Theme 1:Introduction to Molecular and Cellular Biology Flashcards
What is biochemistry?
Biochemistry is the branch of science concerned with the chemical and physio-chemical processes and substances which occur within living organisms
What is studied in biochemistry?
Biochemistry is the study of chemical components of the body
It studied chemical reactions that govern living processes.
what did Feng Zhang do?
Zhang pioneered the development of CRISPR-cas9 as a genome editing tool and its use in eukaryotic cells
What is CRISPR?
CRISPR is a genetic system that conveys immunity to virus infection in bacteria.
Gives access to every single geno
It is a revolutionary experimental tool
What components are used as a molecular scalpel to cut DNA at a specific site?
- a guide RNA
- a CRISPR-associated endonuclease(Cas protien)
Cas9 RNA programmable endonuclease
what do Engineered CRISPR systems do?
Engineered CRISPR systems cut DNA at a specific site to edit a genome which can convey immunity to a virus infection in bacteria
What ethical problems arise with CRISPR in the clinic?
A chinese scientist used CRISPR to make the first genetically edited babies.He claims to have disabled a gene called CCR5, which encodes a protein that allows HIV to enter cells.But He might have inadvertently caused mutations in other parts of the genome, which could have unpredictable health consequences
What is CAR T-cell therapy?
Chimeric antigen receptor (CAR) T-cell therapy is a way to get immune cells called T cells (a type of white blood cell) to fight cancer by changing them in the lab so they can find and destroy cancer cells
What are T-cells?
T-cells are specialised white blood cells of the immune system
T cells are engineered to express CARs that recognise cancer cells
How does CAR T-cell therapy work?
T-cells are specialised white blood cells of the immune system
They are isolated from a patient and a custom designed gene is introduced into the cells.
Cells containing the gene are grown in culture to prepare an inoculum
CAR T-cells are infused back into the patient
T-cells target cancer cells for killing
Is there any evidence of CAR T-cell therapy working?
yes- young girl (emily whitehead) went into remission and was giving low rate to survive. recieved cells age 7 and is now age 16.
How has biochemistry informed
our understanding of the virus and
our approach to managing it?
RNA sequence - determines the
functional genes of the virus
- Origin of the virus
- Possible drug targets
- Possible vaccine candidates
What is key to understanding how to target VIRUSES with drugs?
knowing how it mutates is key to understanding how to target with drugs?
Typically what do vaccines contain?
Typically vaccines contain either killed virus or a
protein fragment of the virus
What are antibodies?
Antibodies are specialized, Y-shaped proteins that bind like a lock-and-key to the body’s foreign invaders
How can antibodies work?
by binding to a viral protein and
preventing its function
What is leading to a potential arms race with the virus?
Some variants are less susceptible to monoclonal
antibodies
How does biochemistry underpin advances in life sciences and biotechnologies.
By providing a description of the chemical
components and mechanisms of living
cells,
How is monoclonal antibodies used today?
Currently over 75 monoclonal antibodies are approved
for a variety of conditions ranging from cancer to
autoimmune diseases to haemophilia and macular
degeneration
How is biochemistry involved in creating monocolonal antibodies?
Creating monoclonal antibodies involves
biochemistry at every level -
- Generating antibodies by immunisation
- Characterizing antibody reactivity
• Creating
monoclonal antibodies -
molecular cell biology
• Humanizing antibodies - adapting from
other species
• Purifying antibodies - for use in
patients
What are the main elements that compose the human body (and their %)
Oxygen (65%) carbon(18%) hydrogen(10%) Nitrogen (3%) Others (less than 1%)
What are some of the other eements that make up cless than 1% of the human body?
Calcium phosphorus sulfur sodium chlorine magnesium
structure
and functional groups in Carbon
tetravalent,
tetrahedral
geometry,
the backbone of
biomolecules,
low electronegativity
structure
and functional groups in Oxygen
- divalent,
highly
electronegative
structure
and functional groups in Nitrogen
trivalent,
somewhat
electronegative
structure
and functional groups in Hydrogen
monovalent,
least
electronegative
structure
and functional groups in phosporus
pentavalent,
low
electronegativity –
labile bonds
structure
and functional groups in Sulphur
divalent,
moderate
electronegativity; redox
What is Chemical bonding driven by?
