Molecular Biology Flashcards
1
Q
Catabolism
A
breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers
2
Q
Anabolism
A
synthesis of complex molecules from simpler molecules, including the formation of macromolecules from monomers using condensation reactions
3
Q
Metabolism
A
web of all enzyme-catalyzed reactions in a cell or organism
4
Q
four biochemical groups
A
- carbohydrates
- lipids
- proteins
- nucleic acids
5
Q
Why is life based on carbon
A
- it can form four covalent bonds; creates stable molecules
- allows for a diversity of molecules (bonds easily)
Not very reactive
Very small
6
Q
elements in living organisms
A
- hydrogen
- oxygen
- nitrogen
- phosphorous
- carbon
7
Q
monomers/dimers/polymers of carbohydrates
A
monomer; monosaccharides
dimers; disaccharaides
polymers; polsaccharides
8
Q
monomers/dimers/polymers of lipids
A
monomers; glycerol, fatty acids, phosphate groups
dimers/polymers; triglycerides, phopholipids, steroids (FAT)
9
Q
monomers/dimers/polymers of proteins
A
monomer; amino acids
dimer/polymer; polypeptides
10
Q
monomers/dimers/polymers of nucleic acids
A
monomer; nucleotide
11
Q
What determines if a reaction occurs or not?
A
- identity of colliding molecules
- orintantation of colliding molecules
- speed/kinetic energy of molecules
12
Q
why do cells use enzymes
A
to icnrease the likelihood that a succesfull collision wil lead to a useful reaction
13
Q
what are enzymes
A
protein molecules with a specific shape that a react can fit into at the active site
- act as catlyusts
- increase rate of reaction
- lower activation energy
14
Q
what explains the properties of water?
A
- dipolarity
- hydrogen vonding
15
Q
what makes water so special
A
its polar and hydrogen bonds form between them
16
Q
why is water polar
A
due to the unequal sharing of electrons within the water molecule that makes oxygen slightly negative and hydrogen slightly positiveq
17
Q
cohesive properties of water
A
Cohesion: attraction of water molecules to other water molecules
- due to hydrogen bonds that form between water molecules due to polarity
explains;
- why water forms into droplets when it is spilt
- why water has a surface tension that allows for some animals to walk/run on it
- why water can move as a water column in the xylem
18
Q
thermal properties of water
A
- high latent heat of vapourization
- high specific heat capacity
explains;
- water can absorb a great deal of heat (good for chemical reactions)
- act as a coolant
19
Q
solvent properties of water
A
excellent solvent;
water molecules are polar and therefore can dissolve other polar molecules (e.g. ‘like dissolves like’)
- disolves glucose, amino acids, fibringoen and hydrogen carbonate ions in BLOOD
- if there is a non-polar substance, plasma membranes, blood proteins, vesicle or transport proteins are used to transport it
20
Q
specific heat capacity
A
large amount of heat causes a small increase in temperature (energy required to raise the temperature of 1 g of a substance)
21
Q
latent heat of vaporization
A
a large amount of heat energy is needed to vaporize/evaporate water
22
Q
adhesive properties of water
A
Adhesion: is the formation of hydrogen bonds between the water molecules and F, N and O (attraction between unlike molecules)
explains;
why water sticks to the vascular tissue in plants (fight gravity!) and can be pulled up
23
Q
bonds formed during condensation reactions
A
BONDS:
- ester bond (triglycerides)
- glycosidic bond (maltose)
- peptide bond (amino acids)
24
Q
hydrophyllic
A
- water loving
- polar substance
25
hydrophobic
- water hating
| - non polar substance
26
General formula of carbhydrates
General formula: (CH2O)#
27
function of carbohydrates
primary source of energy (e.g glycogen is a short term energy source for the body)
28
Monosaccharides
glucose
fructose
galactose
ribose
29
Disaccharides
sucrose
maltose
lactose
30
Polysaccharides
starch
cellulose
glycogen
31
cellulose
- major component of cell walls
- helps give rigidity.support to plant parts such as roots, stems and leaves
Structural polysaccharide in plants
B-glucose
1:4 glycosidic bond
Unlike starch, cellulose is very strong and prevents cells from bursting when they take excess water
Consists of long chains of glucose molecules
32
starch
- organic products of photosynthsis are stored in plants as starch
- typically as starch granules in chloroplasts or in plant storage areas such as roots or root structures
- two sub-componenents; amylopectin and amylose
33
glycogen
- animals stores excess glucose in this form
| - stored in liver and muscle areas
34
Lipids function
- long term storage of energy
- they are important components of the cell membrane
- they are used as a heat insulator
- can act as a shock absorber
35
3 MAIN TYPES:Lipid
1. triglycerides (Fats + Oils)
2. Phospholipids (components of cell membrane)
3. Steroids (Cholesterol, progesterone, estrogen, testosterone)
36
what are TRIGLYCERIDES composed of
