Protein Synthesis

 

Details of DNA transcription and translation

Amino acids are made of a carboxyl group and amine group and an R group.  
they are the subunits for polypeptide chains which ultimately make a protein.

There are twenty one amino acids which correspond to a CODON. This forms the GENETIC CODE

Transcription: mRNA is made from the DNA strand
1.   DNA unwinds and a promoter region is exposed.  There is a SENSE STRAND (TEMPLATE STRAND) of DNA to make RNA.
2.  RNA polymerase synthesizes the mRNA from a 5' to 3' direction.  RNA nucleotides are attached only on the 3' end.
3.  When the mRNA is complete it undergoes processing
 a.EDITING THE mRNA STRAND:  INTRONS are removed and EXONS remain.
b.  A polyA tail and 5' cap are placed on the mRNA in order to protect the strand from exonuclease.  Exonucleases digest and recycle mRNA.  We want them to avoid digesting the mRNA while it is being read by the ribosome
4.  mRNA is now ready for the ribosome.  IN EUKARYOTES, it leaves the nucleus.  IN PROKARYOTES, protein synthesis starts right away

Translation:  mRNA gets read by the ribosome and a polypeptide chain is formed
 Initiation: 
1. METHIONINE is the first amino acid brought by a tRNA.  tRNA has an ANTICODON which is complementary to the mRNA CODON.  The START CODON IS ALWAYS AUG. Meanwhile, the small ribosomal subunit attaches to the strand.
2.  Next the large ribosomal subunit arrives with its P site and A site.

AMINO ACYL T-RNA is the name of the tRNA attached to the amino acid.

the following is excerpted from  mrsdaintreysonlineclassroom. retrieved
january 20, 2016:  

"Elongation
more amino acids are added and connected together to form a polypeptide, as specified by the mRNA sequence.
i. an incoming amino-acyl-tRNA (lets call this AA2-tRNA2) recognizes the codon in the A site and binds there.
ii. a peptide bond is formed through dehydration synthesis between the new amino acid and the growing polypeptide chain.
iii. the amino acid is removed from tRNA1 (bond breaks between aa1 and tRNA1)
iv. the tRNA1 that was in the P site is released, and the tRNA in the A site is translocated to the P site.
v. the ribosome moves over one codon along the mRNA (to the right in our diagram, or more specifically in the 5' ----> 3' direction.)
vi. This movement shifts the tRNA2 (which is attached to the growing amino acid chain) to the P site.
vii. tRNA3 with aa3 can now move into A site and bind with the next codon on mRNA.
viii. THIS PROCESS REPEATS, and the CHAIN ELONGATES as long as there are new codons to read on the mRNA. 

Termination
The process above repeats until a special codon, called a STOP CODON, is reached. There are 3 Stop codons: UAA, UAG, UGA.
i. the stop codons do not code for amino acids but instead act as signals to stop translation.
ii. a protein called release factor binds directly to the stop codon in the A site. The release factor causes a water molecule to be added to the end of the polypeptide chain, and the chain then separates from the last tRNA.

3. the protein is now complete. The mRNA is now usually broken down by exonuclease  and the ribosome splits into its large and small subunits.
   
4. the new protein is sent for final processing into the endoplasmic reticulum and golgi apparatus " 
   

Examine and Identify Vertebrate Skulls

 

   

  

Next we will. introduce the idea of  Using Dichotomous Keys to help identify things. 

We will use this key to do a lab on identifying mammalian skulls.  Be careful with these skulls!  They are very fragile.  We will take two periods to complete this lab.

CLASS NOTES: 
STUDY QUESTIONS TODAY:


1.  What is meant by the word "Adaptation"?
2.  Skull adaptations for predators/prey include the placement of the eyes.  Explain why eye socket anatomy is different in predator vs prey.  Give examples
3.  What teeth do predators have compared to prey?
4.  How are the skulls HOMOLOGOUS TRAITS?  What is a homologous trait?


IDENTIFICATION LAB:

Purpose:
1.  To identify a set of mammalian skulls and determine whether the animal is a predator or prey
2.  Demonstrate an ability to use a dichotomous key
3.  Draw each specimen and demonstrate your ability to observe using the skill of drawing.
4. Make conclusions about what animal this might be.  note that one of the specimens does not clearly fit the key exactly. Just try your best to identify it. 