•Chemical bonding is driven by the
outermost electrons of atoms
What occurs in covalent bonding?
In covalent bonding, atoms
share electrons to form
molecular orbitals that comprise
electron pairs.
What are molecular orbitas?
In chemistry, a molecular orbital is a mathematical function describing the location and wave-like behavior of an electron in a molecule. … When multiple atoms combine chemically into a molecule, the electrons’ locations are determined by the molecule as a whole, so the atomic orbitals combine to form molecular orbitals.
What is – stereochemistry
Stereochemistry is the study of the three‐dimensional structure of molecules
what are molecules specific shape based on?
Molecules adopt specific shape – stereochemistry – based on their bond systems, a key to molecular structure
when are ions formed?
•Ions are formed when
atoms lose or gain electrons
and acquire FIXED
CHARGE
what are ionic bonds?
•Ion pair interactions
•Ionized groups such as acids
and bases can form ionic
bonds
are ionic compund soluable or insoluable in water ?
•Ionic compounds are
soluble in water due to
solvent polarity
What is poarity?
In chemistry, polarity is a separation of electric charge leading to a molecule or its chemical groups having an electric dipole moment, with a negatively charged end and a positively charged end.
What is polar?
•Polar is the term for bonds
and compounds with
asymmetric charge distribution
What is electronegatiity?
“relative strength of
attraction of atomic nucleus for electrons”
What does asymmetry in e- lead to within a molecule?
Asymmetry in e- distrubution leads to
asymmetry in charge within a molecule
what is dipole?
A bond or molecule whose ends have opposite charges.
structured
distribution of charge in space.
How can covalent bonds have ‘partial ionic charcter?
• Atoms have different tendencies to attract electrons: ‘electronegativity’
• asymmetric sharing of electrons in a
covalent bond
• AND THUS, a partial charge across
the bond, or dipole
Many important bonds in
biochemistry are noncovalent. name some of these bonds.
•Van der Waals interactions •Hydrogen bonds •Ion-dipole interactions •Ionic bonds – paired charge interactions
What are noncovalent bonds?
a relatively weak bond formed between molecules without sharing electrons
what energy do chemical bonds have ?
•Energy of formation and
dissociation
name 3 features of van der waals interactions
•A proximity effect, the induced
dipole
- Very short range
- Molecular packing
what is an example of van der waal interactions?
•Design of gecko feet has inspired
dynamically adhesive “van der Waals
materials”
•biomimetic design
•COOPERATIVITY
– many small
bonds add up to great energy
Name four features of hydrogen bonds
•Dipole interactions involving a
shared proton = H atom •Polar interaction •H2O can form H-bonds •A great deal of biomolecular
structure is driven by H
-bonding
What are charged- based interactions?
•Electrostatic interactions take place between charged groups and a) other charged groups b) dipoles
•Can be highly influenced by
solvent and other environmental
effects
What are iconic bonds?
ionic bonds involve complete transfer of electrons between
donor and acceptor atoms
e.g. NaCl = Na+ : Cl
How do ions interact?
ions have fixed electrical charges and interact by complementary attraction (coulombic forces) – like magnets
How do charged groups have a profound influence on the structure of water?
charged groups have a profound influence on the structure of
water, by organizing it through charge:dipole interactions.
What are hydrophobic bonds?
– van der Waal’s interactions
in polar solvent: increased energy due to
“repulsion” by solvent
Properties of water (6)
Solvent
Highly polar molecule
Interacts with charged moities as
well as polar groups in molecules
Self-interacts to form hydrogen
bond network in bulk water
Disruption of the H-bond network
and ordering of water around
hydrophobic surfaces leads to
hydrophobic bonding potential
Strong entropic effect due to
changes in ordering of water
molecules
what is bioenergetics?
