Module 2 : Basic components of living systems , biological molecules (dna) , plasma membranes Flashcards
Primary structure
a sequence of amino acids which are bound together by peptide bonds to form a polypeptide chain, this is encoded for by the DNA. The sequence of amino acids will determine the folding and bonding of the overall protein.
Secondary structure:
the polypeptide coils or pleats to form Alpha-Helices or Beta-pleated sheets, these are bonded by Hydrogen bonds between the OH- and –H groups on parallel chains
Tertiary structure:
the final level of 3-D structure composed of 4 bonds;
-Disulfide bridges: S=S bonds between cysteine groups of amino acids
-Hydrophobic/Hydrophilic interactions- dependent on the nature of the side chains they may be oriented towards the inner or outer of the protein
-Ionic bonds form between oppositely charged side chains facing each other
-Hydrogen bonds are also present in the tertiary structure
ATP structure
- Adenine, ribose and 3 phosphate groups
Macromolecule: DNA/RNA
Monomer-Nucleotides
Functions- control genes
type of reaction-condensation
type of bond-phosphodiester
Nitrogenous Bases differ between DNA and RNA
DNA contains Adenine, Thymine, Guanine and Cytosine(ACGT) (A&G purine bases ,T&C pyrimidines RNA contains Adenine, Uracil, Guanine and Cytosine(AGCU)
Nitrogenous Bases differ between DNA and RNA
DNA contains Adenine, Thymine, Guanine and Cytosine(ACGT) (A&G purine bases ,T&C pyrimidines RNA contains Adenine, Uracil, Guanine and Cytosine(AGCU)
DNA / RNA features and functions
- double stranded ( double helix ) , deoxyribose sugar , ATCG nitrogenous bases
- single stranded , ribose as sugar , ACGU
- DNA acts as a template for RNA during transcription - RNA then is translated into protein
how do polypeptide chains form between nucleotides?
Adjacent nucleotides bind together via a condensation reaction to form a phosphodiester bond in the sugar-phosphate backbone( protects the reactive bases on the inside of the molecule and makes it very stable)Hydrogen bonds form between opposite bases A-T and C-GA-T (2 H bonds) C-G (3 H bonds)
Why is DNA replication Important?
DNA replication is important as it MUST happen prior to Mitosis to ensure that daughter cells contain the DNA needed to do their job.
so that unwanted mutations do not occur.
We have cellular machinery (enzymes and proteins) which specifically check the DNA after being replicated.
Semi-Conservative Model of DNA replication
universally accepted model of DNA replication‘Semi-Conservative’ replication is because one of the parent strands which acts as a template for the daughter DNA is Conserved.
If DNA replication was conservative then the daughter DNA would not contain any of the original strands at all.
DNA replication
- DNA HELICASE UNZIPS the DNA (DNA Helicase breaks the hydrogen bonds between the bases in the double helix)
2.Free nucleotides bind in a complimentary manner to the bases attached to the parent strands. A-T C-G.
3.DNA POLYMERASE binds the free nucleotides together at the template ,DNA polymerase does this by forming phosphodiester bonds between the free nucleotides(3’ and 5’ direction) - DNA POLYMERASE CONTINUES UNTIL 2 NEW STRANDS OF DNA ARE PRESENT- EACH CONTAINING 1 STRAND FROM THE PARENT DNA
What is a gene? Why are genes Important?
- section of DNA that contains a sequence which codes for a protein.
- Genes are responsible for development of organisms
- Genes code proteins which make enzymes
- Mutations in genes can cause a VAST array of diseases -
- Genes can be engineered in Biotechnology
-Genes are responsible for many heritable characteristics - Genes can be a therapeutic targe in ‘gene therapies’
The Genetic Code
degenerate(20 amino acids which are coded for have multiple codons for them.) , non-overlapping, (each base in the sequence is only read ONCE.) ,universal(Each triplet codes for the same amino acid across ALL organisms.)triplet combinations do not code foramino acids ‘UAA’ ‘UAG’ and ‘UGA’ – theseare called ‘stop codons’
introns
Non-coding regions that need removing from the pre-mRNA before it is translated.The introns are removed from Eukaryotic genes during ‘splicing’
Transcription- Produces mRNA using DNA as a template
DNA helicase breaks the hydrogen bonds between the DNA strands to expose the nucleotide bases
- RNA polymerase reads the DNA template strand from the 3’ end and adds complimentary nuecleotides (A,U,G,C) to the template strand. It catalyses phosphodiester bonds between them
- As the RNA polymerase adds nucleotides, the DNA strands reform behind it- as such only about 12bp of DNA are exposed at a time.
- When the RNA polymerase reaches a ‘STOP’ triplet it detaches from the DNA molecule and pre-mRNA production is Complete.
-The mRNA will later leave the nucleus where it will associate with a ribosome
PROCESS OF TRANSLATION
Ribosome attaches to the start codon (AUG) which encodes Methionine
-tRNA carrying a complimentary Anticodon moves to the start codon- the tRNA carries a specific amino acid
- The ribosome moves along the mRNA bringing tRNA molecules to each codon. Therefore adding 1 amino acid per codon
. -Peptide bonds are formed between amino acids using an enzyme and ATP .
- tRNA is released following each peptide formation allowing it to go an collect amino acids from the pool in the cell.
- This continues until the ribosome reaches a ‘STOP CODON’. And here the ribosome, tRNA
and polypeptide all separate.The polypeptide will then fold into the 3-D protein.