For each specimen: 10 marks per specimen:
1.  Make a half page drawing where you measure and label parts     
5 marks - your color drawing is in ink, and  half a page and every part is labeled, and you have measured it in cm
3-4 marks, drawing is not in colour, it is in pencil, or less than half a page or some parts not labeled.  or you did not measure, or it is a rushed drawing
1-2 marks - it is incomplete

2.  observe the eye sockets and the teeth and conclude whether the skull belongs to a predator or prey
3 marks - you explain yourself very clearly and give your reasons and they seem logical
2 marks - your reasons are logical
1 - you are correct and need to provide more evidence for your point of view

3.  Take your best shot at identifying this specimen, give reasons for your conclusion.
2 marks - you are spot on!  or, if it is inconclusive, you give your best evidence for what it might be
1 mark- you are making a pretty good guess and you provide some evidence



Some useful information:

Dichotomous key for rodents
 Dichotomous Key for Mammals in the USA
Mammals of Alaska
The following quote is from
https://www.earthlife.net/mammals/teeth.html

"Teeth in mammals come in four different sorts: Incisors, Canines, Premolars and Molars. Not all mammals have all, or even any of them and the roles any particular sort of teeth play in an animal's life can be quite diverse. The arrangement of teeth in any given mammals mouth can be expressed as a 'dental formula'. This formula gives the arrangement of one side of an animal's jaw such that incisors are always written first then canines then premolars and then molars.

For humans 2123-2123 is upper and lower jaws respectively signifying 2 incisors, 1 canine, 2 premolars and 3 molars on each side in both the upper and lower jaw.

In total this adds up to 8 incisors, 4 canines, 8 premolars and 12 molars = 32 teeth in humans. Other mammals have different numbers of each sort of teeth in their upper and lower jaws. Hence Smoky Bats (family Furipteridae) have the dental formula 2123-3133 whilst Hyenas have 3141-3131 normally.

Incisors = Cutting teeth - these are the front most teeth in the jaw primarily used for the initial biting of food. They have a straight, sharp cutting edge and one root. In many Rodents they grow continually throughout the animals life, this is because they get warn down gnawing through things.

Canines = Stabbing teeth - normally only 2 pairs (one each side) per jaw. They have a sharp, pointed edge and are used with the incisors to bite into food and or to kill prey. Like incisors they have one root. The tusks of many animals such as elephants are modified canines. They are missing in rodents and most large herbivores (Perissodactyls and Artiodactyls). The gap where the canines would have been is often enlarged and is called a 'diastema'.

Premolars = Next back from the canines. They are generally similar to molars in form and function in both herbivores and omnivores, but in carnivores some of them at least are slimmer and are used to cut flesh. When they (the first lower premolar and last upper premolar) are modified like this they are called the carnassials. Otherwise premolars are teeth we use to crush and grind our food. Their upper surfaces have a broad, lumpy top instead of a sharp biting edge. These small irregular lumps are called cusps. Premolars are called bicuspids in some books, this is because, in most cases, they have two cusps. The prefix bi meaning two. The first upper premolars normally have two roots. The other premolars have one root.

Molars = These are larger than premolars and extremely variable depending on the animal's diet. Like premolars they are used for crushing and grinding food, and like premolars their upper surfaces have ridges called cusps on them. Molars normally have three to five cusps and two or three roots. In humans we call the third molars, those closest to the back of the mouth 'Wisdom Teeth'. If the jaw bone is not large enough to accommodate all the teeth in it, as sometimes happens with humans, these wisdom teeth can become painfully wedged between the back of the jaw bone and the 2nd molars. This condition is known as 'impacted wisdom teeth'."

Example:  Domestic Cat

a rabbit skull has a rostrom a rostral fenestra is a window or hole(s) in that area of the skull

this picture is from the following website 

https://www.backyardnature.net/yucatan/rabbit.htm

Classification activity

 Read these notes on classification

Answer these questions 

1.  What is classification?  Who invented it?
2. Explain the term binomial nomenclature
3.  What are the taxons of life, in order of largest to smallest?
4.  Define species.
5.  Cell respiration is a universal energy equation.  Where does it happen?  Write the equation.
6.  What is ATP, ADP.  Give an analogy for how this works
7.  Define Heterotroph and Autotroph
8.   What is the definition of
a. Animal
b. plant
c. Fungus
d. Protozoa
e. Monera

TAXONOMY EXERCISE 

There are specimens around the class. Examine each specimen.

1. Draw or photograph the specimen

2. Make observations on colour, texture, etc...

3.  What taxons do you think this specimen belongs to? What *body part* if it is a part of an organism? What is your evidence? 

4. Classify your specimen.

27-30. You did an exceptional job and you completed all the questions and you made careful drawings of each specimen.  You draw in ink and colour.  Your observations are excellent and this work exceeds expectations. Excellent evidence

22-26 you did an excellent job  you draw in ink and colour.  Your photographs are very good . Your observations are excellent

17-20 You did a good job of completing the questions . Your photographs are good.  You made observations 

<15. You have a good start but you did not finish your work.  

Create a powerpoint on the criteria of living things

Create a powerpoint that covers the following topics.  Due date is To Be Announced 50 points

Include photos of any observations you made in class

1. What are the criteria of living things

2.  What is the Energy equations for living things?

3.  Compare and contrast Eukaryotes and Prokaryotes

4.  Classification.  What are the key points of Classification?

5.  Acknowledgements:  let me know who did what if you worked in a group

40-50.  Your powerpoint is creative, organized and covers the topic thoroughly and includes all the key words

30-40. your powerpoint  is creative and covers most of the key words

25 your power point is not complete 

Hey Eu! Eukaryotes and Prokaryotes

 watch this intro video on Eukaryotes and Prokaryotes

This video is an intro to some of the similarities and differences between eukaryotes and prokaryotes. It is meant to accompany our class notes.