Bioenergetics is the branch of biochemistry that focuses on how cells transform energy, often by producing, storing or consuming adenosine triphosphate (ATP).
what does biological organisation require?
Biological organisation requires the flow of energy
in the concept of bioenergetics where is energy stored and how is it moved?
Energy is stored in covalent bonds and
moved through high energy compounds
What is the primary source of biological energy?
solar radiation
how does solar radiation work?
– Photosynthesis
– light mobilizes electrons in chlorophyll
– electrons provide reducing power
= electrochemical energy
– Energy is stored by synthesis of organic
molecules – carbohydrates
– Chloroplasts accomplish this in plants
– Mitochondria coordinate energy metabolism
in animal and plant cells
what is ATP?
adenosine
triphosphate
Is a major carrier of chemical
energy.
Free energy of
hydrolysis of terminal
phosphate donates energy to
biochemical reactions.
what is the role of covalent bonds in DNA
• establish the structure of the
nucleotide bases
• their linkage to the sugars
• the continuous phosphodiester
backbone
what is the role of hydrogen bonds in DNA
• establish the linkage between complementary bases that defines the double strands and template character of DNA and RNA
what is the role of van der waals interactions in DNA
• lead to base stacking that
stabilizes the double helix
What is the role of charge interactions in DNA
between the phosphate groups
of the backbone and water and
with proteins …
what is the primary function of DNA
: its primary function is the
storage and replication of biological
information.
what is the role of RNA
acts as a carrier of DNA - based information into dynamic cellular metabolism AS WELL AS playing catalytic roles
what is protein?
polymers of amino acids the main products of genes function as chemical machines to carry out cellular tasks, chemical and structural. Information has been translated into structural form
what are protein rna and dna all?
polymers of building blocks(nucleotides and amino acids)
what is dnas code?
linear code ≅ one - dimensional information
what is rna role in codes
functions to carry linear code and also folds into 3 - dimensional molecules
what is proteins shapes
fold into 3 -dimensional shapes, arranging chemical groups in space
what is DNA
deoxyribose nucleic acid
the molecule that stores and
transmits biological information in
the form of genes
DNA is a linear polymer of
deoxyribonucleotides, formed by
condensation polymerization
It possesses a double stranded
structure comprised of two
complementary strands basepaired together(double helix structure)
what are the building blocks of dna?
sugar phosphste (backbone)
base(hydrogen bonded base pair)
nucleotide
what does the sequence of nucleotides contain?
information content of the genes
how is the nucleotide sequence read and decoded?
nucleotide sequence is read in triplets and decoded by ribosomes for synthesis of proteins during the process of translation
during what process is nucleotide read and decoded?
translation
how does dna self regulate?
DNA also contains information
for its own regulation
Specialized DNA sequences, bind
to proteins that regulate
what does transcription contain
promoters and enhancers
what does replication contain
origins of replication ,telomeres
what does segregation contain
centromeres
is DNA information content solely directed towards encoding genes?
no
what does DNA represent?
a storage form of information
what happens to DNA information?
It is transcribed into RNA by RNA polymerase
Why is dna transcribed into rna?
in order to carry out function in the cell, a condensation polymerization
name 5 types of RNA
- mRNA
- rRNA
- tRNA
- miRNA
- ncRNA
What is mRNA
transcripts of genes;
translated into protein
what is rRNA
structural and catalytic RNA that makes up ribosomes
what is tRNA
transfer RNA that adapts
amino acids for protein translation
what is miRNA
microRNA that regulates
gene expression
what is ncRNA
long non
-coding RNAs
that regulate genome function
where is the catalytic centre for protein synthesis?
it was discovered from solution of the structure of the ribosome that rna comprises the catalytic centre for protein synthesis
what are proteins encoded by?
the sequence of nucleotides in their gene
as proteins are the main functional machines of cells , what do the provide?
• catalysis – making and breaking essential bonds throughout metabolism • structure – from cellular filaments to hair and skin • motility – molecular motors and tracks • signaling – circuitry for sensing and conveying • transport – membrane channels •& etc