U3 AOS1 Flashcards
1
Q
what are proteins?
A
large complex molecules that are made of monomers (amino acids)
2
Q
what are proteins made of?
A
all proteins contain nitrogen, hydrogen, carbon and oxygen. some contain sulfur and phosphorus
3
Q
what are the 4 structures in an amino acid?
A
- alpha carbon
- carboxyl group (-COOH)
- amino group (NH2)
- R-group
4
Q
what is the primary structure of proteins?
A
order of amino acids determined by the genetic code (list of 3-letter amino acids)
5
Q
dipeptide
A
2 amino acids joined together
6
Q
polypeptide
A
3+ amino acids joined together
7
Q
how many amino acids join together made a protein?
A
50+
8
Q
what is a peptide bond?
A
the bond created through joining together at the carboxyl group and amino group through a condensation reaction
9
Q
what is a biomacromolecule?
A
large molecules composed of smaller things
10
Q
examples of macromolecules:
A
proteins, nucleic acids & carbohydrates
11
Q
polymer
A
3 or more subunits together
12
Q
structures of proteins
A
all proteins have a primary, secondary and tertiary structure, only some have quaternary
13
Q
describe the polymerisation of amino acids
A
the -OH group is broken of the -COOH group of 1 amino acid, then forms a covalent bond with a hydrogen from the other amino acid, forming water and forms a peptide bond
14
Q
if we have 4 amino acids, how many peptide bonds are made?
A
3 peptide bonds
15
Q
if we had 60 AA how many peptide bonds are made?
A
59 peptide bonds
16
Q
what is the secondary structure of proteins?
A
formed by hydrogen bonds between R- and amino groups that make up the polypeptide backbone and causes the molecule to either bend and fold or spiral around
(interactions between amino acids)
17
Q
what can be formed in the secondary structure of proteins?
A
alpha helices -> spiral coils
beta sheets -> grooved sheets
18
Q
what is the tertiary structure of protiens?
A
the 3D shape of the protein - caused by the irregular folding of secondary structures help together by ionic/hydrogen bonds
19
Q
in an exam, how do you know if the proteins is tertiary?
A
“protein is functional” / “works” / “does its job”
20
Q
what structure does a protein need to be to be functional?
A
tertiary / quaternary
21
Q
what is the quaternary structure of a protein?
A
two or more polypeptide chains interacting
22
Q
what is a proteome?
A
all proteins an organsim can make at a given time - more diverse than genomes
23
Q
what are proteomes influenced by?
A
- individual’s genes
- environmental factors (epigenetics)
24
Q
why are proteomes larger than the number of genes?
A
- gene sequences may be alternatively spliced following transcription to generate multiple protein variants from a single gene
- proteins may be modified following translation to promote further variations
25
what are enzymes?
biological catalysts : all metabolic reactions in living organisms require enzymes to work
26
catalyst vs enzyme
catalyst: substances that increase/decrease rate of chemical reaction, remain unchanged
enzyme: protein that only increase rate of chemical reactions converting substrate into product
27
what do enzymes do to activation energy?
lower the activation energy to help speed the reaction up. reactions can still occur without an enzyme, but at a much lower rate than with an enzyme present.
28
what is a substrate?
molecule that enzymes work on (reactant)
29
what is a product?
what is produced in reaction
30
what is the active site?
part of enzyme that substrate molecule fits into
31
are enzymes used up in a reaction?
enzymes are not changed by the reaction
- only used temporarily
- re-used again for the same reaction with other molecules
- very little enzyme needed to help in many reactions
32
describe the lock and key model of enzymes:
only one key (substrate with specific shape) can fit into the lock (enzyme)
33
describe the induced0fit model of enzymes:
the enzyme is forced to change shape in order for multiple substrates to fit into 1 enzyme
34
competitive inhibitors:
* bind directly to active site - direct competition with substrate
* reversible by increasing amount of substrate
* maximum rate of enzyme activity can still be achieved
35
non-competitive inhibitors:
* bind to allosteric site - changes shape of enzyme
* maximum rate of enzyme activity is reduced
36
what affectts enzyme action?
* inhibitors
* concentration of enzyme & substrate
* correct protein structure
* temperature
* pH (acids & bases)
37
how does increasing concentration impact reaction rate?
increasing concentration does not affect reaction rate - when all enzymes' active site are occupied with substrate, the reaction halts
38
how does order of amino acids impact reaction rate?
if the amino acids are in the wrong order, the protein is folded wrongly leaving it unable to do its job
39
how does temperature impact enzyme activity?
at the optimum temperature enzymes experience the greatest number of collisions between substrates - increasing ROR
raising the temperature causes proteins to denature & lose shape (permanent - unfunctional)
lowering temperature causes molecules to move slower and lessen collisions between enzyme and substrate
40
how does pH affect enzyme activity?
change in pH changes protein shape - most human enzymes live in pH or 6-8
41
what is the pH level in pepsin (stomach)?
