of the leaf referring to the important components (6).

A
  • waxy cuticle: top + bottom of leaf
  • upper epidermis: transparent, allowing max light penetration for max Phs rate
  • palisade mesophyll: contains chloroplasts which contain chlorophyll, the main photosynthetic pigment
  • vascular bundle: xylem delivers H2O to cells for Phs, phloem transports glucose produced from Phs
  • spongy mesophyll: spaced out for gas exchange
  • stomata (pores): controlled by guard cells, facilitate GE (CO2 in, O2 out)
41
Q

Describe ways of measuring the rate of Phs (directly/indirectly).

A

DIRECTLY
- production of O2 (e.g. count bubbles produced by water plants)
- uptake of CO2 (e.g. enviro pH increase)

INDIRECTLY
- increase in biomass (total mass of plant)

42
Q

State the limiting factors of Phs and describe the shape of the graph when rate of Phs is on the Y axis.

A

TEMP
- increase in temp = more KE = more frequent collisions = higher rate of Phs
- graph has increase, then optimum, then decrease due to denaturing

LIGHT INTENSITY
- increase in light = more energy to drive reaction = higher Phs rate
- graph will increase then plateau when chloroplasts are working at max efficiency

CO2 CONC
- increase in CO2 = more substrate = higher Phs rate
- graph will increase then plateau due to another limiting factor

43
Q

PHS VS CR
- the reactions are complementary
- products vs inputs
- state equations for both

  • differences
  • similarities
A
  • complementary reactions within the environment
  • products of Phs are inputs of CR, vice versa
  • PHS: CO2 + H2O = C6H12O6 + O2
  • CR: O2 + C6H12O6 = H2O + CO2

DIFFERENCES
- Phs: anabolic, synthesises/builds glucose
- CR: catabolic, breaks down glucose
- producers perform both, consumers perform just CR

SIMILARITIES
- both involve ATP production
- Phs: ATP produced via light energy, used to make glucose
- CR: ATP produced via breakdown of glucose
- both require enzymes to complete the reaction

44
Q

COMPENSATION POINT GRAPHS
- what are they used to measure
- what do they show
- what is a comp point, when do they occur
- what does above/below a comp point represent

  • describe how CR/Phs depends on time of day
A
  • used to measure O2/glucose production, CO2/H2O use
  • demonstrates the relationship between CR + Phs (time of day/light on X axis, glucose/carb production on Y axis)
  • COMP POINT: when what is produced by Phs = what is used by CR (no excess), Phs rate = CR rate, usually occur at dusk/dawn
  • ABOVE CP: plant is producing more glucose then it is using
  • BELOW CP: plant is using more glucose than it is producing

TIME OF DAY
- rate of Phs is dependent (due to light availability)
- highest rate is at midday

  • rate of CR is not dependent
  • rate remains relatively stable throughout day
  • goes up slightly when Phs increases, as needs small amount of ATP to start up
45
Q

DNA
- role of DNA
- name complementary base pairs + bonds
- sugar phosphate backbone structure + function
- double helix: how is it formed

REPLICATION
- 2 stages, enzyme involved + process
- the entire process is…

A
  • Role of DNA: contains/carries all genetic information/genes for all cells
  • A + T (double H bond), G + C (triple H bond)

BACKBONE
- sugar phosphate backbone formed by the phosphates/sugars of nucleotides bonding to form a polynucleotide (polymer)
- function: provide support + protection to N bases

DOUBLE HELIX
- caused by antiparallel strands (strands run in opposite directions)
- causes twisting of strands to form an energy stable structure (the helix)
- a fold occurs every 10-15 base pairs

REPLICATION
Stage 1
- Helicase enzyme moves along helix and unwinds DNA strands
- each parent strand is a template for a new complementary daughter strand

Stage 2
- DNA polymerase enzyme synthesises both new strands
- the strands have complementary bases to parent strands

  • both stages happen at once
  • the process is semi-conservative (uses half of already formed material, half is created)
46
Q

PROTEIN SYNTHESIS
- why?
- stages (2), their location, + process

A

WHY
- DNA is too large and unstable to leave the nucleus
- protein synthesis allows for singular genes to be transferred outside the nucleus, using mRNA, for a protein to be made

TRANSCRIPTION
- in nucleus
- DNA is unwound at the location of the specific gene
- a complementary strand of mRNA is made (U instead of T)
- after it is formed, exits nucleus via a nuclear pore

TRANSLATION
- in cytoplasm
- mRNA binds to a ribosome
- ribosome translates mRNA one codon at a time
- tRNA (transport) with complementary anti-codons (same as og DNA gene, but with U) drops off the specific AA that corresponds to the codon
- the AAs bond together to form a PP chain
- after entire mRNA strand is translated, the PP chain is formed

47
Q

codon

A

3 bases, a set
- code for a specific AA
- translated together by a ribosome during protein synthesis

48
Q

mRNA

A

messenger RNA
- a smaller, more stable nucleic acid used to transfer specific genes outside the nucleus during protein synthesis

49
Q

tRNA

A

transport RNA
- a T shaped RNA molecule
- has anticodons to the mRNA strand
- brings a specific AA for each codon to form the PP chain

50
Q

GENE (POINT) MUTATIONS
- define
- ways they can occur (4)
- types of effects (4)
- define degenerate

A
  • a change in a single nucleotide in the DNA code, leading to a gene mutation

WAYS
- Substitution: base is replaced with a different one (ATG to ACG)
- Inversion: two bases next to each other swap places (ATG to AGT)
- Insertion: base is added in
- Deletion: base is deleted

EFFECTS
- Missense mutation: mutation alters a single AA, leading to genetic variation, not always bad
- Nonsense mutation: mutation causes a premature stop codon, PP chain is incomplete and dysfunctional, usually bad
- Frameshift mutation: insertion/deletion shifts the entire DNA strand, PP chain is dysfunctional, usually very bad
- Silent mutation: base changes but still codes for correct AA, no effect (this is possible as the DNA code = degenerate: alternate substances can perform the same function)

Biology 315 (5 decks)

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