Module 2 (C & D) Flashcards
Are involved in nearly every biological process within the cell
Protein
Example of biological process
Catalyzing biochemical reactions
Regulating (turning on and off) biochemical processes
Transporting molecules across cell membranes from cell to cell, or from cell to another part)
Proteins are also involved in _____ (self- induced movement of the cell)
Cell motility
Protein roles
- Physics of protein folding
- Conformational transitions
- Binding is crucial to understand
Process by which a protein structure assumes its functional shape or conformation
Protein folding
All protein molecules are _____
Heterogeneous unbranched chains of amino acids
Protein folding is a process by which
A polypeptide chain folds to become a biologically active protein in its native 3D structure
The structure of a protein is hierarchically arranged from a ____ to ____ structure
Primary to Quarternary
Refers to the linear sequence of amino acid residues in the polypeptide chain
Primary structure
Generated by formation of hydrogen bonds between atoms in the polypeptide backbone
Secondary structure
Secondary structure folds the chains into either ____ or ____
Alpha helices or beta sheets
Formed by the folding of the secondary structure sheets or helices into one another
Tertiary structure
Usually a geometric shape and has polypeptide chain as a backbone
Tertiary structure
Determined by the interactions and bonding of the amino acid side chains in the protein
Tertiary structure
Results from folded amin-acids chains in tertiary structures interacting further with each other to give rise to functional protein like hemoglobin or DNA polymerase
Quarternary structure
Primary structure is also known as
Amino acid structure
Secondary structure is also known as
Regular sub- structures
Tertiary structure is also known as
Three- dimensional structure
Quaternary structure is also known as
Complex of protein molecule
External factors influencing the sensitive process of protein folding
- Electric and Magnetic field
- Temperature
- pH
- Chemicals
- Space Limitation
- Molecular crowding
The hydrophobic effect constrains the _____ ____ of a protein to escape water
Apolar residues
The apolar residues converge to form an apolar core of the protein leaving more ______
Polar residues at the surface where they form hydrogen bonds with water molecules (upper panel)
The ____ contribution to the folding reaction is illustrated in the lower panel
Enthalpic
Lower panel is
electrostatic interaction between the positive N- terminus and the negative C- terminus
Disappears from the surface when the protein folds
Apolar surfaces
Apolar means
No charge
An example of neurodegenerative condition cause by protein misfolding
Alzheimers, Huntingtons, Parkinsons
This branch of biophysics studies the energy flow in living systems
Bioenergenetics
Most life forms get their energy from
Sun
Cellular processes such as the building and breaking down of complex molecules occur through ___
Stepwise chemical reactions
During the light reactions of photosynthesis, energy is provided by a molecule called
Adenosine Triphosphate (ATP)
Describe how energy behaves in physical systems and biological
Law s of thermodynamics
States that energy cannot be created nor destroyed
First law of thermodynamics ( can be transferred from place to place)
States that in a closed system the orderliness (entropy) of the system can never increase but only decrease over time
Second law of thermodynamics
High disorder and low energy =
High entropy
______ increases as molecules at a ____ concentration in one place diffuse and spread out
Entropy at a high
Living thighs are highly ordered, requiring constant energy to be maintained at ____
State of low entropy
Application of probability and statistics to large populations of molecules
Statistical mechanics
A mathematical description of how the molecules move
Model
Allows us to interpret the things we can measure in terms of what specific molecules are doing
Statistical mechanics
Branch that deals with measuring the rate or speed of biological process
Kinetics
Biological processes examples
- Biochemical reactions
- Conformational transitions
- Binding or unbinding of biomolecules
Tells us whether a given process or biochemical reaction will occur
Thermodynamics
How fast this process will occur
Kinetics
This model is a hypothesis as to what the molecular mechanisms is that causes some process
Models in statistical thermodynamics
A device that can alter the direction or size of a force
Machine
Examples of machine
Pulley, lever or an inclined plane