TRIGLYCERIDES;
tri: refers to 3 fatty acids chains
- glycerol
- fatty acids
37
SATURATED FATTY ACID:
if the bonds between carbon atoms are SINGLE
the fatty acids contain as much hydrogen as they possibly could
animal sources (red meats, milk, etc.) >>> FATS
38
UNSATURATED FATTY ACID
UNSATURATED FATTY ACIDS
when the fatty acids contain 1 or more DOUBLE BONDS
contains less hydrogen atoms than it could (unfulfilled)
Plants (Oil)
can be polyunsatured or monoundsatured
39
CIS and TRANS unsaturated Fatty acids
CIS:(can be poly)
same side C=C bond
when hydrogen atoms are on the same side with respect to the double bond
TRANS:(can be poly)
-when the hydrogen atoms are on the opposite side with respect to the double bond
```
CIS= Healthy
Trans= unhealthy
```
cis-fatty acids cannot line next to each other, thats why the are lipid at room temperature
cis fatty acids are ‘slippery’ and will not clog arteries
Trans Fatty Acids
-hydrogenation of vegetable or fish oils
-modification of natural, healthy oils
-hydrogenation changes the shape of the oil
-trans fats are illegal
-turns it from liquid>> solid
40
PHOSPHOLIPIDS
these are modified triglycerides that have one fatty acid chain by a phosphate group
41
Scientific Evidence of trans unsatured fats health risk
Coronary heart disease: arteries become blocked due to fatty deposits
High intake of transfat
CHD: found in patients who take more cis unsaturated fatty acids
42
BMI
BMI: body mass index, reflects heigh and weight
18. 5> underweight
18. 5-24.9 Normal weight
25. 0-29.9 Overweight
30. 0< Obese
43
BMI formula
FORMULA: weight (kg)/[height (m)x height (m)]
44
energy storage in humans
- storing glucose as glycogen in liver and muscle cells
| - storing triglyceride lipids within adipose (fat) cells
45
FUNCTIONS OF PROTEINS:
FUNCTIONS OF PROTEINS:
| structural, catalytic, signalling, immunological
46
how man naturally occuring amino acids are there
20 (humans produce 10; rest have to be injested)
47
what is the AA sequence coded for
genes
48
rubisco
short hand name for enzyme that catalyzes the first reaction of carbon fixing reactions of photosynthesis
49
insulin
a protein hormone produced by the pancreas that results in a decrease of blood sugar levels and an increase of sugar inside body cells
50
immunoglobin
an antibody that recognizes an antigen as part of the immune response
51
rhodopsin
pigment found in eye retina for low light conditions
52
collagen
main protein component of connective tissuem which is in skin, tendons and ligaments
53
spider silk
fibrous protein spun by spiders for webs, lines, nest bulding, hunting
54
how do the proteins differ from each other?
Length: different # of amino acids
Types: different types
Order: different order
55
primary structure of protein
- linear sequence of AAs
- contains only peptide bonds
- in nature: proteins are almost never found in this structure because they fold to produce more complex molecules
56
secondary structure of protein
- the polypeptide chain folds to form: alpha helix or beta pleated sheet
examples: keratin (alpha helix) and silk (beta pleated sheet)
- these structures are held together by hydrogen bonds
57
tertiary structure of protein
- alpha helix and beta pleated sheets fold into compact globules
- the structures are held together by: hydrogen bonds, ionic bonds and disulphide bonds
- example: enzymes
58
quaternary structure of protein
- examples: hemoglobin, collagen, insulin
| - held together by: hydrogen bonds, ionic bonds, disulphide bonds
59
Fibrous Protein
Shape: Long and narrow
Role: Structural (strength and support)
Solubility: Generally insoluble in water
Sequence: Repetitive amino acid sequence
Stability: Less sensitive to change in heart and pH
Examples
Collagen, myosin, fibrin, actin, keratin, elastin
60
Globular Protein
Shape: Rounded/spherical
Role:Functional (catalytic, transport, etc)
Solubillity: Generally soluble in water
Sequence: Irregular amino acid sequence
Stability;More sensitive to change in heat, pH, etc
Examples:
Catalase, haemoglobin, lipase, insulin, immunoglobulin, DNA Polymerase, Oestrogen
61
PROTEOME:
PROTEOME: all of the proteins produced by a cell, tissue or organ in a human
- as cells can differentiate they dont have to produce the same proteins to have the same genome
62
Protein Denatureation
- proteins can denature by heat and pH environment alteration (bonds broken and proteins get broken down into simpler forms/become inactive)
- each protein has an optimum temperature
63
ENZYMES
ENZYMES “special proteins”
Functions:- speed up reactions, they act as a catalyst
Long chain of amino acids (globular protein in tertiary structure)
Substrate>>>enzyme>>>product
64
Active site
a small region on the enzyme where the substrate binds to and the reaction takes place, enzymes are substrate specific
65
Catalyst:
increase rate of reaction without themselves reaction without being being used up.