Vocabulary words and ideas in the video:

Eukaryote Prokaryote DNA nuclear membrane protozoan multicellular organisms unicellular organisms cell membrane, cytoplasm, DNA, RNA, ribosome, protein, endoplasmic reticulum vacuole mitochondria Plant cell chloroplast cell wall made of cellulose cell wall made of peptidoglycan Bacteria in the environment and the gut

Make a creative summary of these notes.  The summary must cover all of the points below:

 1. What are the 4 criteria to life? 

2. What are the two main types of cells on earth? 

 3. Give an example of a. UNICELLULAR organism b. MULTICELLULAR organism 

4. I gave an example of the cell as a chocolate factory. Make your own analogy of the cell and include EVERY ORGANELLE. You may choose a plant cell or an animal cell.

 5. How are plant cells different from animal cells?

 6. What are four ways that cells can interact with each other. below

evaluation: 20 points

Cellular respiration is a fundamental energy equation

 In today's lesson, we reviewed the fundamental criteria of living things and looked at the Textbook to see what it had to say about these criteria.  We also explored cell respiration and did a class demo where, after some aerobic exercise, we observed our body system respond to the energy requirement of running on the spot.  

Our breathing rate increased. Our hearts beat faster.  Our muscles began to feel sore. 

All living things get energy using biochemical reactions.  Many living things on earth get their energy using cell respiration.  All human body systems support cells doing cell respiration.

a. Cardiovascular System and Respiratory system deliver Oxygen and remove Carbon dioxide for all cells

b. Digestive system provides glucose

c. Excretory system removes excess water 

If muscles do not receive enough Oxygen for cellular respiration then they undergo a fermentation reaction which generates less energy and also generates lactic acid.  Lactic acid can persist in muscles and make your muscles sore.  

Dead or Alive, notes on the cell

For your first assignment, I would like you to go outside and find the following objects  Photograph them or draw them and write about them in a little paragraph of no more than a third of a page.  You may answer in the form of a type written response under your photo, OR you may write it out in hand writing and draw your answers. 

1.  Find something dead.  How do you know it is dead? 

2.  find something alive.  What is it about this object that makes it alive?

3.  Find something that has never, ever been alive.  What characteristics does this object have that tells you that it is neither dead nor alive. It is nonliving.

4. Find something that is not alive, but an important PART of something alive.  Explain your answer

5. What is something that is not alive but a living thing depends upon it to survive? 

Look at your responses and ask yourself:  What is the criteria of being alive?

Criteria for living things:

What are the criteria for living things?
1.   MOTILITY - the ability to move
2.   IRRITABILITY - it responds to stimulus
3.   REPRODUCTION - it can reproduce and make offspring

a. it can grow

b. it can make another one of itself
4.  It is made of CELLS 

5. a.   HAS METABOLISM -total of all biochemical reactions

occurring in a living thing. If metabolism stops...then that

is death.

    b. TAKES IN NUTRIENTS and MAKES WASTE

CELLS (definition)

-A membrane bound organism that has cytoplasm and genetic material. It also has METABOLISM happening inside it.

-ORGANISMS CAN BE UNICELLULAR (made of a single cell) or MULTICELLULAR (made of many cells)

-ORGANISMS CAN BE EUKARYOTES or PROKARYOTES

Eukaryotic cells have DNA inside a nucleus.  Prokaryotic cells have DNA in the cytoplasm but no nucleus. Prokaryotes are bacteria

Eukaryotes are animals, plants, fungi, unicellular protozoans, seaweed.

6.  CELLS have HOMEOSTASIS - maintaining the status quo for temp,
pH, levels of hormones, levels of enzymes.

7. CELLS CAN adapt to change in the environment.






Organelle systems provide everything for the cell
1.  energy for the cell - this is in the form of ATP made
by mitochondria.The mitochondria needs GLUCOSE and OXYGEN.
GLUCOSE IS FROM DIGESTIVE SYSTEM.
OXYGEN IS FROM SYSTEM AND
RESPIRATORY SYSTEM.



2.   eating and drinking - cell receives building blocks such as
AMINO ACIDS, LIPIDS, NUCLEIC ACIDS from the
DIGESTIVE SYSTEM AND CIRCULATORY SYSTEM

3.  waste is taken away by diffusion

4. communication for the cell 
5.  cells defend themselves

6.  Reproduction of the cell 

ANY ANIMAL CELL inside a mammal...

Eating building material such as amino acids, lipids nucleic acids

Energy:  glucose and oxygen goes to mitochondria and carbon
dioxide leaves mitochondria

Waste:  ammonia and water 

Drinking water

cell product:  made by the cell as specified by the DNA. For example,
a pancreatic cell makes INSULIN