MODULE 1 Flashcards
1
Q
Carbon
A
- inherently neutral (uncharged)
- non-polar/hydrophobic
2
Q
O, N, P (sometimes S)
A
make compounds
* polar/hydrophilic
* partly (dipoles) or fully charged (i.e. molecules with those atoms/colours will be polar)
3
Q
Covalent bond
A
holds molecules together
4
Q
Eukaryote
A
organism has cells with a defined nucleus (can be single celled or multicellular)
5
Q
Prokaryotic
A
single celled organism without a nucleus
6
Q
Main molecules types in bio
A
- Water
- Carbs
- Lipids
- Amino acids
- Nucelotides
7
Q
Water…
A
- Stabilise temp
- Ice floats (insulate water/floating platforms)
- Water tensions (H bonding)/capillary action
- Good solvent for polar molecules
- Poor solvent of hydrophobic molecules (cell membranes)
8
Q
Monosaccharides
A
Usually form rings
* Glucose (6 atom ring)
* Fructose
* Galactose
* Ribose (5 atom ring)
9
Q
Carbs/sugars/saccharides
A
Composed of C,H,O with general formula Cn(H2O)n
* ‘n’ # of carbon atoms
* Lots of O = very polar
10
Q
Disaccharides
A
2 mono joined together
* Lots of different connections
* Lactose
* Sucrose
* Trehalose (glucose/glucose)
11
Q
Sugar polymers
A
Long chains of mono
* Starch - Storage
* Chitin - Protection
* Cellulose - Structure
12
Q
Saturated lipid
A
all single bonds
Liquid typically
13
Q
Unsaturated lipids
A
one or more double bonds
Solids typically
14
Q
triglycerols
A
Energy stores
* Adipocyte (fat deposit)
15
Q
steroids
A
Signalling molecules
Lipid
16
Q
Phospholipids
A
Form cell membranes
* Mostly H-phobic but with polar end
* Polar parts interact with aq enviro, H-phobic parts cluster together
* Lipid bilayers separate inside + outside cell
17
Q
amino acids
A
Building blocks of protein
18
Q
In aq sol. the amino and acid group…
A
Are charged (NH3+ and COO-)
* This is the NORMAL STATE for amino acids in nature
19
Q
Nucleotides
A
- Phosphate group (-ve charge)
- Sugar (ribose or deoxyribose)
- Nucleobase (A,G,C,T,U)
20
Q
Mono/di/tri-nucleotides
A
dAMP (mono)
dADP (di)
dATP (tri)
21
Q
Capillary action
A
ability of liquid to flow in narrow spaces, even against gravity
22
Q
Purine
A
- double ring, flat aromatic base (A, G)
23
Q
Pyrimidine
A
- single ring flat aromatic base (C, T, U)
24
Q
5’ to 3’
A
Nucleic acids
25
**N**-terminus (or amino terminus) to **C**-terminus (or carboxy terminus)
Proteins
26
Residues
Some of monomer is **lost on polymerisation**, leaving residue incorporated in the *growing chain*
* For these molecules, the residue is usually the *biggest* part
27
Biopolymer synthesis relies on...
**dehydration** reactions and are **anabolic**
28
Common sugar phosphate backbone
* **Negative** charge on **phosphates**
* **Hydrophilic** (sugars and phosphates)
* 5’ and 3’ ends
29
Things in DNA vs. RNA
**D**eoxyribose (DNA)
**R**ibose (RNA)
**Uracil** (RNA)
**Thymine** (DNA)
30
Electrophoresis
Nucleic acids **migrate** in an electric field because they are **charged**.
* **Distance** they migrate dependent on **size**
31
<50 amino acid residues
NB peptides
32
>50 residues
protein
33
Aromatic protein side chains and nucleobases have a characteristic *absorbance*...
~2**8**0 nm (**proteins**) or ~2**6**0 nm (**bases**)
34
Record spectra
A2**6**0:A2**8**0 **PROTEINS**
A2**6**0:A2**3**0 **CARBS**/PHENOL
35
C and G complement
**3** hydrogen bonds
*stronger*
36
A and T complement
**2** hydrogen bonds
A bit *weaker*
37
beta DNA
1. Strands run in **opposite** directions
2. **Flat** bases **stack** on top of one another (reduced A260nm intensity)
3. **Negative** phosphates *repel* each other
4. **Right handed** double helix
5. *Major* and *minor* grooves
38
N-glycosidic bond
**covalent** bond between **sugar** and **base** in RNA/DNA
39
Phosphodiester bond
**covalent** bond between **nucleotides** in RNA/DNA
40
Deamination
loss of an amine
41
dsDNA
double stranded DNA
42
ssDNA
single stranded DNA
43
Tm/Melting point
when **50%** of the molecule is **unfolded/separated**
44
Information flow
Going from DNA >transcription> RNA >translation> PROTEINS
45
Genome
Complete genetic information
**DNA**
46
Transcriptome
all the **RNA** expressed in a cell/tissue at a give time
47
Proteome
all the **proteins** expressed in a *cell/tissue* at a give time
48
Prokaryotes have ____ genomes
**Small**
* Bacteria and archaea have **circular** chromosomes (plasmids)
49
Eukaryotes have ____ genomes
**Big**
* **Linear** chromosomes
* Condensed into **chromatin**
* Wrapped around **histone** protein
50
mRNA
**message** for making proteins
* Often *multiple* copies made, designed to be **used** then **degraded**
51
MicroRNA and snRNA
**regulatory** roles
52
Ribosomal RNA & Transfer RNA
Important for **protein synthesis**
53
role of proteins
**shape**, they form **receptors**, **enzymes**, **hormones** and growth factors, **toxins**, **transporters** and **antibodies**
54
Epigenetic regulation
Expression of *some* genes is altered by **chemical** modifications of DNA and proteins but NOT to the DNA sequence itself - epigenetics.