66
STEPS OF AN ENZYMATIC REACTION
1. substrate enters active site
2. enzyme-substrate complex is formed
3. substrate is changed into a different chemical (product)
at the end of the reaction, the product leaves the active site
AT THE END:
-enzymes are never permanently modified, they can return into their original state, to be used over + over again
67
two enzymatic reaction theories
Lock and key
| Induced Fit
68
Lock and Key Hypothesis
Lock and Key Hypothesis
the substrate molecular shape is the exact match to the enzyme's active site
the substrate fits perfectly into the enzyme's active site, the way a key fits into a lock. Each substrate has a particular corresponding enzyme
69
Induced-Fit Hypothesis
-the substrate binds to the enzyme's active site
the enzyme changes shape to fit and hold the substrate
now the enzyme active site fits,
Forces substrate into distorted active site= makes or breaks substrate by force
the strain to fit breaks/makes bonds
70
Factors affecting enzyme activity
Temperature
-as temperature increases so does enzyme activity
this is because:
molecules move faster (most often substrate moves around, but enzyme can as well) causing more of a chance for the enzyme and the substrate to find each other and bind
Optimum temperature
when the activity of an enzyme is at its greatest (any point beyond that the activity declines because they begin to break)
SUBSTRATE CONCENTRATION
Denaturation
change in the shape of an enzyme, for example:
-an active enzyme is tridimensional
-when it is heated it loses shape because heat causes the enzyme to twist and bend, and the hydrogen bonds to break
-this affects its activity to recognize the substrate (because of the change in the shape of the active site
71
Stages of Denaturation
- Quaternary Structure lost = protein subunits are dissociated
- Tertiary structure lost = interaction between side chains of amino acids are lost (hydrogen bonds/ionic bonds)
- Binary Structure lost = proteins lose patterns such as alpha helix and beta pleated sheet and become random coil configurations
- Primary structure = the sequence of amino acids (peptide bonds) remains
72
Change in pH
each enzyme has an optimum pH
-change in pH could result in change in the shape of the enzyme (new shape may not be active)
optimum pH of pepsin is 2
optimum pH of lipase is 8
73
```
Optimum pH of/location:
pepsin
amylase
lipase
lactase
```
Pepsin.>> PH2 (Stomach
Amylase>> PH7 (mouth, small intestine, pancreas)
Lipase>> PH8 (small intestine)
Lactase >> PH7 (small intestine)
74
Use of immobilized enzymes
- used as catalysts in industry
- enzymes can be held in tiny pores on beads called calcium alginate (trapped there; immoblixed) so enzymes can be recovered and reused in processes
-used in the production of lactose-free milk for lactose intolerant people (enzyme lactase is immoblized to break dont lactose into glucose and galatcose and digest it)
75
Nucleotide
a molecule containing a phosphate group attached to a pentose sugar and base
76
DNA
deoxyribose nucleic acid, code for life and all the functions in a living organism
- a double stranded helix
- sugar phosphate backbone
- anti parallel
- nitrogen containing
- hydrogen bonding and phosphdiester bonds
- found in nucleos
- pentose sugar- deoxyribose
77
Crick and Watson and Rosalind Franklin:
discovered the structure of DNA
78
nucleotide bases
PURINE:
- adenine
- guanine
PYRAMIDINE:
- thymine
- cytosine
- uracil (only in RNA)
79
RNA
Single stranded
Ribose sugar
Uracil (GCUA)
Nucleic Acid
Found in nucleus and outside of it (can travel out)
Has pentose sugar
Three types: tRNA, mRNA, rRNA
80
Matthew Meselson and Franklin Stahl
Geneticists and molecular biologists that worked together to discover the semi-conservative replication of DNA
81
what did Matthew Meselson and Franklin Stahl do
They found a way to mark the parent DNA molecule using an isotope of nitrogen with an extra neutron (N14 and N15), allowing them to show 1 old strand and a newly synthesized strand
They used E.Coli bacteria in the experiment
82
SEMI CONSERVATIVE REPLICATION:
Theory: mechanism of DNA replication where two new copies of DNA are produced from an original DNA strand consisting of one of the original strands and one new strand
83
What did Meselson and Stahl do?