Magnification/Resolution/ types of microscopes
- how many times bigger the image produced by the microscope is than the real-life object you are viewing
- ability to distinguish between objects that are close together
- light microscopes
Electron microscopes
Laser scanning confocal microscopes
Advantages and disadvantages of light and electron microscopes
ad- easy to use, small /portable, cheap, show large organelles /cells, living tissues observed, image in colour
disad- magnification up to 1500x , resolution is limited
ad- use beam of electrons , over 500,000 magnification , specimens dead
disad- expensive, black and white , vacuum required, large not portable
TEM(transmission electron microscope )
SEM(scanning electron microscope )
Laser scanning confocal microscopes
2d image , max magnification 500,000x , higher resolution
3d image
max magnification 100,000x
lower resolution
The cells being viewed must be stained with fluorescent dyes
Advantages:used on thick or 3-D specimens, external, 3-D structure of specimens to be observed, high resolution
Disadvantages:
It is a slow process and takes a long time to obtain an image - The laser has the potential to cause photodamage to the cell
Preparing a slide using a liquid specimen/solid specimen
Liquid :
- Add a few drops of the sample to the slide using a pipette
Cover the liquid/smear with a coverslip and gently press down to remove air bubbles
Wear gloves to ensure there is no cross-contamination of foreign
Solid :
Peel away or cut a very thin layer of cells from the tissue sample to be placed on the slide (using a scalpel or forceps)
The tissue needs to be thin so that the light from the microscope can pass through
Apply a stain
Gently place a coverslip on top and press down to remove any air bubbles
Unclear or blurry images:
Switch to the lower power objective lens and try using the coarse focus to get a clearer image
Consider whether the specimen sample is thin enough for light to pass through to see the structures clearly
graticule
- A graticule is a small disc that has an engraved ruler
It can be placed into the eyepiece of a microscope to act as a ruler in the field of view - As a graticule has no fixed units it must be calibrated for the objective lens that is in use. This is done by using a scale engraved on a microscope slide (a stage micrometer)
- By using the two scales together the number of micrometers each graticule unit is worth can be worked out
- After this is known the graticule can be used as a ruler in the field of view
Limitations:
- The size of cells or structures of tissues may appear inconsistent in different specimen slides
- Optical microscopes do not have the same magnification power as other types of microscopes and so there are some structures that can not be seen
Guidelines for microscope drawings
The drawing must have a title
The magnification under which the observations shown by the drawing are made must be recorded
A sharp HB pencil should be used (and a good eraser!)
Drawings should be on plain white paper
Lines should be clear, single lines (no thick shading)
No shading
The drawing should take up as much of the space on the page as possible
Well-defined structures should be drawn
The drawing should be made with proper proportions
Label lines should not cross or have arrowheads and should connect directly to the part of the drawing being labelled
Label lines should be kept to one side of the drawing (in parallel to the top of the page) and drawn with a ruler
Calculations with magnification
- Magnification = I/A
magnification of eyepiece/objective lens : mag of eyepiece x mag of objective lens
Process of protein synthesis in eukaryotes
RER ( rough endoplasmic reticulum) contains ribosomes which produces a transport vesicles which consist of a protein .
TV moves to Golgi apparatus in via cisface and gets modified and moves out via transface and becomes a secretory vesicle
which either leaves the plasma membrane as it is or becomes a lysosomes
Exosytosis / Endocytosis
Exocytosis - bulk movement out of cell
Endocytosis - bulk movement in to the cell
Chorelostol/ lipids in the phospholipid bilayer
affects fluidity and stability of cell membrane, disrupts close-packing of phospholipids (increases flexibility)
Resists effects of temp change
used to produce steroid- based hormones
heads - hydrophilic, tails- hydrophobic, water can’t pass through due to tails, only lipid soluble molecules pass through, small non polar molecules
Role membrane and mosaic model
regulates transport of materials in(out of cells
antigens, immune system recognise the cell as being ‘ self ‘ not attack it - Site of chemical reactions. - Compartmentalisation
Membrane is lipid bilayer - made of 2 phospholipid molecules - 1972 - singer & Nicholson
Membrane proteins/ glycoprotein/Glycolipids
Providing structural support
water molecules transport across membrane )
active transport ( carrier proteins change shape molecule)
cell adhesion, receptors
cell recognition sites
cell adhesion to form tissues
cell receptor sites
Act as cell surface receptors for specific
Molecules
cell recognition sites
maintaining membrane stability
help cell adhesion
What process carrier/channel proteins involved in / factors effect permeability
carrier. - active transport
channel - facilitated diffusion
temperature
short diffusion pathway(thin)
solvents
concentration gradient
Temperature effect membrane permeability / solvent concentration
Increase temp increase rate of diffusion
channel/membrane proteins denature
allowing more substances through
lipids more fluid
ke of molecules increases
organic solvents tends to increase
membrane permeability
dissolves lipids in cell membrane
cause phospholipid bil over molecules lose
structure
Osmosis definition / Water potential & units
- net movement of water molecules from a region of high water potential to low water potential through a partially semi- permeable membrane
- tendency of water molecules to move around in a system
units - Kpa
Role / process / examples of Active Transport
movement of molecules (ions), into or out a cell from region of lower concentration to a region of higher concentration using ATP.and carrier proteins
roots absorbing mineral ions, villi absorbing glucose, selective reabsorption from kidneys
generate through aerobic respiration
ATP directly move molecules during AT
use a set up concentration gradient(co-transport)
carrier proteins bind to molecule/ion to be
transported across membrane (specific receptor site)
- ATP binds to carrier protein & hydrolysed
to adp&p ( cp changes shape opens to other side of membrane
- molecule/ion released opposite side
- when phosphate (from ATP) released
from cp its reverted to original shape