* Can be passed through generations of cells (and individuals)
55
Start Codon
Met
* **AUG**
56
Stop Codons
* UAA
* UAG
* UGA
57
OPEN READING FRAME (ORF)
**start** to the **stop** codon of a gene that encodes the protein/peptide
58
Missense
Mistake in the DNA code, **one** of the DNA **base pairs** is changed
59
Silent
Mutation of the **protein-coding region** that has **no effect** on the protein *sequence*
60
Nonsense
**Single** change in DNA **code** produces **stop** codon, prematurely terminates protein synthesis
61
Insertion
**Addition** of one (or more) **nucleotide base pairs** into the DNA sequence
62
Deletion
A piece of DNA is **removed** from the sequence
63
Point mutation
**Single amino** acid has been *changed* (can also refer to a small # of bases being modified, added or lost in the nucleotide sequence)
64
Frameshift
Insertion or deletion mutation results in a change to a gene's **reading frame**
65
Duplication mutation
Incorrect **copying** leads to **repeated** sequences
66
Redundant/degenerate
some amino acids are encoded by **more than one codon**
67
DNA Polymerases
* Make a DNA copy from **template**
* Need **primer** to start
* Use **deoxynucleotide triphosphate**s as *substrate*
68
Semi-conservative
each newly generated dsDNA contains one **original** (the template) and one **new** strand
69
Topoisomerase enzymes
**cut** strands, allow to unwind and stick back together (**religate**)
70
Biopolymer synthesis
1. Initiation
2. Chain elongation
3. Termination
71
ORI (Origin) Sites
* **AT**-rich (easier to pull strands apart because *less stable*)
* DNA **binding protein**s open up the site
* DNA helicase unwinds - **replication forks**
72
Both original/parental strands are copied at the same time
true
73
Leading strands
Primase makes an **RNA primer** to begin
* DNA polymerase III makes a DNA copy of the strand in the 5’ -> 3’ direction
* **Continuous** copying
74
Lagging
Primase makes *multiple* **RNA primers**
* polymerase synthesises, until it runs into the **next primer** making **Okazaki fragments**
75
When the two replication forks come together...
* DNA **polymerase I** **replaces** the RNA primer with DNA
* DNA **ligase** **joins** pieces
* **Discontinuous** copying
76
Termination
* **Joining** up the new strands
* Roughly **opposite** the *origin*
77
Eukaryotic DNA Replication
* **Multiple** origins on each linear chromosome
* Need to **strip off nucleosomes** before replication and **reform** afterwards
* Special mechanisms (**telomerase**) for the ends telomeres of the chromosomes
78
Chain elongation
main phase of polymerisation
79
ssBP/single stranded binding proteins
**bind** to ssDNA and **protect** from *tangling/reforming* dsDNA
80
Supercoiling
overwinding DNA
81
RNA Polymerases
* Make an **RNA** copy from a **DNA** template
* DON’T NEED A PRIMER to start
* Use **ribonucleotide triphosphates** as **substrate**
* Limited proofreading
82
Promoter region
* **Upstream** 5’ end
* **RNA polymerase** binds
* -10 and -35
83
Transcription factor(s)
**proteins** capable of **recognising** a *specific base sequence*
84
Promoter strength
**Strong** binding = **more** RNA copies made
**Weak** binding = **fewer** RNA copies made
85
Transcription Regulation: Repression
Protein repressor **binds**.
