Module 2 : Basic components of living systems , biological molecules (dna) , plasma membranes

Question 1

Primary structure

Answer 1

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.

Question 2

Secondary structure:

Answer 2

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

Question 3

Tertiary structure:

Answer 3

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

Question 4

ATP structure

Answer 4

• Adenine, ribose and 3 phosphate groups

Question 5

Macromolecule: DNA/RNA

Answer 5

Monomer-Nucleotides
Functions- control genes
type of reaction-condensation
type of bond-phosphodiester

Question 6

Nitrogenous Bases differ between DNA and RNA

Answer 6

DNA contains Adenine, Thymine, Guanine and Cytosine(ACGT) (A&G purine bases ,T&C pyrimidines RNA contains Adenine, Uracil, Guanine and Cytosine(AGCU)

Question 7

Nitrogenous Bases differ between DNA and RNA

Answer 7

DNA contains Adenine, Thymine, Guanine and Cytosine(ACGT) (A&G purine bases ,T&C pyrimidines RNA contains Adenine, Uracil, Guanine and Cytosine(AGCU)

Question 8

DNA / RNA features and functions

Answer 8

• 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

Question 9

how do polypeptide chains form between nucleotides?

Answer 9

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)

Question 10

Why is DNA replication Important?

Answer 10

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.

Question 11

Semi-Conservative Model of DNA replication

Answer 11

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.

Question 12

DNA replication

Answer 12

1. 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)
2. DNA POLYMERASE CONTINUES UNTIL 2 NEW STRANDS OF DNA ARE PRESENT- EACH CONTAINING 1 STRAND FROM THE PARENT DNA

Question 13

What is a gene? Why are genes Important?

Answer 13

• 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’

Question 14

The Genetic Code

Answer 14

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’

Question 15

introns

Answer 15

Non-coding regions that need removing from the pre-mRNA before it is translated.The introns are removed from Eukaryotic genes during ‘splicing’

Question 16

Transcription- Produces mRNA using DNA as a template

Answer 16

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

Question 17

PROCESS OF TRANSLATION

Answer 17

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.

Question 18

Magnification/Resolution/ types of microscopes

Answer 18

• 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

Question 19

Advantages and disadvantages of light and electron microscopes

Answer 19

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

Question 20

TEM(transmission electron microscope )

SEM(scanning electron microscope )

Laser scanning confocal microscopes

Answer 20

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

Question 21

Preparing a slide using a liquid specimen/solid specimen

Answer 21

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

Question 22

Unclear or blurry images:

Answer 22

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

Question 23

graticule

Answer 23

• 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

Question 24

Guidelines for microscope drawings

Answer 24

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

Question 25

Calculations with magnification

Answer 25

• Magnification = I/A
  magnification of eyepiece/objective lens : mag of eyepiece x mag of objective lens

Question 26

Process of protein synthesis in eukaryotes

Answer 26

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

Question 27

Exosytosis / Endocytosis

Answer 27

Exocytosis - bulk movement out of cell
Endocytosis - bulk movement in to the cell

Question 28

Chorelostol/ lipids in the phospholipid bilayer

Answer 28

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

Question 29

Role membrane and mosaic model

Answer 29

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

Question 30

Membrane proteins/ glycoprotein/Glycolipids

Answer 30

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

Question 31

What process carrier/channel proteins involved in / factors effect permeability

Answer 31

carrier. - active transport
channel - facilitated diffusion

temperature
short diffusion pathway(thin)
solvents
concentration gradient

Question 32

Temperature effect membrane permeability / solvent concentration

Answer 32

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

Question 33

Osmosis definition / Water potential & units

Answer 33

• 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

Question 34

Role / process / examples of Active Transport

Answer 34

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