Is a type of machine that also has the ability to convert potential energy into mechanical energy into a mechanical force or motion
Motor
Uses our bones as levers to redirect and in some cases magnify or decrease the forces they apply
Muscles
These are hairlike projections on the surface of some cells that move, allowing the cell to swim,
Cillia
Longer, whiplike stricture that stick out from the body of some cells and move to proper the cell forward
Flagella
Some cells move by temporarily pushing out their membrane at one or more location
Pseudopodia
Cells that manufacture proteins or other substances to be used elsewhere in the body
Secretions
Have various mechanisms for packaging and moving the substances they make
Secretory cells
When a cell is getting ready to divide it first duplicates its chromosmes
Separation of chromosomes (DNA) during cell divisions
Binding in one part of a molecule affects activity in another part of the same molecule
Allosterics
Allostery from the greek word ____ meaning ___
allos - other
stereos - object / solid object
Allostery allows two things to take place
Allosteric regulation and cooperativity
The control of a biological process by a cell or organism
Regulation
Directly involved in carrying out the protein’s function
Active site
Usually happens simply by controlling binding directly at the molecule’s active site
Regulation of the process
Regulation of a process is achieved through binding somewhere other than the active site
Allosteric site
When a biochemical process is controlled via long distance
Exhibits allosteric regulation
Sites behave as active sites and as allosteric sites at the same time it is called
Cooperativity
The occurrence of separate events together in a nonindependent manner
Cooperativity
Events occur only slightly more together than they would if they were completely independent
Slightly cooperative process
A set of otherwise independent events occurs in a mostly all or none manner
Highly cooperative process
Regulates the substrates to bind
Regulatory molecule
No rejection happened
Allosteric inhibitor
Rejection of substrate happened
Allosteric inhibition
Regulates substrates to bind
Regulatory molecule
There’s binding at active site
Allosteric activator
This branch of biophysics studies the physics of DNA and RNA
DNA and Nucleic Acid Biophysics
DNA and RNA stands for
alam mo n dapat to beh
Can act as a catalyst for certain chemical reactions
RNA
Controls our physical heriditary
DBA
Can bend and twist to form a helix as wel
Double helix
Helix of a helix is called a
Superhelix
Process of forming a superhelix in DNA is known as
Supercoiling
A quarternary structure in DNA occurs when the DNA Superhelix wraps itself around protein complexes known as
Histones
Function of DNA
Long term storage of genetic information; transmission of genetic infos to make other cells and new organisms
Function of RNA
Used to transfer the genetic code from the nucleus to the ribosomes to make proteins
RNA is used to
Transmit genetic information in some organisms and may have been the molecule used to store genetic blueprints in primitive organisms
DNA is
responsible for storing and transferring genetic informations
RNA directly codes
For amino acids and acts as a messenger between DNA and ribosomes to make proteins
Structural features of DNA
B- form double helix - double stranded molecule consisting of a long chain of nucleotides
Structure features of RNA
A- form helix, single stranded helix - shorter chains of nucleotides
Composition of Bases and Sugars
Deoxyribose sugar
phosphate backbone
Adenine
Guanine
Cytosine
Thymine bases
Composition of Bases and Sugars
Ribose sugar
Phosphate backbone
Adenine
Guanine
Cytosine
Uracil bases
Propagation of DNA
Self- replicating
Propagation of RNA
Synthesized from DNA on an as needed basis
Base Pairing of DNA
AT (Adenine - Thymine)
GC (Guanine - Cytosine)
Base pairing of RNA
AU (Adenine- Uracil)
GC ( Guanine - Cytosine)
Reactivity of DNA
Reactivity of C-H bonds in DNA make it fairly stable, plus the body destroys enzymes that would attack DNA, the small grooves in the helix also serves as protection, providing minimal space for enzymes to attach
Reactivity of RNA
The O-H bond in the ribose of RNA makes the molecule more reactive, not stable under alkaline conditions, the large grooves in the molecule make it susceptible to enzyme attack, It is constantly produced, used, degraded, and recycled
Ultraviolet Damage of DNA
DNA is susceptible to UV damage
Ultraviolet Damage of RNA
Compared with DNA, RNA is relatively resistant to UV damage