mRNA
rRNA
tRNA
84
OTHER REPLICATION THEORIES:
Conservative: parental DNA is conserved
| Dispersive (fragmented) : mixture of old and new DNA within the same chromosome
85
mRNA
messenger RNA. Copy of a gene, carries information to make a protein
86
rRNA
ribosomal RNA, component of ribosomes. Large and small subunit
87
tRNA
transfer RNA. Brings amino acids to ribosomes during protein synthesis, has a site for the AA to attach and an anticodon (determines which of the 20 AA’s is attached to the tRNA)
88
enzymes in replication
DNA Helicase: separates the two DNA strands before replication
DNA Polymerase I: catalyzes the formation of new polynucleotide chain
DNA ligase: joins together short sections of the lagging strand
Single-stranded binding protein: keeps the separated DNA strands apart during replication
89
DNA Helicase
DNA Helicase: separates the two DNA strands before replication
90
DNA Polyermase I
| DNA Polymerase II
DNA Polymerase I:
Removes the primer and replaces it with DNA
DNA POLYERMASE III;Synthesized new strand by adding nucleotides onto the primer in a 5’ to 3’ direction
91
DNA Ligase
DNA ligase: joins together short sections of the lagging strand (okazaki fragments)
92
Single-stranded binding protein:
Single-stranded binding protein: keeps the separated DNA strands apart during replication
93
Polymerase Chain Reaction
developed in 1970's
- artificial DNA replication
- duplicates short segments of DNA
- scientists can produce large quantities of DNA this way for study
- used for forensics studies and paterntity testing
- Process consists of fluctuating temperatures
94
Cell respiration:
```
Cell respiration: controlled release of energy from organic compounds to produce ATP
Its how the body gains energy
Chemical reaction within all cells
TYPES:
Aerobic
Anaerobic
```
95
AEROBIC:
AEROBIC:
Normal form of respiration through breathing (muscular contraction)
Glucose + oxygen -----> carbon dioxide + water + energy (ATP)
C6H12O6 + 6O2------> 6CO2 + 6H2O + 36ATP
96
ANAEROBIC: respiration
ANAEROBIC:
When the body is getting no oxygen from breathing, so the cell creates energy just with glucose (inefficient)
In humans: glucose -----> Lactic Acid + Energy
C6H12O6-----> 2C3H6O3 + 2 ATP
97
anaerboic respiration
Anaerobic respiration is the act gaining ATP without oxygen from the pyruvate
- only 1-2 ATP produced
98
alcoholic fermentation
- yeast
- produces ethanol, carbon dioxide
- use of fermentation in baking and alochol production
99
lactic acid fermentation
-organisms can respire without oxygen
-produce lactic acid by breaking down pyruvate
-e.g. during excersize
Lactic acid causes muscular fatigue and pain, forms crystals in the muscle tissue that makes the movement hard, toxic to body
OXYGEN DEBT: oxygen needed to break down lactic acid into carbon dioxide and water
100
Why are leaves green?
Chlorophyll in chloroplasts
101
PHOTOSYNTHESIS
CO2 + H2O --------> O2 + C6H12O6
Photosynthesis is the production of carbon compounds in cells using light energy
Oxygen is produced from the photolysis of water (splitting of light)
102
what wavelengths does visible light have
between 400-700 nm
103
Electromagnetic spectrum
light energy is needed to produce carbon compounds from carbon dioxide
Visible spectrum: green is in the middle
- violet is the shortest and red the longest wavelength
-IR and UV
104
what do substances do when hit with a particular wavelength of light
- absorb it
| - reflect it
105
what does chlorphyll do when hit by light (and why are plants green?)
- its a green pigment; reflects green light and absorbs all other wavelengths of the visible light spectrum (red and blue are absobved and used for photosynthesis)
106
PHOTOSYNTHETIC PIGMENT:
PHOTOSYNTHETIC PIGMENT: colored biological compound that is present in chloroplasts and photosynthetic bacteria, and which captures light energy for photosynthesis
107
LIMITING FACTORS OF PHOTOSYNTHESIS:
LIMITING FACTORS:
1. Temperature: has an optimum temperature, when it gets an higher, the rate goes down, as the plants begin to deteriorate
2. Carbon Dioxide: reaches a max concentration, after there is no change in the rate
3. Light Intensity: reaches a max intensity, after there is no change in the rate
108
steps of photosynthesis
1. light dependent; photolysis
| 2. light indepdent; production of carbon compounds
109
measuring rate of photosynthesis?
- by oxygen consumed
- by carbon dioxide produced
- by water used