* This *blocks* the binding of the **sigma factor/RNApol** complex
* no gene expression
86
Transcription Regulation: Accelerators
**Transcriptional Activator** (protein) binds at a specific DNA sequence
* **alters** the *structure* of the **promoter** so the transcription factor can now bind more **frequently**
87
Transcription bubble
local **unwinding** of DNA for **transcription**
88
Translation
Converts a **nucleotide** sequence to a **protein** sequence
89
Peptide bond formation is very thermodynamically ____
unfavourable
90
Messenger RNA (mRNA)
contains **template** for protein synthesis/information about which amino acids to **add** in which **order**
91
Transfer RNA (tRNA)
**matches** the correct amino acids to the template
92
Ribosomal RNA (rRNA)
**combines** with *proteins* to form the machinery for **protein synthesis**/catalyses peptide bond formation
93
Aa-tRNA synthetases
* **attach** the **amino** acid to the **tRNA**
* **Catalyse** the **activation** of amino acids
94
Ribosome
**E-Site** - Used tRNAs move here before **exiting**
**P-Site** - For **growing** protein chain
**A-Site** - *Accepts* incoming **tRNA-aa**
95
The stages of protein synthesis
1. Initiation
2. Elongation
3. Termination
96
96
Prokaryotic VS. Eukaryotic Translation
**Initiation** - *different mechanism* for **finding** the **start** codon, special tRNA but normal Met as first amino acid.
**Elongation** - same
**Termination** -
* in EU - a **single** release factor recognises all three stop codons
* prokaryotes have** 2-3**
97
Peptidyl transferase
**enzyme** component of the ***ribosome*** that transfers the activated amino acids from tRNA to the *growing* peptide chain
98
Primary structure
Amino acid sequence
99
Secondary structure
**Local features** allow formation of structure - backbone-backbone hydrogen bonding
* **Alpha helix** & **Beta sheet**
100
Tertiary structure
Overall **3D** arrangement of a **polypeptide chain**
* Held together by lots of *different* interactions/bonds
101
Quaternary structure
Organisation of **subunits** (Many but not all proteins have multiple subunits)
102
Hydrophobic effect
driving force for **protein folding**
103
Protein Folding
* Info encoded in amino acid sequence
* **Burial** of **hydrophobic** surfaces/side chains in aqueous **solvent**
* **Collapse** of protein chain/formation of **secondary** structure
* Firming up **tertiary** structure by interactions in protein
104
unfolding proteins
Proteins much more easily lose their **unique 3-D** shape if they are **heated**
105
α-Helices and B-DNA
α-helices are a perfect size to **fit** into the **major groove**
106
Single strands of protein can fit in the ____
**minor** groove
107
Beta Strand
**extended** form of protein **secondary** structure
108
Beta Sheet
**Assembly** of beta **strands**
109
Beta turn
form of protein **secondary** structure, often formed *between* beta **strands** in a beta **sheet**
110
Energy
capacity to do work
111
Potential energy
* *stored* in **chem bonds**
112
Kinetic energy
* expressed as **movement**, heat etc.
113
1st law of thermo
Energy can be **neither** created or destroyed
* **Transferred**
114
2nd law of thermo
* **Entropy** of universe is **increasing**
* Physical and chemical process **favour randomness**
* If you apply **energy** you can push a state towards **order**
115
Favourable reaction
*give* out energy/**exergonic**
116
Unfavourable reaction
*need* energy/**endergonic**
117
substrate molecules
contain more free energy
118
Activation energy/barrier
The energy *required* to **initiate** a reaction
119
Entropy
measure of disorder
120
Equilibrium
**rates** of *forward* and *reverse* reactions are the **same**; **concentrations** of substrates and products don’t change; overall energies are **balanced**
121
Kinetics
how **quickly** an event happens; *rates*
122
Thermodynamics
measures and transitions of **intrinsic** energy
123
Enzymes
Use catalysts to lower energy barrier
124
Enzyme process
1. E + S
2. **ES** (enzyme-substrate **complex**)
3. **E'S** (**Enzyme-Transition state** complex
4. E + P
125
Lock and key model
substrate molecules fits **directly** into the **active site**
126
Induced-fit model
substrate induces a **shape change** for *optimal* substrate bonding and activity
127
Selection model
enzyme exists in **multiple** forms in equilibrium, only *one* of which (A) **binds** substrate
128
Enzyme regulation
* inhibited by **compound** that *binds* to the active site, **prevents** substrate from binding
* Or binds **outside** the active site and stops the **motions** of the enzymes required for activity
129
129
Pyrophosphate (PPi)
released by *hydrolysis* of **NTPs** into **NMPs**; spontaneously forms phosphates (**2Pi**); provides energy for **unfavourable** reactions
130
How do tRNA and aminoacyl RNA synthetases work together to correctly translate an mRNA sequence translated into a protein/peptide sequence?
aminoacyl RNA synthetases make sure that the *correct* **amino** acid is attached to the *correct* **tRNA**
131
Kinetic control
relates to the **energy required** to go beyond the activation barrier
132
Thermodynamic control
start or end, how **quickly** is it going to take place
133
How can the hydrolysis of pyrophosphate drive unfavourable interactions?
**Coupling** reactions so the net energy is gained even though one step is unfavoured
* Driving the reaction in **one direction**
