Biology 2120 recitation

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Biology 2120 recitation

• (Date)

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Todays schedule

• Lecture review
• Quiz
• Review Quiz
• How to Read a Paper, Part III The Logical
  Argument

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• Chapter 3 Proteins
•  
• A The Big Picture Fig. 3-14 
• A Amino acids form a linear polymer called a
  polypeptide  
• B A peptide bond joins two amino acids
  together 
• C Amino acids in proteins are classified into
  three structural categories Figs. 3-1, 3-2
• C A peptide bond forms a rigid, planar
  structure Fig. 3-3
• C The amino acid side chain does not
  participate in the formation of a peptide bond
• C Amino acids joined by a peptide bond maintain
  structural polarity 
• B Definitions Proteins vs. polypeptides vs.
  peptides vs. subunits 
• C Proteins are polymers of amino acids that
  possess three important traits
• All proteins adopt at least two stable,
  three-dimensional shapes
• All proteins bind to at least one target molecule
• All proteins perform a least one cellular
  function 
• C Peptides are short polymers of amino acids
• C Polypeptides are long polymers of amino
  acids 
• Monomeric proteins contain a single polypeptide 
• C Subunits are polypeptides that associate
  together to form a single protein
• Multimeric proteins contain more than one
  polypeptide subunit Fig. 3-4

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• A Protein structure is classified into four
  categories Table 3-4, Figure 3-6 
• B Five classes of chemical bonds stabilize
  protein structure Fig. 3-5
• C Hydrogen bonds are formed by the polypeptide
  backbone and by some amino acid side chains
• C Ionic bonds are formed at the ends of
  polypeptides and by ionic amino acid side chains
• C Hydrophobic interactions occur in nonpolar
  amino acid side chains
• C van der Waals interactions occur between all
  atoms in a polypeptide
• C Disulfide bonds are formed by the side chain
  cysteine 
• B Primary structure is defined by the linear
  sequence of amino acids Fig. 3-7 
• B Secondary structure is defined by regions of
  repetitive, predictable organization in the
  primary structure Fig. 3-8
• C An alpha helix is shaped like a coil
• C A beta sheet forms a plane
• C Motifs are specific combinations of secondary
  structures Fig. 3-9
• B Tertiary structure is defined by the
  arrangement of the primary structure in three
  dimensions
• C Some proteins can fold into their proper
  tertiary structure spontaneously
• C Many proteins are classified into one of
  three tertiary structure categories 
• Fibrous proteins are rich in secondary structures
  and often form filamentous complexes Fig. 3-10
• Globular proteins adopt a condensed, rounded
  shape Figs. 3-11, 3-12
• Transmembrane proteins span both sides of a
  cellular membrane Fig. 7-5 
• C A domain is a portion of a protein that
  adopts a characteristic shape Fig. 3-13

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• B Quaternary structure is defined by the
  three-dimensional arrangement of polypeptide
  subunits in a multimeric protein Fig. 3-4
• A Changing protein shape and protein function 
• B All proteins adopt at least two different
  shapes
• C When proteins change shape they also change
  their function
• C Proteins change shape in response to changes
  in their environment 
• B Cells chemically modify proteins to control
  their shape and function
• C Covalent modifications are relatively
  long-lasting 
• Disulfide bonds are formed primarily in proteins
  at the cell surface and in the extracellular
  space
• Sugars are covalently attached primarily to
  proteins at the cell surface
• Lipids are covalently attached to membrane
  proteins
• Phosphate groups are covalently attached to a
  wide variety of cellular proteins
• All covalent modifications are reversible 
• C Noncovalent modifications are relatively
  short-lived 
• Most proteins contain more than one binding site
• Short-term binding, cleavage, and release of
  nucleotides is a common way to regulate protein
  activity
• Binding and release of calcium ions also
  regulates the activity of many proteins 
• B Proteins are classified into nine categories
  according to their function Table 3-1 

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• A Where do proteins go to die? 
• B Proteins in the cytosol are broken down in
  the proteasome Fig. 23-38
• B Proteins in organelles are digested in
  lysosomes Fig. 4-18
• B Proteins in the extracellular space are
  digested by proteinases
• Lecture 5 Membranes structure
•  
• The Big Picture Fig. 7-2
•  Phospholipids are the basic building blocks of
  cellular membranes
•  Phospholipids contain three structural elements
  Fig. 7-6
• Glycerol is a three carbon sugar-alcohol
• The lipid portion of a phospholipid can vary
  widely in structure
• Polar head groups confer additional specificity
  on the structure of phospholipids 