1-3
42
what is the pH level in trypsin (small intestines?)
8
43
what are nucleic acids?
monomers that join together to make a polymer (DNA or RNA)
made of nucleotides (A, T, G, C & U)
44
structure of nucleic acids:
each nucleic acid is made of nucleotides containing:
1. nitrogenous base
2. phosphate group
3. pentose sugar
45
what are nucleic acids?
stores code that tells a cell what proteins do - code determined by order of nitrogenous bases
46
what does adenine bond with? (DNA)
thymine
47
what does adenine bond with? (RNA)
uracil
48
what does guanine bond with?
cytosine
49
what are the bases in nucleic acids held by?
hydrogen bonds
50
describe the role of nucleic acids?
* DNA provides directions for its own cell division
* DNA/genes directs synthesis of mRNA -> controls proteins synthesis
51
what is RNA responsible for?
making ribosomes for each protein synthesis - rRNA
RNA transports the right AA to ribosome using small molecules of rRNA
52
what does mRNA do?
carries genetic information from nucleus to ribosomes to make proteins
53
what does rRNA do?
helps with protein synthesis
54
what does tRNA do?
delivers amino acids to ribosomes after recognising specific nucleotide sequences
55
what is dogma?
a principle or set of principles
56
dogma of genetics:
DNA → RNA → Protein:
1. DNA replicated to form RNA
2. DNA transcribed to RNA
3. RNA translated to Protein
4. Proteins Carry Out Functions:
57
how does DNA make proteins?
sequence of nitrogenous bases are copied as short segments of RNA
58
how is a RNA template made?
* double helix of DNA is unwound & unzipped to expose 1 strand
* free nucleotides bind with exposed bases & form chain of RNA - mRNA
* mRNA forms template
59
transcription
process of unwinding, unzipping & copying
60
what is the difference between exposed bases and free nucleotides in RNA template making?
Exposed Bases: These are the parts of the DNA that show up when it unzips. They guide the appearance of the RNA.
Free Nucleotides: These are the tiny building blocks of RNA floating around the cell. They stick to the exposed DNA bases and combine to make the RNA strand.
61
DNA to mRNA
1. RNA polymerase attaches to specific sequence of DNA in upstream region of the template strand. double stranded DNA unwinds
2. complementary mRNA is copied from exposed template strand, joining free RNA nucleotides. working in the 3' to 5' direction to make 5' to 3' mRNA strand
3. RNA polymerase encounters termination signal in template DNA strand to unbind & stop transcription. found after coding region is copied
62
what is pre-mRNA?
the mRNA sequence that is copied after transcription
63
exons:
genes contining coding regions
64
introns:
genes containing sections that do not contain instructions for a protein
65
alternative splicing
Introns Are Removed: During RNA processing, the introns are cut out, and exons are joined together.
Exons Can Be Rearranged: Sometimes, exons are combined in different ways, creating multiple RNA versions.
Creates Different Proteins: This allows one gene to make many types of proteins.
66
what is a cap?
small chemical structure added to the start of the mRNA (at the 5' end)
protects pre-mRNA from enzyme attack
67
what is a poly-adenine tail?
long string of adenine (A) bases added to the end of the mRNA molecule (the 3' end).
Helps prevent the mRNA from being broken down too quickly by enzymes.
Keeps the mRNA stable so it can be used to make proteins.
68
what is a triplet?
Refers to a set of three bases in DNA.
These triplets are the "codes" that direct the creation of proteins.
Example: In DNA, a triplet might look like "AGT" (adenine, guanine, thymine
69
what is a codon?
Refers to a set of three bases in mRNA.
A codon is what actually gets read during protein synthesis. It is complementary to the DNA triplet.
Example: In mRNA, the codon for the DNA triplet "AGT" would be "UCA" (uracil, cytosine, adenine).
70
triplet vs codon?
a triplet is the original "code" in DNA, and the codon is the "message" in mRNA that is used to make proteins
71
steps to translating mRNA
1. single strand leaves to cytoplasm & encounters ribosomes that translates it into protein chain
2. tNA brings free AA that complement codon to the ribosome
72
what are secretory proteins?
proteins that a cell makes that will be released out of a cell
73
provide an example of secretory proteins:
insulin made in beta cells of pancreas is released out into the bloodstream
74
what is exocytosis?
process of releasing a large molecule out of the cell
75
describe what occurs during exocytosis?
* creates a membrane-bound vesicle
* vesicle will fuse with cell membrane & release contents out into extracellular environment
76
what is the extracellular environment?
area outside the cell
77
where are secretory proteins found?
ribosomes on the rough endoplasmic reticulum
78
what is the job of the rough ER?
to fold and modify the polypeptide into the correct protein
* done by adding carbohydrate chain to make a glycoprotein
* lumen of rough ER will help fold polypeptide into correct 3D shape
79
what are the 3 functions of exocytosis?
* allows cells to secrete waste substances & molecules (e.g. hormones & proteins)
* important for chemical signal messaging & cell to cell communication
* used to rebuild cell membrane by fusing lipids & protein removed through endocytosis back into the membrane
80
where does the secretory protein go after the RER?
golgi apparatus
81
what is the role of the golgi apparatus?
final modifications of the protein & packaging into secretory vesicles to be exocytosed out of the cell
82
describe the secretory pathway:
1. secreted proteins enter rough ER as ribosomes are synthesising them
2. protein exits RER in vesicle
3. protein travels through the cisternae of the golgi apparatus
4. protein enters secretory vsicle that fuses with cell membrane
5. protein is secreted from cell
83
what are the 2 types of secretion?
constitutive & regulated
84
what is constitutive secretion?
default pathway - used to replenish material at the plasma membrane & certain membrane-bound organelles
85
what is regulated secretion?
Terminates in secretory vesicles that store secreted material until a signal triggers fusion with the plasma membrane
86
constitutive vs regulated secretion
constitutive is always flowing
regulated is only open when needed
87
what is gene regulation?
helps ensure cells will produce functional proteins for that cell type
* turns cells on and off
88
what are structural genes?
genes that are expressed continuously
* genes that encode proteins that are required constantly are expressed
* 'housekeeping' genes that are required for basic functions of the cell
89
what are regulator genes?
switching genes on and off
* not always expressed
* not needed at all times - helps somatic cells specialise in function
90
what is unregulated gene expression?
can result in uncontrolled expression of unwanted genes
91
how do prokaryotes control their expression of genes?
use operons to regulate which genes are made and when
92
what are operons?
group of prokaryotic genes with a related function that are often grouped & transcribed together
* has only 1 promoter region for the entire operon
93
what is an operon composed of?
* structural genes - genes that are related & used in biochemical pathway
* promoter - nucleotide sequence that can bind with RNA polymerase to start transcription
* operator - nucleotide sequence that can bind with repressor protein to inhibit transcription
94
what is a regulatory gene?
produces a protein (repressor) that can inhibit the transcription of an operon by attaching it to the operator
95
what does a repressor do?
block RNA polymerase from moving along the operon to transcribe the structural genes until it reaches a terminator sequence
96
what is the function of the trp operon?
to synthesise the AA trytophan in E. coli
* includes 5 structural genes to make 5 enzymes needed to make tryptophan
97
what is attenuation?
another form of regulation in prokaryotes
* The cell starts making RNA from a gene but might stop partway through if it doesn’t need the gene’s product.
* the leader region helps the cell save energy and resources by not making something it doesn’t need.
98
what is the attenuator?
It acts like a switch to pause or stop making RNA.
Found in certain genes, especially in bacteria.
If conditions aren’t right, the attenuator stops RNA production early.
99
what does the attenuator do?
as leader sequence is transcribed, forms mRNA strand that can bind itself to hairpin structures - give 3 main outcomes
1. pause
2. continue
3. terminate
100
3 ethical approaches
consequences-based
duty-based
virtues-based
101
what is consequences-based?
considering the consequences of an action, with the aim to achieve maximisation of positive outcomes and minimisation of negative effects
102
what is duty-based?
considers how people act and places importance on that people have a duty to act a particular way, and that ethical rules must be followed, regardless of the consequences
103
what is virtues-based?
consideration is given to the virtue/moral character of the person carrying out the action
104
what are the 5 ethical concepts in biology?
* integrity - doing the right thing even when no-one is looking
* justice - people get what they deserve (fairness)
* beneficence - doing good to others
* non-maleficence - doing no harm
* respect - Valuing the dignity, autonomy, and rights of all living beings
105
what are endonucleases?
general term for enzymes that cut off the sugar-phosphate backbone of DNA
106
what are restriction enzymes used for?
to cut long double stranded DNA into small fragments to be modified
107
what are plasmids?
small, self-replicating, circular DNA molecules that are separate from the bacterial chromosome
108
what is horizontal gene transfer?
movement of genetic material between organisms without it being passed down from parent to offspring.