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Figure 3-3
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Figure 3-6
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Figure 3-5
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Figure 3-9 Common Structural Motifs
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Figure 3-13 GAPDH, An Example of a Protein
Containing Two Functional Domains
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Antibodies 4 structure
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Figure 7-6 The Three Major Classes of Membrane
Lipids
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How to Read a Paper, Part III

• The logical argument. Technically, the kind of
  logical argument (also called a syllogism) used
  to support a hypothesis contains at least three
  terms At least two premises, and a conclusion.
• The general form looks like this Premise A,
  Premise B, therefore Conclusion C. A classic
  example is Omne animal est substantia (all
  animals have substance), omnis homo est animal
  (all men are animals), ergo omnis homo est
  substantia (therefore, all men have substance).
  Often, several premises are aligned this way to
  reach a conclusion- there is no limit to how many
  one can use.
•  
• To support a scientific hypothesis, one has to
•  
• First, decide what conclusion will best
  prove/disprove the hypothesis.
• Second, decide what premises need to be gathered
  to best support the conclusion. Most cell biology
  articles use several premises to support multiple
  conclusions. The reason so many are used is that
  one has to consider at least one alternative
  hypothesis (sometimes called the null hypothesis,
  which states that the premises do not support the
  conclusion) to explain the known facts the
  scientists hypothesis is proposing. (In common
  parlance, it could be called covering ones
  back.)
•  

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How to Read a Paper, Part III (cont)

• Exercise (1) Have the students decide which one
  of the following statements is a scientifically
  valid hypothesis 
• A. I hypothesize that tomorrow the sun will rise
  in the east, and it will set in the west.
• B. I hypothesize that red light has a longer
  wavelength than green light.
• C. I hypothesize that eating hamburgers causes
  heart disease.
•  
• A is incorrect because it is simply a prediction
  of what will happen, not an explanation of why it
  will happen. Note that statement A can still be
  disproven, but that doesnt make it a valid
  hypothesis.
•  
• B is also incorrect, because it is simply a
  prediction of what might already be true. It does
  not attempt to explain why the wavelengths are
  different. Like A, this statement can be
  disproven, but it still isnt a valid hypothesis.
•  
• C is correct, because it identifies something
  that is already known (the condition of heart
  disease) and offers an explanation as to why it
  exists. It doesnt have to be the only correct
  explanation. It simply has to be one explanation
  for why something is true, and it has to be
  disprovable.
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How to Read a Paper, Part III (cont)

• (2) Have your students list some premises that
  they would gather to support the hypothesis given
  above. Some examples might include
•  
• Hamburgers contain a higher amount of fat than
  most other foods (premise A)
• A high fat diet correlates with increased risk of
  heart disease (premise B)
• Therefore, eating hamburgers causes heart disease
  (conclusion C)
•  
• Hamburger is a high calorie food (premise A)
• Consumption of excess calories causes the body to
  store calories as fat (premise B)
• The presence of fat in the body correlates with
  increased risk of heart disease (premise C)
• Therefore, eating hamburgers causes heart disease
  (conclusion D)
•  
• Hamburger is composed of animal tissue (premise
  A)
• Animal tissue typically contains high
  concentrations of fat (premise B)
• Fat is high in calories (premise C)
• Consumption of excess calories causes the body to
  store calories as fat (premise D)
• The presence of fat in the body correlates with
  increased risk of heart disease (premise E)
• Therefore, eating hamburgers causes heart disease
  (conclusion F)
•  
• Note that there are several ways of arguing in
  support of a hypothesis, and one does not need to
  use them all to reach a conclusion. There is no
  right answer to this problem. The construction
  of the premises in an argument is entirely up to
  the researcher, and the reader is left to decide
  whether they agree that the argument supports the
  hypothesis or not.

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For next week

• Find one logical argument in each of the two
  research articles you have downloaded and printed
  out.
• Write them down and hand them in at the beginning
  of next weeks recitation.
• Bring two written questions from lecture
  material, hand them in.