109
what does bacterial plasmids contain and what do they do?
the origin of replication
* where DNA replication begins
110
what is cleavage?
the process when restriction enzymes attach to cut the DNA strand
111
what is the sticky end?
when the resulting ends have overhanging exposed sequences with no base pair
* can only recombine with complementary sticky ends
112
what is the blunt end?
when the cut is clean and results in no overhangning area
* can be combined with any other bunt end fragment
113
how to stick fragments together?
cutting the gene of interest with the same restriction enzyme so sequences match
114
what is the gene of interest?
gene wanted to insert into a plasmid
115
what is DNA ligase and why is it used?
an enzyme that helps "glue" pieces of DNA together
* create bonds in the phosphate sugar backbone to glue fragments together
116
what is recombinant DNA?
type of DNA that is made by combining genes or DNA sequences from different sources.
117
bacterial protein factories?
a gene is inserted into bacteria and since bacterial reproduces rapidly, it makes them ideal to produce large amounts of target protein in a short time
118
what is transformation?
uptake of a plasmid into bacterial cells
119
why does bacterial transformation rarely occur naturally?
bacterial cell walls & membranes prevent the plasmid from entering as it is negatively charged
120
how can scientists force the plasmid to enter bacteria/plant cells?
by adding calcium ions & using different temperature that heat shocks the cell to create adhesion zones where the membrane becomes more permeable
121
what is electroporation?
when scientists apply short high voltage pulses to create adhesion zones
122
what is the non-recombinant plasmid?
It’s the original plasmid without any new genes inserted into it - plasmid that didn't get digested by a restriction enzyme
123
what is bacterial selection?
process where scientists determine which bacteria has taken up the recombinant plasmid
* can check if recombinant plasmid has been taken in by bacteria by adding extra genes that help select out cells that have been successfully transformed
124
what are the 2 types of added genes?
antibiotic resistance genes: helps bacteria survive a particular antibiotic
reporter genes: genes added in the plasmid before the gene of interest
125
what is insulin?
essential hormone produced by the pancreas to reduce high blood glucose levels in the blood
126
what is human insulin composed of?
51 amino acids
* A-chain (21 amino acids long)
* B-chain (30 amino acids long)
127
what needs to be removed from human genes before insertation into the plasmid and why?
introns as they are non-coding regions
128
what are genetically modified organisms (GMOs)?
any organisms that have had their genomes altered in some way
129
what are the 5 diffeerent techniques for genetic modification?
* gene therapy - alter genes to correct genetic defects & cure/prevent genetic diseases
* gene editing - changing the DNA code by adding a gene/removing a gene at a specific region
* cloning - creating a genetically identical copy of an organism
* transgenic modification - inserting a gene from another species into the DNA of an organism
* gene silencing - removing a faulty gene or stopping it from being read completely
130
transgenic organisms vs genetically modified organisms
All transgenic organisms are GMOs, but not all GMOs are transgenic.
Transgenic specifically involves adding genes from different species.
131
what does crispr stand for?
clustered regularly interspaced short palindromic repeats
132
what is crispr?
bacterial immune system that recognises & cuts DNA of an invading bacteriophage
133
what are cas genes?
adjacent to the crispr region - code for proteins that act on DNA/RNA in different ways
134
steps of DNA profiling
1. isolate DNA samples
2. make copies of specific portions of DNA
3. analyse and compare amplified DNA portions
135
what is DNA amplification?
takes whatever DNA is available & replicates it exponentially to produce more DNA segments available
136
what is DNA polymerrase?
builds DNA strands using the original sample as a template
* works in 5' to 3' direction
137
what does PCR stand for?
polymerase chain rrreaction
138
steps to PCR:
1. denaturation at 94 degrees
2. annealing at 55 degrees
3. extension at 72 degrees
139
denaturation (PCR)
Heat the DNA to separate the two strands.
This breaks the hydrogen bonds between the DNA strands, creating two single strands.
140
annealing (PCR)
Cool the mixture to allow short DNA primers to attach to the ends of the target gene.
2 primers needed that attaches to the beginning/end of target DNA region
141
extension (PCR)
Heat the mixture again to a moderate temperature, allowing the enzyme Taq polymerase to attach & build the sequence
142
what is gel electrophoresis?
process to separate different sized DNA molecules
143
what is an STR?
short tandem repeats - stretches of DNA that are repetitive
